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5xog

RNA Polymerase II elongation complex bound with Spt5 KOW5 and Elf1

Method: X-RAY DIFFRACTION Dmax: 164.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed RNA polymerase subunit

OrganismNot specified

UniProt C4R4Y0

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 14 DNA 2 RNA 1 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain A； UniProt 1–1743 Not recorded DNA-directed RNA polymerase subunit beta × 1 （C4QZQ7） RNA polymerase II third largest subunit B44, part of central core × 1 （C4R7L2） RNA polymerase II subunit B32 × 1 （C4R2U9） RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III × 1 （C4R3P8） RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III × 1 （C4R1V1） RNA polymerase II subunit × 1 （C4R9A1） RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III × 1 （C4R273） DNA-directed RNA polymerase subunit × 1 （F2QPE6） RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III × 1 （C4R009） RNA polymerase II subunit B12.5 × 1 （C4R3Z5） RNA polymerase subunit ABC10-alpha × 1 （F2QMI1） ;RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3') ; × 1 DNA (39-MER) × 1 DNA (30-MER) × 1 Transcription elongation factor 1 homolog × 1 （A0A1B2JER8） Spt4/5 complex component × 1 （F2QUC3） ZN ZINC ION × 9 MG MAGNESIUM ION × 1 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；50 mM potassium malonate (pH 6.0), 150 mM Tris malonate (malonic acid titrated with Tris(hydroxymethyl) aminomethane, pH 6.0), 6.67% (v/v) glycerol, 6.67% (w/v) trehalose dihydrate and 10% PEG20000 Resolution 3.00 Å R-free 0.225

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5XOG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5X4Z RNA Polymerase II from Komagataella Pastoris (Type-1 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M sodium citrate, 8% PGA-LM, 10% glycerol
Resolution 7.80 Å R-free 0.357
5X4Z RNA Polymerase II from Komagataella Pastoris (Type-1 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain M 1–1743（1743 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M sodium citrate, 8% PGA-LM, 10% glycerol
Resolution 7.80 Å R-free 0.357
5X50 RNA Polymerase II from Komagataella Pastoris (Type-2 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；287 K；0.2 M sodium citrate, 8% PGA-LM and 1 % dextran sulfate sodium salt
Resolution 4.29 Å R-free 0.296
5X51 RNA Polymerase II from Komagataella Pastoris (Type-3 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M sodium citrate, 10% PGA-LM, 0.5% dextran sulfate sodium salt, 15 mM Tris, and 35 mM Hepes
Resolution 7.00 Å R-free 0.335
5X51 RNA Polymerase II from Komagataella Pastoris (Type-3 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain M 1–1743（1743 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M sodium citrate, 10% PGA-LM, 0.5% dextran sulfate sodium salt, 15 mM Tris, and 35 mM Hepes
Resolution 7.00 Å R-free 0.335
5XON RNA Polymerase II elongation complex bound with Spt4/5 and TFIIS Deposited 2017-05-29 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.83 Å
6A5L RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA Deposited 2018-06-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.60 Å
6A5O RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.90 Å
6A5P RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å
6A5R RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
6A5T RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.70 Å
6A5U RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
6INQ RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position) Deposited 2018-10-26 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
6IR9 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome Deposited 2018-11-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6J4W RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-5) of the nucleosome Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.90 Å
6J4X RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1A) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Y RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Z RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6J50 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
6J51 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7WBV RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7WBW RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3.5) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.10 Å
7WBX RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7XN7 RNA polymerase II elongation complex containing Spt4/5, Elf1, Spt6, Spn1 and Paf1C Deposited 2022-04-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7XSE RNA polymerase II elongation complex transcribing a nucleosome (EC42) Deposited 2022-05-13 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7XSX RNA polymerase II elongation complex transcribing a nucleosome (EC49) Deposited 2022-05-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7XSZ RNA polymerase II elongation complex transcribing a nucleosome (EC115) Deposited 2022-05-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7XT7 RNA polymerase II elongation complex transcribing a nucleosome (EC49B) Deposited 2022-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7XTD RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) Deposited 2022-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7XTI RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) Deposited 2022-05-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8H0V RNA polymerase II transcribing a chromatosome (type I) Deposited 2022-09-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8H0W RNA polymerase II transcribing a chromatosome (type II) Deposited 2022-09-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8HE5 RNA polymerase II elongation complex bound with Rad26 and Elf1, stalled at SHL(-3.5) of the nucleosome Deposited 2022-11-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.95 Å
8JH2 RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.70 Å
8JH3 RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8JH4 RNA polymerase II elongation complex containing 60 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8YFQ Cryo EM structure of Komagataella phaffii RNAPII-Rat1-Rai1 pre-termination complex Deposited 2024-02-25 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.30 Å
8YFR Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex bound within the RNAPII cleft Deposited 2024-02-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.40 Å
9II7 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome containing histone variant H2A.B Deposited 2024-06-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9UJS RNA polymerase II elongation complex stalled at SHL(-4) of the H3-H4 octasome Deposited 2025-04-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain A 1–1743（1743 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
9UJT RNA polymerase II elongation complex stalled at SHL(-0.5) of the H3-H4 octasome (tetrasome) Deposited 2025-04-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain A 1–1743（1743 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.54 Å
9WMS Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type B) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9WMT Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type A) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
9WMU Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type A) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.28 Å
9WMV Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type B) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.66 Å
9WMW Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, FACT-hexamer) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain A 1–1743（1743 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å

44 other PDB entries and 46 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C4R4Y0_KOMPG
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–1743； UniProt 1–1743

DNA-directed RNA polymerase subunit beta

OrganismNot specified

UniProt C4QZQ7

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 14 DNA 2 RNA 1 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain B； UniProt 1–1227 Not recorded DNA-directed RNA polymerase subunit × 1 （C4R4Y0） RNA polymerase II third largest subunit B44, part of central core × 1 （C4R7L2） RNA polymerase II subunit B32 × 1 （C4R2U9） RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III × 1 （C4R3P8） RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III × 1 （C4R1V1） RNA polymerase II subunit × 1 （C4R9A1） RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III × 1 （C4R273） DNA-directed RNA polymerase subunit × 1 （F2QPE6） RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III × 1 （C4R009） RNA polymerase II subunit B12.5 × 1 （C4R3Z5） RNA polymerase subunit ABC10-alpha × 1 （F2QMI1） ;RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3') ; × 1 DNA (39-MER) × 1 DNA (30-MER) × 1 Transcription elongation factor 1 homolog × 1 （A0A1B2JER8） Spt4/5 complex component × 1 （F2QUC3） ZN ZINC ION × 9 MG MAGNESIUM ION × 1 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；50 mM potassium malonate (pH 6.0), 150 mM Tris malonate (malonic acid titrated with Tris(hydroxymethyl) aminomethane, pH 6.0), 6.67% (v/v) glycerol, 6.67% (w/v) trehalose dihydrate and 10% PEG20000 Resolution 3.00 Å R-free 0.225

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5XOG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5X4Z RNA Polymerase II from Komagataella Pastoris (Type-1 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M sodium citrate, 8% PGA-LM, 10% glycerol
Resolution 7.80 Å R-free 0.357
5X4Z RNA Polymerase II from Komagataella Pastoris (Type-1 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain N 1–1227（1227 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M sodium citrate, 8% PGA-LM, 10% glycerol
Resolution 7.80 Å R-free 0.357
5X50 RNA Polymerase II from Komagataella Pastoris (Type-2 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；287 K；0.2 M sodium citrate, 8% PGA-LM and 1 % dextran sulfate sodium salt
Resolution 4.29 Å R-free 0.296
5X51 RNA Polymerase II from Komagataella Pastoris (Type-3 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M sodium citrate, 10% PGA-LM, 0.5% dextran sulfate sodium salt, 15 mM Tris, and 35 mM Hepes
Resolution 7.00 Å R-free 0.335
5X51 RNA Polymerase II from Komagataella Pastoris (Type-3 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain N 1–1227（1227 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M sodium citrate, 10% PGA-LM, 0.5% dextran sulfate sodium salt, 15 mM Tris, and 35 mM Hepes
Resolution 7.00 Å R-free 0.335
5XON RNA Polymerase II elongation complex bound with Spt4/5 and TFIIS Deposited 2017-05-29 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.83 Å
6A5L RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA Deposited 2018-06-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.60 Å
6A5O RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.90 Å
6A5P RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å
6A5R RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
6A5T RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.70 Å
6A5U RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
6INQ RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position) Deposited 2018-10-26 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
6IR9 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome Deposited 2018-11-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6J4W RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-5) of the nucleosome Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.90 Å
6J4X RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1A) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Y RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Z RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6J50 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
6J51 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7WBV RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7WBW RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3.5) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.10 Å
7WBX RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7XN7 RNA polymerase II elongation complex containing Spt4/5, Elf1, Spt6, Spn1 and Paf1C Deposited 2022-04-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7XSE RNA polymerase II elongation complex transcribing a nucleosome (EC42) Deposited 2022-05-13 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7XSX RNA polymerase II elongation complex transcribing a nucleosome (EC49) Deposited 2022-05-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7XSZ RNA polymerase II elongation complex transcribing a nucleosome (EC115) Deposited 2022-05-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7XT7 RNA polymerase II elongation complex transcribing a nucleosome (EC49B) Deposited 2022-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7XTD RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) Deposited 2022-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7XTI RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) Deposited 2022-05-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8H0V RNA polymerase II transcribing a chromatosome (type I) Deposited 2022-09-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8H0W RNA polymerase II transcribing a chromatosome (type II) Deposited 2022-09-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8HE5 RNA polymerase II elongation complex bound with Rad26 and Elf1, stalled at SHL(-3.5) of the nucleosome Deposited 2022-11-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.95 Å
8JH2 RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.70 Å
8JH3 RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8JH4 RNA polymerase II elongation complex containing 60 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8YFQ Cryo EM structure of Komagataella phaffii RNAPII-Rat1-Rai1 pre-termination complex Deposited 2024-02-25 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.30 Å
8YFR Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex bound within the RNAPII cleft Deposited 2024-02-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.40 Å
9II7 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome containing histone variant H2A.B Deposited 2024-06-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9UJS RNA polymerase II elongation complex stalled at SHL(-4) of the H3-H4 octasome Deposited 2025-04-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain B 1–1227（1227 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
9UJT RNA polymerase II elongation complex stalled at SHL(-0.5) of the H3-H4 octasome (tetrasome) Deposited 2025-04-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain B 1–1227（1227 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.54 Å
9WMS Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type B) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9WMT Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type A) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
9WMU Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type A) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.28 Å
9WMV Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type B) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.66 Å
9WMW Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, FACT-hexamer) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain B 1–1227（1227 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å

44 other PDB entries and 46 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C4QZQ7_KOMPG
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–1227； UniProt 1–1227

RNA polymerase II third largest subunit B44, part of central core

OrganismNot specified

UniProt C4R7L2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 14 DNA 2 RNA 1 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain C； UniProt 1–304 Not recorded DNA-directed RNA polymerase subunit × 1 （C4R4Y0） DNA-directed RNA polymerase subunit beta × 1 （C4QZQ7） RNA polymerase II subunit B32 × 1 （C4R2U9） RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III × 1 （C4R3P8） RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III × 1 （C4R1V1） RNA polymerase II subunit × 1 （C4R9A1） RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III × 1 （C4R273） DNA-directed RNA polymerase subunit × 1 （F2QPE6） RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III × 1 （C4R009） RNA polymerase II subunit B12.5 × 1 （C4R3Z5） RNA polymerase subunit ABC10-alpha × 1 （F2QMI1） ;RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3') ; × 1 DNA (39-MER) × 1 DNA (30-MER) × 1 Transcription elongation factor 1 homolog × 1 （A0A1B2JER8） Spt4/5 complex component × 1 （F2QUC3） ZN ZINC ION × 9 MG MAGNESIUM ION × 1 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；50 mM potassium malonate (pH 6.0), 150 mM Tris malonate (malonic acid titrated with Tris(hydroxymethyl) aminomethane, pH 6.0), 6.67% (v/v) glycerol, 6.67% (w/v) trehalose dihydrate and 10% PEG20000 Resolution 3.00 Å R-free 0.225

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5XOG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5X4Z RNA Polymerase II from Komagataella Pastoris (Type-1 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M sodium citrate, 8% PGA-LM, 10% glycerol
Resolution 7.80 Å R-free 0.357
5X4Z RNA Polymerase II from Komagataella Pastoris (Type-1 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain O 1–304（304 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M sodium citrate, 8% PGA-LM, 10% glycerol
Resolution 7.80 Å R-free 0.357
5X50 RNA Polymerase II from Komagataella Pastoris (Type-2 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；287 K；0.2 M sodium citrate, 8% PGA-LM and 1 % dextran sulfate sodium salt
Resolution 4.29 Å R-free 0.296
5X51 RNA Polymerase II from Komagataella Pastoris (Type-3 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M sodium citrate, 10% PGA-LM, 0.5% dextran sulfate sodium salt, 15 mM Tris, and 35 mM Hepes
Resolution 7.00 Å R-free 0.335
5X51 RNA Polymerase II from Komagataella Pastoris (Type-3 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain O 1–304（304 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M sodium citrate, 10% PGA-LM, 0.5% dextran sulfate sodium salt, 15 mM Tris, and 35 mM Hepes
Resolution 7.00 Å R-free 0.335
5XON RNA Polymerase II elongation complex bound with Spt4/5 and TFIIS Deposited 2017-05-29 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.83 Å
6A5L RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA Deposited 2018-06-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.60 Å
6A5O RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.90 Å
6A5P RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å
6A5R RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
6A5T RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.70 Å
6A5U RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
6INQ RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position) Deposited 2018-10-26 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
6IR9 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome Deposited 2018-11-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6J4W RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-5) of the nucleosome Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.90 Å
6J4X RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1A) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Y RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Z RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6J50 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
6J51 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7WBV RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7WBW RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3.5) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.10 Å
7WBX RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7XN7 RNA polymerase II elongation complex containing Spt4/5, Elf1, Spt6, Spn1 and Paf1C Deposited 2022-04-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7XSE RNA polymerase II elongation complex transcribing a nucleosome (EC42) Deposited 2022-05-13 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7XSX RNA polymerase II elongation complex transcribing a nucleosome (EC49) Deposited 2022-05-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7XSZ RNA polymerase II elongation complex transcribing a nucleosome (EC115) Deposited 2022-05-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7XT7 RNA polymerase II elongation complex transcribing a nucleosome (EC49B) Deposited 2022-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7XTD RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) Deposited 2022-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7XTI RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) Deposited 2022-05-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8H0V RNA polymerase II transcribing a chromatosome (type I) Deposited 2022-09-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8H0W RNA polymerase II transcribing a chromatosome (type II) Deposited 2022-09-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8HE5 RNA polymerase II elongation complex bound with Rad26 and Elf1, stalled at SHL(-3.5) of the nucleosome Deposited 2022-11-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.95 Å
8JH2 RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.70 Å
8JH3 RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8JH4 RNA polymerase II elongation complex containing 60 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8YFQ Cryo EM structure of Komagataella phaffii RNAPII-Rat1-Rai1 pre-termination complex Deposited 2024-02-25 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.30 Å
8YFR Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex bound within the RNAPII cleft Deposited 2024-02-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.40 Å
9II7 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome containing histone variant H2A.B Deposited 2024-06-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9UJS RNA polymerase II elongation complex stalled at SHL(-4) of the H3-H4 octasome Deposited 2025-04-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain C 1–304（304 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
9UJT RNA polymerase II elongation complex stalled at SHL(-0.5) of the H3-H4 octasome (tetrasome) Deposited 2025-04-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain C 1–304（304 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.54 Å
9WMS Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type B) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9WMT Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type A) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
9WMU Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type A) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.28 Å
9WMV Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type B) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.66 Å
9WMW Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, FACT-hexamer) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain C 1–304（304 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å

44 other PDB entries and 46 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C4R7L2_KOMPG
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 1–304； UniProt 1–304

RNA polymerase II subunit B32

OrganismNot specified

UniProt C4R2U9

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 14 DNA 2 RNA 1 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain D； UniProt 1–186 Not recorded DNA-directed RNA polymerase subunit × 1 （C4R4Y0） DNA-directed RNA polymerase subunit beta × 1 （C4QZQ7） RNA polymerase II third largest subunit B44, part of central core × 1 （C4R7L2） RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III × 1 （C4R3P8） RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III × 1 （C4R1V1） RNA polymerase II subunit × 1 （C4R9A1） RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III × 1 （C4R273） DNA-directed RNA polymerase subunit × 1 （F2QPE6） RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III × 1 （C4R009） RNA polymerase II subunit B12.5 × 1 （C4R3Z5） RNA polymerase subunit ABC10-alpha × 1 （F2QMI1） ;RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3') ; × 1 DNA (39-MER) × 1 DNA (30-MER) × 1 Transcription elongation factor 1 homolog × 1 （A0A1B2JER8） Spt4/5 complex component × 1 （F2QUC3） ZN ZINC ION × 9 MG MAGNESIUM ION × 1 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；50 mM potassium malonate (pH 6.0), 150 mM Tris malonate (malonic acid titrated with Tris(hydroxymethyl) aminomethane, pH 6.0), 6.67% (v/v) glycerol, 6.67% (w/v) trehalose dihydrate and 10% PEG20000 Resolution 3.00 Å R-free 0.225

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5XOG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5X4Z RNA Polymerase II from Komagataella Pastoris (Type-1 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M sodium citrate, 8% PGA-LM, 10% glycerol
Resolution 7.80 Å R-free 0.357
5X4Z RNA Polymerase II from Komagataella Pastoris (Type-1 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain P 1–186（186 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M sodium citrate, 8% PGA-LM, 10% glycerol
Resolution 7.80 Å R-free 0.357
5X50 RNA Polymerase II from Komagataella Pastoris (Type-2 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；287 K；0.2 M sodium citrate, 8% PGA-LM and 1 % dextran sulfate sodium salt
Resolution 4.29 Å R-free 0.296
5X51 RNA Polymerase II from Komagataella Pastoris (Type-3 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M sodium citrate, 10% PGA-LM, 0.5% dextran sulfate sodium salt, 15 mM Tris, and 35 mM Hepes
Resolution 7.00 Å R-free 0.335
5X51 RNA Polymerase II from Komagataella Pastoris (Type-3 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain P 1–186（186 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M sodium citrate, 10% PGA-LM, 0.5% dextran sulfate sodium salt, 15 mM Tris, and 35 mM Hepes
Resolution 7.00 Å R-free 0.335
5XON RNA Polymerase II elongation complex bound with Spt4/5 and TFIIS Deposited 2017-05-29 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.83 Å
6A5L RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA Deposited 2018-06-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.60 Å
6A5O RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.90 Å
6A5P RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å
6A5R RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
6A5T RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.70 Å
6A5U RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
6INQ RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position) Deposited 2018-10-26 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
6IR9 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome Deposited 2018-11-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6J4W RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-5) of the nucleosome Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.90 Å
6J4X RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1A) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Y RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Z RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6J50 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
6J51 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7WBV RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7WBW RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3.5) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.10 Å
7WBX RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7XN7 RNA polymerase II elongation complex containing Spt4/5, Elf1, Spt6, Spn1 and Paf1C Deposited 2022-04-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7XSE RNA polymerase II elongation complex transcribing a nucleosome (EC42) Deposited 2022-05-13 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7XSX RNA polymerase II elongation complex transcribing a nucleosome (EC49) Deposited 2022-05-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7XSZ RNA polymerase II elongation complex transcribing a nucleosome (EC115) Deposited 2022-05-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7XT7 RNA polymerase II elongation complex transcribing a nucleosome (EC49B) Deposited 2022-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7XTD RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) Deposited 2022-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7XTI RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) Deposited 2022-05-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8H0V RNA polymerase II transcribing a chromatosome (type I) Deposited 2022-09-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8H0W RNA polymerase II transcribing a chromatosome (type II) Deposited 2022-09-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8HE5 RNA polymerase II elongation complex bound with Rad26 and Elf1, stalled at SHL(-3.5) of the nucleosome Deposited 2022-11-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.95 Å
8JH2 RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.70 Å
8JH3 RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8JH4 RNA polymerase II elongation complex containing 60 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8YFQ Cryo EM structure of Komagataella phaffii RNAPII-Rat1-Rai1 pre-termination complex Deposited 2024-02-25 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.30 Å
8YFR Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex bound within the RNAPII cleft Deposited 2024-02-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.40 Å
9II7 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome containing histone variant H2A.B Deposited 2024-06-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9UJS RNA polymerase II elongation complex stalled at SHL(-4) of the H3-H4 octasome Deposited 2025-04-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain D 1–186（186 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
9UJT RNA polymerase II elongation complex stalled at SHL(-0.5) of the H3-H4 octasome (tetrasome) Deposited 2025-04-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain D 1–186（186 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.54 Å
9WMS Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type B) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9WMT Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type A) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
9WMU Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type A) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.28 Å
9WMV Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type B) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.66 Å
9WMW Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, FACT-hexamer) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain D 1–186（186 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å

44 other PDB entries and 46 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C4R2U9_KOMPG
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 1–186； UniProt 1–186

RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III

OrganismNot specified

UniProt C4R3P8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 14 DNA 2 RNA 1 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain E； UniProt 1–214 Not recorded DNA-directed RNA polymerase subunit × 1 （C4R4Y0） DNA-directed RNA polymerase subunit beta × 1 （C4QZQ7） RNA polymerase II third largest subunit B44, part of central core × 1 （C4R7L2） RNA polymerase II subunit B32 × 1 （C4R2U9） RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III × 1 （C4R1V1） RNA polymerase II subunit × 1 （C4R9A1） RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III × 1 （C4R273） DNA-directed RNA polymerase subunit × 1 （F2QPE6） RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III × 1 （C4R009） RNA polymerase II subunit B12.5 × 1 （C4R3Z5） RNA polymerase subunit ABC10-alpha × 1 （F2QMI1） ;RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3') ; × 1 DNA (39-MER) × 1 DNA (30-MER) × 1 Transcription elongation factor 1 homolog × 1 （A0A1B2JER8） Spt4/5 complex component × 1 （F2QUC3） ZN ZINC ION × 9 MG MAGNESIUM ION × 1 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；50 mM potassium malonate (pH 6.0), 150 mM Tris malonate (malonic acid titrated with Tris(hydroxymethyl) aminomethane, pH 6.0), 6.67% (v/v) glycerol, 6.67% (w/v) trehalose dihydrate and 10% PEG20000 Resolution 3.00 Å R-free 0.225

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5XOG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5X4Z RNA Polymerase II from Komagataella Pastoris (Type-1 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M sodium citrate, 8% PGA-LM, 10% glycerol
Resolution 7.80 Å R-free 0.357
5X4Z RNA Polymerase II from Komagataella Pastoris (Type-1 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain Q 1–214（214 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M sodium citrate, 8% PGA-LM, 10% glycerol
Resolution 7.80 Å R-free 0.357
5X50 RNA Polymerase II from Komagataella Pastoris (Type-2 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；287 K；0.2 M sodium citrate, 8% PGA-LM and 1 % dextran sulfate sodium salt
Resolution 4.29 Å R-free 0.296
5X51 RNA Polymerase II from Komagataella Pastoris (Type-3 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M sodium citrate, 10% PGA-LM, 0.5% dextran sulfate sodium salt, 15 mM Tris, and 35 mM Hepes
Resolution 7.00 Å R-free 0.335
5X51 RNA Polymerase II from Komagataella Pastoris (Type-3 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain Q 1–214（214 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M sodium citrate, 10% PGA-LM, 0.5% dextran sulfate sodium salt, 15 mM Tris, and 35 mM Hepes
Resolution 7.00 Å R-free 0.335
5XON RNA Polymerase II elongation complex bound with Spt4/5 and TFIIS Deposited 2017-05-29 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.83 Å
6A5L RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA Deposited 2018-06-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.60 Å
6A5O RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.90 Å
6A5P RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å
6A5R RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
6A5T RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.70 Å
6A5U RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
6INQ RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position) Deposited 2018-10-26 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
6IR9 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome Deposited 2018-11-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6J4W RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-5) of the nucleosome Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.90 Å
6J4X RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1A) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Y RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Z RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6J50 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
6J51 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7WBV RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7WBW RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3.5) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.10 Å
7WBX RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7XSE RNA polymerase II elongation complex transcribing a nucleosome (EC42) Deposited 2022-05-13 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7XSX RNA polymerase II elongation complex transcribing a nucleosome (EC49) Deposited 2022-05-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7XSZ RNA polymerase II elongation complex transcribing a nucleosome (EC115) Deposited 2022-05-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7XT7 RNA polymerase II elongation complex transcribing a nucleosome (EC49B) Deposited 2022-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7XTD RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) Deposited 2022-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7XTI RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) Deposited 2022-05-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8H0V RNA polymerase II transcribing a chromatosome (type I) Deposited 2022-09-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8H0W RNA polymerase II transcribing a chromatosome (type II) Deposited 2022-09-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8HE5 RNA polymerase II elongation complex bound with Rad26 and Elf1, stalled at SHL(-3.5) of the nucleosome Deposited 2022-11-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.95 Å
8JH2 RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.70 Å
8JH3 RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8JH4 RNA polymerase II elongation complex containing 60 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8YFQ Cryo EM structure of Komagataella phaffii RNAPII-Rat1-Rai1 pre-termination complex Deposited 2024-02-25 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.30 Å
8YFR Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex bound within the RNAPII cleft Deposited 2024-02-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.40 Å
9II7 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome containing histone variant H2A.B Deposited 2024-06-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9UJS RNA polymerase II elongation complex stalled at SHL(-4) of the H3-H4 octasome Deposited 2025-04-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain E 1–214（214 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
9UJT RNA polymerase II elongation complex stalled at SHL(-0.5) of the H3-H4 octasome (tetrasome) Deposited 2025-04-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain E 1–214（214 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.54 Å
9WMS Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type B) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9WMT Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type A) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
9WMU Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type A) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.28 Å
9WMV Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type B) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.66 Å
9WMW Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, FACT-hexamer) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain E 1–214（214 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å

43 other PDB entries and 45 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C4R3P8_KOMPG
Isoform —
PDB entities 5
Chains and sequence ranges Author chain E； PDBConstruct 1–214； UniProt 1–214

RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III

OrganismNot specified

UniProt C4R1V1

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 14 DNA 2 RNA 1 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain F； UniProt 1–155 Not recorded DNA-directed RNA polymerase subunit × 1 （C4R4Y0） DNA-directed RNA polymerase subunit beta × 1 （C4QZQ7） RNA polymerase II third largest subunit B44, part of central core × 1 （C4R7L2） RNA polymerase II subunit B32 × 1 （C4R2U9） RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III × 1 （C4R3P8） RNA polymerase II subunit × 1 （C4R9A1） RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III × 1 （C4R273） DNA-directed RNA polymerase subunit × 1 （F2QPE6） RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III × 1 （C4R009） RNA polymerase II subunit B12.5 × 1 （C4R3Z5） RNA polymerase subunit ABC10-alpha × 1 （F2QMI1） ;RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3') ; × 1 DNA (39-MER) × 1 DNA (30-MER) × 1 Transcription elongation factor 1 homolog × 1 （A0A1B2JER8） Spt4/5 complex component × 1 （F2QUC3） ZN ZINC ION × 9 MG MAGNESIUM ION × 1 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；50 mM potassium malonate (pH 6.0), 150 mM Tris malonate (malonic acid titrated with Tris(hydroxymethyl) aminomethane, pH 6.0), 6.67% (v/v) glycerol, 6.67% (w/v) trehalose dihydrate and 10% PEG20000 Resolution 3.00 Å R-free 0.225

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5XOG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5X4Z RNA Polymerase II from Komagataella Pastoris (Type-1 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M sodium citrate, 8% PGA-LM, 10% glycerol
Resolution 7.80 Å R-free 0.357
5X4Z RNA Polymerase II from Komagataella Pastoris (Type-1 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain R 1–155（155 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M sodium citrate, 8% PGA-LM, 10% glycerol
Resolution 7.80 Å R-free 0.357
5X50 RNA Polymerase II from Komagataella Pastoris (Type-2 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；287 K；0.2 M sodium citrate, 8% PGA-LM and 1 % dextran sulfate sodium salt
Resolution 4.29 Å R-free 0.296
5X51 RNA Polymerase II from Komagataella Pastoris (Type-3 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M sodium citrate, 10% PGA-LM, 0.5% dextran sulfate sodium salt, 15 mM Tris, and 35 mM Hepes
Resolution 7.00 Å R-free 0.335
5X51 RNA Polymerase II from Komagataella Pastoris (Type-3 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain R 1–155（155 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M sodium citrate, 10% PGA-LM, 0.5% dextran sulfate sodium salt, 15 mM Tris, and 35 mM Hepes
Resolution 7.00 Å R-free 0.335
5XON RNA Polymerase II elongation complex bound with Spt4/5 and TFIIS Deposited 2017-05-29 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.83 Å
6A5L RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA Deposited 2018-06-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.60 Å
6A5O RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.90 Å
6A5P RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å
6A5R RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
6A5T RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.70 Å
6A5U RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
6INQ RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position) Deposited 2018-10-26 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
6IR9 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome Deposited 2018-11-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6J4W RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-5) of the nucleosome Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.90 Å
6J4X RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1A) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Y RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Z RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6J50 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
6J51 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7WBV RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7WBW RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3.5) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.10 Å
7WBX RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7XN7 RNA polymerase II elongation complex containing Spt4/5, Elf1, Spt6, Spn1 and Paf1C Deposited 2022-04-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7XSE RNA polymerase II elongation complex transcribing a nucleosome (EC42) Deposited 2022-05-13 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7XSX RNA polymerase II elongation complex transcribing a nucleosome (EC49) Deposited 2022-05-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7XSZ RNA polymerase II elongation complex transcribing a nucleosome (EC115) Deposited 2022-05-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7XT7 RNA polymerase II elongation complex transcribing a nucleosome (EC49B) Deposited 2022-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7XTD RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) Deposited 2022-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7XTI RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) Deposited 2022-05-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8H0V RNA polymerase II transcribing a chromatosome (type I) Deposited 2022-09-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8H0W RNA polymerase II transcribing a chromatosome (type II) Deposited 2022-09-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8HE5 RNA polymerase II elongation complex bound with Rad26 and Elf1, stalled at SHL(-3.5) of the nucleosome Deposited 2022-11-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.95 Å
8JH2 RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.70 Å
8JH3 RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8JH4 RNA polymerase II elongation complex containing 60 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8YFQ Cryo EM structure of Komagataella phaffii RNAPII-Rat1-Rai1 pre-termination complex Deposited 2024-02-25 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.30 Å
8YFR Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex bound within the RNAPII cleft Deposited 2024-02-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.40 Å
9II7 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome containing histone variant H2A.B Deposited 2024-06-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9UJS RNA polymerase II elongation complex stalled at SHL(-4) of the H3-H4 octasome Deposited 2025-04-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain F 1–155（155 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
9UJT RNA polymerase II elongation complex stalled at SHL(-0.5) of the H3-H4 octasome (tetrasome) Deposited 2025-04-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain F 1–155（155 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.54 Å
9WMS Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type B) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9WMT Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type A) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
9WMU Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type A) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.28 Å
9WMV Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type B) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.66 Å
9WMW Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, FACT-hexamer) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain F 1–155（155 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å

44 other PDB entries and 46 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C4R1V1_KOMPG
Isoform —
PDB entities 6
Chains and sequence ranges Author chain F； PDBConstruct 1–155； UniProt 1–155

RNA polymerase II subunit

OrganismNot specified

UniProt C4R9A1

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 14 DNA 2 RNA 1 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain G； UniProt 1–171 Not recorded DNA-directed RNA polymerase subunit × 1 （C4R4Y0） DNA-directed RNA polymerase subunit beta × 1 （C4QZQ7） RNA polymerase II third largest subunit B44, part of central core × 1 （C4R7L2） RNA polymerase II subunit B32 × 1 （C4R2U9） RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III × 1 （C4R3P8） RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III × 1 （C4R1V1） RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III × 1 （C4R273） DNA-directed RNA polymerase subunit × 1 （F2QPE6） RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III × 1 （C4R009） RNA polymerase II subunit B12.5 × 1 （C4R3Z5） RNA polymerase subunit ABC10-alpha × 1 （F2QMI1） ;RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3') ; × 1 DNA (39-MER) × 1 DNA (30-MER) × 1 Transcription elongation factor 1 homolog × 1 （A0A1B2JER8） Spt4/5 complex component × 1 （F2QUC3） ZN ZINC ION × 9 MG MAGNESIUM ION × 1 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；50 mM potassium malonate (pH 6.0), 150 mM Tris malonate (malonic acid titrated with Tris(hydroxymethyl) aminomethane, pH 6.0), 6.67% (v/v) glycerol, 6.67% (w/v) trehalose dihydrate and 10% PEG20000 Resolution 3.00 Å R-free 0.225

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5XOG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5X4Z RNA Polymerase II from Komagataella Pastoris (Type-1 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M sodium citrate, 8% PGA-LM, 10% glycerol
Resolution 7.80 Å R-free 0.357
5X4Z RNA Polymerase II from Komagataella Pastoris (Type-1 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain S 1–171（171 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M sodium citrate, 8% PGA-LM, 10% glycerol
Resolution 7.80 Å R-free 0.357
5X50 RNA Polymerase II from Komagataella Pastoris (Type-2 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；287 K；0.2 M sodium citrate, 8% PGA-LM and 1 % dextran sulfate sodium salt
Resolution 4.29 Å R-free 0.296
5X51 RNA Polymerase II from Komagataella Pastoris (Type-3 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M sodium citrate, 10% PGA-LM, 0.5% dextran sulfate sodium salt, 15 mM Tris, and 35 mM Hepes
Resolution 7.00 Å R-free 0.335
5X51 RNA Polymerase II from Komagataella Pastoris (Type-3 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain S 1–171（171 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M sodium citrate, 10% PGA-LM, 0.5% dextran sulfate sodium salt, 15 mM Tris, and 35 mM Hepes
Resolution 7.00 Å R-free 0.335
5XON RNA Polymerase II elongation complex bound with Spt4/5 and TFIIS Deposited 2017-05-29 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.83 Å
6A5L RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA Deposited 2018-06-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.60 Å
6A5O RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.90 Å
6A5P RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å
6A5R RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
6A5T RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.70 Å
6A5U RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
6INQ RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position) Deposited 2018-10-26 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
6IR9 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome Deposited 2018-11-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6J4W RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-5) of the nucleosome Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.90 Å
6J4X RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1A) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Y RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Z RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6J50 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
6J51 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7WBV RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7WBW RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3.5) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.10 Å
7WBX RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7XN7 RNA polymerase II elongation complex containing Spt4/5, Elf1, Spt6, Spn1 and Paf1C Deposited 2022-04-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7XSE RNA polymerase II elongation complex transcribing a nucleosome (EC42) Deposited 2022-05-13 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7XSX RNA polymerase II elongation complex transcribing a nucleosome (EC49) Deposited 2022-05-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7XSZ RNA polymerase II elongation complex transcribing a nucleosome (EC115) Deposited 2022-05-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7XT7 RNA polymerase II elongation complex transcribing a nucleosome (EC49B) Deposited 2022-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7XTD RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) Deposited 2022-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7XTI RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) Deposited 2022-05-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8H0V RNA polymerase II transcribing a chromatosome (type I) Deposited 2022-09-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8H0W RNA polymerase II transcribing a chromatosome (type II) Deposited 2022-09-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8HE5 RNA polymerase II elongation complex bound with Rad26 and Elf1, stalled at SHL(-3.5) of the nucleosome Deposited 2022-11-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.95 Å
8JH2 RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.70 Å
8JH3 RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8JH4 RNA polymerase II elongation complex containing 60 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8YFQ Cryo EM structure of Komagataella phaffii RNAPII-Rat1-Rai1 pre-termination complex Deposited 2024-02-25 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.30 Å
8YFR Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex bound within the RNAPII cleft Deposited 2024-02-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.40 Å
9II7 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome containing histone variant H2A.B Deposited 2024-06-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9UJS RNA polymerase II elongation complex stalled at SHL(-4) of the H3-H4 octasome Deposited 2025-04-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain G 1–171（171 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
9UJT RNA polymerase II elongation complex stalled at SHL(-0.5) of the H3-H4 octasome (tetrasome) Deposited 2025-04-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain G 1–171（171 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.54 Å
9WMS Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type B) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9WMT Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type A) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
9WMU Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type A) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.28 Å
9WMV Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type B) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.66 Å
9WMW Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, FACT-hexamer) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain G 1–171（171 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å

44 other PDB entries and 46 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C4R9A1_KOMPG
Isoform —
PDB entities 7
Chains and sequence ranges Author chain G； PDBConstruct 1–171； UniProt 1–171

RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III

OrganismNot specified

UniProt C4R273

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 14 DNA 2 RNA 1 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain H； UniProt 1–145 Not recorded DNA-directed RNA polymerase subunit × 1 （C4R4Y0） DNA-directed RNA polymerase subunit beta × 1 （C4QZQ7） RNA polymerase II third largest subunit B44, part of central core × 1 （C4R7L2） RNA polymerase II subunit B32 × 1 （C4R2U9） RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III × 1 （C4R3P8） RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III × 1 （C4R1V1） RNA polymerase II subunit × 1 （C4R9A1） DNA-directed RNA polymerase subunit × 1 （F2QPE6） RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III × 1 （C4R009） RNA polymerase II subunit B12.5 × 1 （C4R3Z5） RNA polymerase subunit ABC10-alpha × 1 （F2QMI1） ;RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3') ; × 1 DNA (39-MER) × 1 DNA (30-MER) × 1 Transcription elongation factor 1 homolog × 1 （A0A1B2JER8） Spt4/5 complex component × 1 （F2QUC3） ZN ZINC ION × 9 MG MAGNESIUM ION × 1 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；50 mM potassium malonate (pH 6.0), 150 mM Tris malonate (malonic acid titrated with Tris(hydroxymethyl) aminomethane, pH 6.0), 6.67% (v/v) glycerol, 6.67% (w/v) trehalose dihydrate and 10% PEG20000 Resolution 3.00 Å R-free 0.225

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5XOG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5X4Z RNA Polymerase II from Komagataella Pastoris (Type-1 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M sodium citrate, 8% PGA-LM, 10% glycerol
Resolution 7.80 Å R-free 0.357
5X4Z RNA Polymerase II from Komagataella Pastoris (Type-1 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain T 1–145（145 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M sodium citrate, 8% PGA-LM, 10% glycerol
Resolution 7.80 Å R-free 0.357
5X50 RNA Polymerase II from Komagataella Pastoris (Type-2 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；287 K；0.2 M sodium citrate, 8% PGA-LM and 1 % dextran sulfate sodium salt
Resolution 4.29 Å R-free 0.296
5X51 RNA Polymerase II from Komagataella Pastoris (Type-3 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M sodium citrate, 10% PGA-LM, 0.5% dextran sulfate sodium salt, 15 mM Tris, and 35 mM Hepes
Resolution 7.00 Å R-free 0.335
5X51 RNA Polymerase II from Komagataella Pastoris (Type-3 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain T 1–145（145 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M sodium citrate, 10% PGA-LM, 0.5% dextran sulfate sodium salt, 15 mM Tris, and 35 mM Hepes
Resolution 7.00 Å R-free 0.335
5XON RNA Polymerase II elongation complex bound with Spt4/5 and TFIIS Deposited 2017-05-29 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.83 Å
6A5L RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA Deposited 2018-06-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.60 Å
6A5O RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.90 Å
6A5P RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å
6A5R RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
6A5T RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.70 Å
6A5U RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
6INQ RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position) Deposited 2018-10-26 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
6IR9 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome Deposited 2018-11-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6J4W RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-5) of the nucleosome Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.90 Å
6J4X RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1A) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Y RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Z RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6J50 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
6J51 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7WBV RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7WBW RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3.5) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.10 Å
7WBX RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7XN7 RNA polymerase II elongation complex containing Spt4/5, Elf1, Spt6, Spn1 and Paf1C Deposited 2022-04-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7XSE RNA polymerase II elongation complex transcribing a nucleosome (EC42) Deposited 2022-05-13 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7XSX RNA polymerase II elongation complex transcribing a nucleosome (EC49) Deposited 2022-05-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7XSZ RNA polymerase II elongation complex transcribing a nucleosome (EC115) Deposited 2022-05-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7XT7 RNA polymerase II elongation complex transcribing a nucleosome (EC49B) Deposited 2022-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7XTD RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) Deposited 2022-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7XTI RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) Deposited 2022-05-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8H0V RNA polymerase II transcribing a chromatosome (type I) Deposited 2022-09-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8H0W RNA polymerase II transcribing a chromatosome (type II) Deposited 2022-09-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8HE5 RNA polymerase II elongation complex bound with Rad26 and Elf1, stalled at SHL(-3.5) of the nucleosome Deposited 2022-11-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.95 Å
8JH2 RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.70 Å
8JH3 RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8JH4 RNA polymerase II elongation complex containing 60 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8YFQ Cryo EM structure of Komagataella phaffii RNAPII-Rat1-Rai1 pre-termination complex Deposited 2024-02-25 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.30 Å
8YFR Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex bound within the RNAPII cleft Deposited 2024-02-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.40 Å
9II7 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome containing histone variant H2A.B Deposited 2024-06-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9UJS RNA polymerase II elongation complex stalled at SHL(-4) of the H3-H4 octasome Deposited 2025-04-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain H 1–145（145 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
9UJT RNA polymerase II elongation complex stalled at SHL(-0.5) of the H3-H4 octasome (tetrasome) Deposited 2025-04-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain H 1–145（145 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.54 Å
9WMS Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type B) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9WMT Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type A) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
9WMU Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type A) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.28 Å
9WMV Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type B) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.66 Å
9WMW Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, FACT-hexamer) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain H 1–145（145 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å

44 other PDB entries and 46 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C4R273_KOMPG
Isoform —
PDB entities 8
Chains and sequence ranges Author chain H； PDBConstruct 1–145； UniProt 1–145

DNA-directed RNA polymerase subunit

OrganismNot specified

UniProt F2QPE6

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 14 DNA 2 RNA 1 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain I； UniProt 1–115 Not recorded DNA-directed RNA polymerase subunit × 1 （C4R4Y0） DNA-directed RNA polymerase subunit beta × 1 （C4QZQ7） RNA polymerase II third largest subunit B44, part of central core × 1 （C4R7L2） RNA polymerase II subunit B32 × 1 （C4R2U9） RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III × 1 （C4R3P8） RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III × 1 （C4R1V1） RNA polymerase II subunit × 1 （C4R9A1） RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III × 1 （C4R273） RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III × 1 （C4R009） RNA polymerase II subunit B12.5 × 1 （C4R3Z5） RNA polymerase subunit ABC10-alpha × 1 （F2QMI1） ;RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3') ; × 1 DNA (39-MER) × 1 DNA (30-MER) × 1 Transcription elongation factor 1 homolog × 1 （A0A1B2JER8） Spt4/5 complex component × 1 （F2QUC3） ZN ZINC ION × 9 MG MAGNESIUM ION × 1 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；50 mM potassium malonate (pH 6.0), 150 mM Tris malonate (malonic acid titrated with Tris(hydroxymethyl) aminomethane, pH 6.0), 6.67% (v/v) glycerol, 6.67% (w/v) trehalose dihydrate and 10% PEG20000 Resolution 3.00 Å R-free 0.225

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5XOG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5X4Z RNA Polymerase II from Komagataella Pastoris (Type-1 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M sodium citrate, 8% PGA-LM, 10% glycerol
Resolution 7.80 Å R-free 0.357
5X4Z RNA Polymerase II from Komagataella Pastoris (Type-1 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain U 1–115（115 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M sodium citrate, 8% PGA-LM, 10% glycerol
Resolution 7.80 Å R-free 0.357
5X50 RNA Polymerase II from Komagataella Pastoris (Type-2 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；287 K；0.2 M sodium citrate, 8% PGA-LM and 1 % dextran sulfate sodium salt
Resolution 4.29 Å R-free 0.296
5X51 RNA Polymerase II from Komagataella Pastoris (Type-3 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M sodium citrate, 10% PGA-LM, 0.5% dextran sulfate sodium salt, 15 mM Tris, and 35 mM Hepes
Resolution 7.00 Å R-free 0.335
5X51 RNA Polymerase II from Komagataella Pastoris (Type-3 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain U 1–115（115 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M sodium citrate, 10% PGA-LM, 0.5% dextran sulfate sodium salt, 15 mM Tris, and 35 mM Hepes
Resolution 7.00 Å R-free 0.335
6A5L RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA Deposited 2018-06-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.60 Å
6A5O RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.90 Å
6A5P RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å
6A5R RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
6A5T RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.70 Å
6A5U RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
6INQ RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position) Deposited 2018-10-26 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
6IR9 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome Deposited 2018-11-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6J4W RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-5) of the nucleosome Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.90 Å
6J4X RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1A) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Y RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Z RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6J50 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
6J51 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7WBV RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7WBW RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3.5) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.10 Å
7WBX RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7XN7 RNA polymerase II elongation complex containing Spt4/5, Elf1, Spt6, Spn1 and Paf1C Deposited 2022-04-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7XSE RNA polymerase II elongation complex transcribing a nucleosome (EC42) Deposited 2022-05-13 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7XSX RNA polymerase II elongation complex transcribing a nucleosome (EC49) Deposited 2022-05-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7XSZ RNA polymerase II elongation complex transcribing a nucleosome (EC115) Deposited 2022-05-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7XT7 RNA polymerase II elongation complex transcribing a nucleosome (EC49B) Deposited 2022-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7XTD RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) Deposited 2022-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7XTI RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) Deposited 2022-05-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8H0V RNA polymerase II transcribing a chromatosome (type I) Deposited 2022-09-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8H0W RNA polymerase II transcribing a chromatosome (type II) Deposited 2022-09-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8HE5 RNA polymerase II elongation complex bound with Rad26 and Elf1, stalled at SHL(-3.5) of the nucleosome Deposited 2022-11-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.95 Å
8JH2 RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.70 Å
8JH3 RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8JH4 RNA polymerase II elongation complex containing 60 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8YFQ Cryo EM structure of Komagataella phaffii RNAPII-Rat1-Rai1 pre-termination complex Deposited 2024-02-25 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.30 Å
8YFR Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex bound within the RNAPII cleft Deposited 2024-02-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.40 Å
9II7 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome containing histone variant H2A.B Deposited 2024-06-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9UJS RNA polymerase II elongation complex stalled at SHL(-4) of the H3-H4 octasome Deposited 2025-04-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain I 1–115（115 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
9UJT RNA polymerase II elongation complex stalled at SHL(-0.5) of the H3-H4 octasome (tetrasome) Deposited 2025-04-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain I 1–115（115 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.54 Å
9WMS Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type B) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9WMT Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type A) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
9WMU Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type A) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.28 Å
9WMV Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type B) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.66 Å
9WMW Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, FACT-hexamer) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain I 1–115（115 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å

43 other PDB entries and 45 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name F2QPE6_KOMPC
Isoform —
PDB entities 9
Chains and sequence ranges Author chain I； PDBConstruct 1–115； UniProt 1–115

RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III

OrganismNot specified

UniProt C4R009

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 14 DNA 2 RNA 1 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain J； UniProt 1–72 Not recorded DNA-directed RNA polymerase subunit × 1 （C4R4Y0） DNA-directed RNA polymerase subunit beta × 1 （C4QZQ7） RNA polymerase II third largest subunit B44, part of central core × 1 （C4R7L2） RNA polymerase II subunit B32 × 1 （C4R2U9） RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III × 1 （C4R3P8） RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III × 1 （C4R1V1） RNA polymerase II subunit × 1 （C4R9A1） RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III × 1 （C4R273） DNA-directed RNA polymerase subunit × 1 （F2QPE6） RNA polymerase II subunit B12.5 × 1 （C4R3Z5） RNA polymerase subunit ABC10-alpha × 1 （F2QMI1） ;RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3') ; × 1 DNA (39-MER) × 1 DNA (30-MER) × 1 Transcription elongation factor 1 homolog × 1 （A0A1B2JER8） Spt4/5 complex component × 1 （F2QUC3） ZN ZINC ION × 9 MG MAGNESIUM ION × 1 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；50 mM potassium malonate (pH 6.0), 150 mM Tris malonate (malonic acid titrated with Tris(hydroxymethyl) aminomethane, pH 6.0), 6.67% (v/v) glycerol, 6.67% (w/v) trehalose dihydrate and 10% PEG20000 Resolution 3.00 Å R-free 0.225

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5XOG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5X4Z RNA Polymerase II from Komagataella Pastoris (Type-1 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M sodium citrate, 8% PGA-LM, 10% glycerol
Resolution 7.80 Å R-free 0.357
5X4Z RNA Polymerase II from Komagataella Pastoris (Type-1 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain V 1–72（72 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M sodium citrate, 8% PGA-LM, 10% glycerol
Resolution 7.80 Å R-free 0.357
5X50 RNA Polymerase II from Komagataella Pastoris (Type-2 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；287 K；0.2 M sodium citrate, 8% PGA-LM and 1 % dextran sulfate sodium salt
Resolution 4.29 Å R-free 0.296
5X51 RNA Polymerase II from Komagataella Pastoris (Type-3 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M sodium citrate, 10% PGA-LM, 0.5% dextran sulfate sodium salt, 15 mM Tris, and 35 mM Hepes
Resolution 7.00 Å R-free 0.335
5X51 RNA Polymerase II from Komagataella Pastoris (Type-3 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain V 1–72（72 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M sodium citrate, 10% PGA-LM, 0.5% dextran sulfate sodium salt, 15 mM Tris, and 35 mM Hepes
Resolution 7.00 Å R-free 0.335
5XON RNA Polymerase II elongation complex bound with Spt4/5 and TFIIS Deposited 2017-05-29 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.83 Å
6A5L RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA Deposited 2018-06-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.60 Å
6A5O RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.90 Å
6A5P RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å
6A5R RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
6A5T RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.70 Å
6A5U RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
6INQ RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position) Deposited 2018-10-26 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
6IR9 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome Deposited 2018-11-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6J4X RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1A) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Y RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Z RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6J50 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
6J51 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7WBV RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7WBW RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3.5) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.10 Å
7WBX RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7XN7 RNA polymerase II elongation complex containing Spt4/5, Elf1, Spt6, Spn1 and Paf1C Deposited 2022-04-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7XSE RNA polymerase II elongation complex transcribing a nucleosome (EC42) Deposited 2022-05-13 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7XSX RNA polymerase II elongation complex transcribing a nucleosome (EC49) Deposited 2022-05-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7XSZ RNA polymerase II elongation complex transcribing a nucleosome (EC115) Deposited 2022-05-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7XT7 RNA polymerase II elongation complex transcribing a nucleosome (EC49B) Deposited 2022-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7XTD RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) Deposited 2022-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7XTI RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) Deposited 2022-05-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8H0V RNA polymerase II transcribing a chromatosome (type I) Deposited 2022-09-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8H0W RNA polymerase II transcribing a chromatosome (type II) Deposited 2022-09-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8HE5 RNA polymerase II elongation complex bound with Rad26 and Elf1, stalled at SHL(-3.5) of the nucleosome Deposited 2022-11-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.95 Å
8JH2 RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.70 Å
8JH3 RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8JH4 RNA polymerase II elongation complex containing 60 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8YFQ Cryo EM structure of Komagataella phaffii RNAPII-Rat1-Rai1 pre-termination complex Deposited 2024-02-25 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.30 Å
8YFR Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex bound within the RNAPII cleft Deposited 2024-02-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.40 Å
9II7 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome containing histone variant H2A.B Deposited 2024-06-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9UJS RNA polymerase II elongation complex stalled at SHL(-4) of the H3-H4 octasome Deposited 2025-04-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain J 1–72（72 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
9UJT RNA polymerase II elongation complex stalled at SHL(-0.5) of the H3-H4 octasome (tetrasome) Deposited 2025-04-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain J 1–72（72 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.54 Å
9WMS Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type B) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9WMT Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type A) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
9WMU Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type A) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.28 Å
9WMV Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type B) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.66 Å
9WMW Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, FACT-hexamer) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain J 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å

43 other PDB entries and 45 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C4R009_KOMPG
Isoform —
PDB entities 10
Chains and sequence ranges Author chain J； PDBConstruct 1–72； UniProt 1–72

RNA polymerase II subunit B12.5

OrganismNot specified

UniProt C4R3Z5

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 14 DNA 2 RNA 1 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain K； UniProt 1–118 Not recorded DNA-directed RNA polymerase subunit × 1 （C4R4Y0） DNA-directed RNA polymerase subunit beta × 1 （C4QZQ7） RNA polymerase II third largest subunit B44, part of central core × 1 （C4R7L2） RNA polymerase II subunit B32 × 1 （C4R2U9） RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III × 1 （C4R3P8） RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III × 1 （C4R1V1） RNA polymerase II subunit × 1 （C4R9A1） RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III × 1 （C4R273） DNA-directed RNA polymerase subunit × 1 （F2QPE6） RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III × 1 （C4R009） RNA polymerase subunit ABC10-alpha × 1 （F2QMI1） ;RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3') ; × 1 DNA (39-MER) × 1 DNA (30-MER) × 1 Transcription elongation factor 1 homolog × 1 （A0A1B2JER8） Spt4/5 complex component × 1 （F2QUC3） ZN ZINC ION × 9 MG MAGNESIUM ION × 1 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；50 mM potassium malonate (pH 6.0), 150 mM Tris malonate (malonic acid titrated with Tris(hydroxymethyl) aminomethane, pH 6.0), 6.67% (v/v) glycerol, 6.67% (w/v) trehalose dihydrate and 10% PEG20000 Resolution 3.00 Å R-free 0.225

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5XOG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5X4Z RNA Polymerase II from Komagataella Pastoris (Type-1 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M sodium citrate, 8% PGA-LM, 10% glycerol
Resolution 7.80 Å R-free 0.357
5X4Z RNA Polymerase II from Komagataella Pastoris (Type-1 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain W 1–118（118 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M sodium citrate, 8% PGA-LM, 10% glycerol
Resolution 7.80 Å R-free 0.357
5X50 RNA Polymerase II from Komagataella Pastoris (Type-2 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；287 K；0.2 M sodium citrate, 8% PGA-LM and 1 % dextran sulfate sodium salt
Resolution 4.29 Å R-free 0.296
5X51 RNA Polymerase II from Komagataella Pastoris (Type-3 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M sodium citrate, 10% PGA-LM, 0.5% dextran sulfate sodium salt, 15 mM Tris, and 35 mM Hepes
Resolution 7.00 Å R-free 0.335
5X51 RNA Polymerase II from Komagataella Pastoris (Type-3 crystal) Deposited 2017-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain W 1–118（118 aa）
Not recorded ZN ZINC ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.15 M sodium citrate, 10% PGA-LM, 0.5% dextran sulfate sodium salt, 15 mM Tris, and 35 mM Hepes
Resolution 7.00 Å R-free 0.335
5XON RNA Polymerase II elongation complex bound with Spt4/5 and TFIIS Deposited 2017-05-29 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.83 Å
6A5L RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA Deposited 2018-06-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.60 Å
6A5O RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.90 Å
6A5P RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å
6A5R RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
6A5T RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.70 Å
6A5U RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
6INQ RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position) Deposited 2018-10-26 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
6IR9 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome Deposited 2018-11-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6J4W RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-5) of the nucleosome Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.90 Å
6J4X RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1A) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Y RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Z RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6J50 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
6J51 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7WBV RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7WBW RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3.5) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.10 Å
7WBX RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7XN7 RNA polymerase II elongation complex containing Spt4/5, Elf1, Spt6, Spn1 and Paf1C Deposited 2022-04-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7XSE RNA polymerase II elongation complex transcribing a nucleosome (EC42) Deposited 2022-05-13 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7XSX RNA polymerase II elongation complex transcribing a nucleosome (EC49) Deposited 2022-05-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7XSZ RNA polymerase II elongation complex transcribing a nucleosome (EC115) Deposited 2022-05-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7XT7 RNA polymerase II elongation complex transcribing a nucleosome (EC49B) Deposited 2022-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7XTD RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) Deposited 2022-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7XTI RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) Deposited 2022-05-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8H0V RNA polymerase II transcribing a chromatosome (type I) Deposited 2022-09-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8H0W RNA polymerase II transcribing a chromatosome (type II) Deposited 2022-09-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8HE5 RNA polymerase II elongation complex bound with Rad26 and Elf1, stalled at SHL(-3.5) of the nucleosome Deposited 2022-11-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.95 Å
8JH2 RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.70 Å
8JH3 RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8JH4 RNA polymerase II elongation complex containing 60 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8YFQ Cryo EM structure of Komagataella phaffii RNAPII-Rat1-Rai1 pre-termination complex Deposited 2024-02-25 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.30 Å
8YFR Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex bound within the RNAPII cleft Deposited 2024-02-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.40 Å
9II7 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome containing histone variant H2A.B Deposited 2024-06-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9UJS RNA polymerase II elongation complex stalled at SHL(-4) of the H3-H4 octasome Deposited 2025-04-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain K 1–118（118 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
9UJT RNA polymerase II elongation complex stalled at SHL(-0.5) of the H3-H4 octasome (tetrasome) Deposited 2025-04-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain K 1–118（118 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.54 Å
9WMS Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type B) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9WMT Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type A) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
9WMU Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type A) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.28 Å
9WMV Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type B) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.66 Å
9WMW Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, FACT-hexamer) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain K 1–118（118 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å

44 other PDB entries and 46 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name C4R3Z5_KOMPG
Isoform —
PDB entities 11
Chains and sequence ranges Author chain K； PDBConstruct 1–118； UniProt 1–118

RNA polymerase subunit ABC10-alpha

OrganismNot specified

UniProt F2QMI1

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 14 DNA 2 RNA 1 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain L； UniProt 1–72 Not recorded DNA-directed RNA polymerase subunit × 1 （C4R4Y0） DNA-directed RNA polymerase subunit beta × 1 （C4QZQ7） RNA polymerase II third largest subunit B44, part of central core × 1 （C4R7L2） RNA polymerase II subunit B32 × 1 （C4R2U9） RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III × 1 （C4R3P8） RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III × 1 （C4R1V1） RNA polymerase II subunit × 1 （C4R9A1） RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III × 1 （C4R273） DNA-directed RNA polymerase subunit × 1 （F2QPE6） RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III × 1 （C4R009） RNA polymerase II subunit B12.5 × 1 （C4R3Z5） ;RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3') ; × 1 DNA (39-MER) × 1 DNA (30-MER) × 1 Transcription elongation factor 1 homolog × 1 （A0A1B2JER8） Spt4/5 complex component × 1 （F2QUC3） ZN ZINC ION × 9 MG MAGNESIUM ION × 1 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；50 mM potassium malonate (pH 6.0), 150 mM Tris malonate (malonic acid titrated with Tris(hydroxymethyl) aminomethane, pH 6.0), 6.67% (v/v) glycerol, 6.67% (w/v) trehalose dihydrate and 10% PEG20000 Resolution 3.00 Å R-free 0.225

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5XOG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6A5L RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA Deposited 2018-06-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.60 Å
6A5O RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 9.90 Å
6A5P RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å
6A5R RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.70 Å
6A5T RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.70 Å
6A5U RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation Deposited 2018-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.60 Å
6INQ RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position) Deposited 2018-10-26 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
6IR9 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome Deposited 2018-11-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6J4W RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-5) of the nucleosome Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.90 Å
6J4X RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1A) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Y RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6J4Z RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6J50 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
6J51 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position) Deposited 2019-01-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7WBV RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
7WBW RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3.5) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.10 Å
7WBX RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome Deposited 2021-12-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7XN7 RNA polymerase II elongation complex containing Spt4/5, Elf1, Spt6, Spn1 and Paf1C Deposited 2022-04-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7XSE RNA polymerase II elongation complex transcribing a nucleosome (EC42) Deposited 2022-05-13 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7XSX RNA polymerase II elongation complex transcribing a nucleosome (EC49) Deposited 2022-05-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7XSZ RNA polymerase II elongation complex transcribing a nucleosome (EC115) Deposited 2022-05-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7XT7 RNA polymerase II elongation complex transcribing a nucleosome (EC49B) Deposited 2022-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7XTD RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) Deposited 2022-05-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7XTI RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) Deposited 2022-05-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8H0V RNA polymerase II transcribing a chromatosome (type I) Deposited 2022-09-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8H0W RNA polymerase II transcribing a chromatosome (type II) Deposited 2022-09-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8HE5 RNA polymerase II elongation complex bound with Rad26 and Elf1, stalled at SHL(-3.5) of the nucleosome Deposited 2022-11-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 25-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.95 Å
8JH2 RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.70 Å
8JH3 RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8JH4 RNA polymerase II elongation complex containing 60 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8YFQ Cryo EM structure of Komagataella phaffii RNAPII-Rat1-Rai1 pre-termination complex Deposited 2024-02-25 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.30 Å
8YFR Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex bound within the RNAPII cleft Deposited 2024-02-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；EMGP2
Resolution 3.40 Å
9II7 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome containing histone variant H2A.B Deposited 2024-06-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES-KOH(pH7.5), 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9UJS RNA polymerase II elongation complex stalled at SHL(-4) of the H3-H4 octasome Deposited 2025-04-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric
Chain L 1–72（72 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
9UJT RNA polymerase II elongation complex stalled at SHL(-0.5) of the H3-H4 octasome (tetrasome) Deposited 2025-04-17 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain L 1–72（72 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.54 Å
9WMS Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type B) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9WMT Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type A) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.59 Å
9WMU Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type A) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.28 Å
9WMV Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type B) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.66 Å
9WMW Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, FACT-hexamer) Deposited 2025-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric
Chain L 1–72（72 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å

40 other PDB entries and 40 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name F2QMI1_KOMPC
Isoform —
PDB entities 12
Chains and sequence ranges Author chain L； PDBConstruct 1–72； UniProt 1–72

Transcription elongation factor 1 homolog

Komagataella pastoris

UniProt A0A1B2JER8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 14 DNA 2 RNA 1 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain M； UniProt 1–82 Fragment：UNP residues 1-82 Mutation：N53G, L54Q, S55R DNA-directed RNA polymerase subunit × 1 （C4R4Y0） DNA-directed RNA polymerase subunit beta × 1 （C4QZQ7） RNA polymerase II third largest subunit B44, part of central core × 1 （C4R7L2） RNA polymerase II subunit B32 × 1 （C4R2U9） RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III × 1 （C4R3P8） RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III × 1 （C4R1V1） RNA polymerase II subunit × 1 （C4R9A1） RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III × 1 （C4R273） DNA-directed RNA polymerase subunit × 1 （F2QPE6） RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III × 1 （C4R009） RNA polymerase II subunit B12.5 × 1 （C4R3Z5） RNA polymerase subunit ABC10-alpha × 1 （F2QMI1） ;RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3') ; × 1 DNA (39-MER) × 1 DNA (30-MER) × 1 Spt4/5 complex component × 1 （F2QUC3） ZN ZINC ION × 9 MG MAGNESIUM ION × 1 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；50 mM potassium malonate (pH 6.0), 150 mM Tris malonate (malonic acid titrated with Tris(hydroxymethyl) aminomethane, pH 6.0), 6.67% (v/v) glycerol, 6.67% (w/v) trehalose dihydrate and 10% PEG20000 Resolution 3.00 Å R-free 0.225

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name A0A1B2JER8_PICPA
Isoform —
PDB entities 16
Chains and sequence ranges Author chain M； PDBConstruct 4–85； UniProt 1–82

Spt4/5 complex component

Komagataella phaffii

UniProt F2QUC3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 14 DNA 2 RNA 1 PDB declaration: heptadecameric（17） Consistent with all polymer counts Chain W； UniProt 736–815 Fragment：UNP residues 736-815 DNA-directed RNA polymerase subunit × 1 （C4R4Y0） DNA-directed RNA polymerase subunit beta × 1 （C4QZQ7） RNA polymerase II third largest subunit B44, part of central core × 1 （C4R7L2） RNA polymerase II subunit B32 × 1 （C4R2U9） RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III × 1 （C4R3P8） RNA polymerase subunit ABC23, common to RNA polymerases I, II, and III × 1 （C4R1V1） RNA polymerase II subunit × 1 （C4R9A1） RNA polymerase subunit ABC14.5, common to RNA polymerases I, II, and III × 1 （C4R273） DNA-directed RNA polymerase subunit × 1 （F2QPE6） RNA polymerase subunit ABC10-beta, common to RNA polymerases I, II, and III × 1 （C4R009） RNA polymerase II subunit B12.5 × 1 （C4R3Z5） RNA polymerase subunit ABC10-alpha × 1 （F2QMI1） ;RNA (5'-R(*UP*UP*UP*UP*UP*UP*UP*AP*UP*CP*GP*AP*GP*AP*GP*GP*U)-3') ; × 1 DNA (39-MER) × 1 DNA (30-MER) × 1 Transcription elongation factor 1 homolog × 1 （A0A1B2JER8） ZN ZINC ION × 9 MG MAGNESIUM ION × 1 APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；50 mM potassium malonate (pH 6.0), 150 mM Tris malonate (malonic acid titrated with Tris(hydroxymethyl) aminomethane, pH 6.0), 6.67% (v/v) glycerol, 6.67% (w/v) trehalose dihydrate and 10% PEG20000 Resolution 3.00 Å R-free 0.225

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5XOG Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7WBV RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome Deposited 2021-12-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain W 1–809（809 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name F2QUC3_KOMPC
Isoform —
PDB entities 17
Chains and sequence ranges Author chain W； PDBConstruct 4–83； UniProt 736–815

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 5xog

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5xog
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5xog
Deposition date deposition_date2017-05-28
Structure title titleRNA Polymerase II elongation complex bound with Spt5 KOW5 and Elf1
Keywords keywordstranscription, complex; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier51.11 Å
Radius of gyration Rg (electron density) rg_electron50.84 Å
Forward intensity I(0) i03533420000.00
Molecular weight molecular_weight481900.0 kDa
Excluded volume excluded_volume596430 ų
Envelope volume envelope_volume838790 ų
Hydration-shell volume shell_volume129120 ų
Envelope diameter envelope_diameter168.3 Å
Shell Rg shell_rg60.18 Å
Envelope Rg envelope_rg50.49 Å
Shape Rg shape_rg50.87 Å
Total Rg total_rg51.01 Å
Total atoms total_atoms33711
Residues n_residues4131
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax164.9 Å
Rg (real space) rg_real50.91 Å
Rg uncertainty (real space) rg_real_error1.32 Å
I(0) (real space) i0_real3.5330e+09
I(0) uncertainty (real space) i0_real_error6.7530e+07
Rg (reciprocal space) rg_reciprocal51.27 Å
I(0) (reciprocal space) i0_reciprocal3535000000.0000
Solution quality estimate total_estimate0.8802
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary63.8 Å
Skewness Skewness skewness0.188
Kurtosis Kurtosis kurtosis-0.424
Angular range angular_range— – 0.1550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha709300000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.869
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (20)

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7. Fold Classification (SCOP + CATH) 19 domains

CATH v4.4 (19 domains)

Domain ID domain_id5xogA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology274 — Enzyme I; Chain A, domain 2
Homologous superfamily homologous superfamily100 — RNA polymerase Rpb1, domain 3
Domain ID domain_id5xogA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily140 —
Domain ID domain_id5xogB01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1110 — Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3
Homologous superfamily homologous superfamily10 — RNA polymerase Rpb2, domain 2
Domain ID domain_id5xogB02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1800 — DCoH-like
Homologous superfamily homologous superfamily10 — RNA polymerase alpha subunit dimerisation domain
Domain ID domain_id5xogC01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily10 — RNA polymerase, RBP11-like subunit
Domain ID domain_id5xogC02
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology120 — RNA Polymerase Alpha Subunit; Chain A, domain 2
Homologous superfamily homologous superfamily12 — DNA-directed RNA polymerase, insert domain
Domain ID domain_id5xogD02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily40 — RNA Polymerase II, Rpb4 subunit
Domain ID domain_id5xogE01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1340 — Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1
Homologous superfamily homologous superfamily10 — RNA polymerase, Rpb5, N-terminal domain
Domain ID domain_id5xogE02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology940 — Eukaryotic RPB6 RNA polymerase subunit
Homologous superfamily homologous superfamily20 — RPB5-like RNA polymerase subunit
Domain ID domain_id5xogF00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology940 — Eukaryotic RPB6 RNA polymerase subunit
Homologous superfamily homologous superfamily10 — RNA polymerase subunit, RPB6/omega
Domain ID domain_id5xogG01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily120 — RNA polymerase Rpb7-like, N-terminal domain
Domain ID domain_id5xogG02
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
Domain ID domain_id5xogH00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
Domain ID domain_id5xogI01
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily10 —
Domain ID domain_id5xogI02
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily10 —
Domain ID domain_id5xogJ00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — Homeodomain-like
Domain ID domain_id5xogK00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily10 — RNA polymerase, RBP11-like subunit
Domain ID domain_id5xogL00
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily30 — RNA polymerase ii, chain L
Domain ID domain_id5xogM00
Class class2 — Mainly Beta
Architecture architecture20 — Single Sheet
Topology topology25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily190 —
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8. Citations (1)

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9. Files and Curves (10)