9xgk

Structure of mammalian RNA polymerase II stalled by Actinomycin D at the N-1 position.

Method: ELECTRON MICROSCOPY D_max: 160.8 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed RNA polymerase II subunit RPB1

OrganismNot specified

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 × 13 DNA 2 RNA 1 PDB declaration: hexadecameric（16） Consistent with all polymer counts	Chain A； UniProt 1–1970	Not recorded	DNA-directed RNA polymerase II subunit RPB2 × 1 （A5PJW8） DNA-directed RNA polymerase II subunit RPB3 × 1 （Q3T0Q3） DNA-directed RNA polymerase II subunit RPB4 × 1 （Q1JQ91） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （Q2T9T3） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （F2Z4C9） DNA-directed RNA polymerase II subunit RPB7 × 1 （Q5E9B8） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （F2Z4H3） DNA-directed RNA polymerase II subunit RPB9 × 1 （Q32P73） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q32P78） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q32P79） DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 （Q3ZBC0） Actinomycin D × 1 DNA (NTS, non-template strand) × 1 RNA × 1 DNA (TS, template strand) × 1 ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.53 Å

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 9XGK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8QQ2 RNAPII elongation complex bound to RECQ5 Deposited 2023-10-03	Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain A 1–1970（1970 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-PROPANE	Resolution 4.20 Å
8QW8 In condensate RNAPII elongation complex bound to RECQ5 Deposited 2023-10-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain A 1–1970（1970 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.70 Å
8QW9 RNAPII elongation complex bound to RECQ5_R502E Deposited 2023-10-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain A 1–1970（1970 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.30 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPB1_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1970； UniProt 1–1970

DNA-directed RNA polymerase II subunit RPB2

OrganismNot specified

UniProt A5PJW8

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 × 13 DNA 2 RNA 1 PDB declaration: hexadecameric（16） Consistent with all polymer counts	Chain B； UniProt 1–1174	Not recorded	DNA-directed RNA polymerase II subunit RPB1 × 1 （G3MZY8） DNA-directed RNA polymerase II subunit RPB3 × 1 （Q3T0Q3） DNA-directed RNA polymerase II subunit RPB4 × 1 （Q1JQ91） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （Q2T9T3） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （F2Z4C9） DNA-directed RNA polymerase II subunit RPB7 × 1 （Q5E9B8） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （F2Z4H3） DNA-directed RNA polymerase II subunit RPB9 × 1 （Q32P73） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q32P78） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q32P79） DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 （Q3ZBC0） Actinomycin D × 1 DNA (NTS, non-template strand) × 1 RNA × 1 DNA (TS, template strand) × 1 ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.53 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9XGK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5FLM Structure of transcribing mammalian RNA polymerase II Deposited 2015-10-26	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric	Chain B 1–1174（1174 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer 150 MM NACL, 5 MM HEPES, 0.01 MM ZNCL2, 10 MM DTT；pH 7.25；150 MM NACL, 5 MM HEPES, 0.01 MM ZNCL2, 10 MM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
5OIK Structure of an RNA polymerase II-DSIF transcription elongation complex Deposited 2017-07-18	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain B 1–1174（1174 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.25；pH was adjusted at 25 degrees Celsius cryo-EM vitrification conditions Cryogen ETHANE；Sample (four microliters) was applied to glow-discharged Quantifoil R 2/1 holey carbon grids, which were then blotted for 8.5s and plunge-frozen in liquid ethane.	Resolution 3.70 Å
8QQ2 RNAPII elongation complex bound to RECQ5 Deposited 2023-10-03	Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain B 1–1174（1174 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-PROPANE	Resolution 4.20 Å
8QW8 In condensate RNAPII elongation complex bound to RECQ5 Deposited 2023-10-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain B 1–1174（1174 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.70 Å
8QW9 RNAPII elongation complex bound to RECQ5_R502E Deposited 2023-10-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain B 1–1174（1174 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.30 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPB2_BOVIN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–1174； UniProt 1–1174

DNA-directed RNA polymerase II subunit RPB3

OrganismNot specified

UniProt Q3T0Q3

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 × 13 DNA 2 RNA 1 PDB declaration: hexadecameric（16） Consistent with all polymer counts	Chain C； UniProt 1–275	Not recorded	DNA-directed RNA polymerase II subunit RPB1 × 1 （G3MZY8） DNA-directed RNA polymerase II subunit RPB2 × 1 （A5PJW8） DNA-directed RNA polymerase II subunit RPB4 × 1 （Q1JQ91） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （Q2T9T3） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （F2Z4C9） DNA-directed RNA polymerase II subunit RPB7 × 1 （Q5E9B8） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （F2Z4H3） DNA-directed RNA polymerase II subunit RPB9 × 1 （Q32P73） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q32P78） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q32P79） DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 （Q3ZBC0） Actinomycin D × 1 DNA (NTS, non-template strand) × 1 RNA × 1 DNA (TS, template strand) × 1 ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.53 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9XGK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5FLM Structure of transcribing mammalian RNA polymerase II Deposited 2015-10-26	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric	Chain C 1–275（275 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer 150 MM NACL, 5 MM HEPES, 0.01 MM ZNCL2, 10 MM DTT；pH 7.25；150 MM NACL, 5 MM HEPES, 0.01 MM ZNCL2, 10 MM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
5OIK Structure of an RNA polymerase II-DSIF transcription elongation complex Deposited 2017-07-18	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain C 1–275（275 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.25；pH was adjusted at 25 degrees Celsius cryo-EM vitrification conditions Cryogen ETHANE；Sample (four microliters) was applied to glow-discharged Quantifoil R 2/1 holey carbon grids, which were then blotted for 8.5s and plunge-frozen in liquid ethane.	Resolution 3.70 Å
8QQ2 RNAPII elongation complex bound to RECQ5 Deposited 2023-10-03	Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain C 1–275（275 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-PROPANE	Resolution 4.20 Å
8QW8 In condensate RNAPII elongation complex bound to RECQ5 Deposited 2023-10-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain C 1–275（275 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.70 Å
8QW9 RNAPII elongation complex bound to RECQ5_R502E Deposited 2023-10-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain C 1–275（275 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.30 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPB3_BOVIN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–275； UniProt 1–275

DNA-directed RNA polymerase II subunit RPB4

OrganismNot specified

UniProt Q1JQ91

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 × 13 DNA 2 RNA 1 PDB declaration: hexadecameric（16） Consistent with all polymer counts	Chain D； UniProt 1–142	Not recorded	DNA-directed RNA polymerase II subunit RPB1 × 1 （G3MZY8） DNA-directed RNA polymerase II subunit RPB2 × 1 （A5PJW8） DNA-directed RNA polymerase II subunit RPB3 × 1 （Q3T0Q3） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （Q2T9T3） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （F2Z4C9） DNA-directed RNA polymerase II subunit RPB7 × 1 （Q5E9B8） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （F2Z4H3） DNA-directed RNA polymerase II subunit RPB9 × 1 （Q32P73） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q32P78） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q32P79） DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 （Q3ZBC0） Actinomycin D × 1 DNA (NTS, non-template strand) × 1 RNA × 1 DNA (TS, template strand) × 1 ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.53 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9XGK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5FLM Structure of transcribing mammalian RNA polymerase II Deposited 2015-10-26	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric	Chain D 1–142（142 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer 150 MM NACL, 5 MM HEPES, 0.01 MM ZNCL2, 10 MM DTT；pH 7.25；150 MM NACL, 5 MM HEPES, 0.01 MM ZNCL2, 10 MM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
5OIK Structure of an RNA polymerase II-DSIF transcription elongation complex Deposited 2017-07-18	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain D 1–142（142 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.25；pH was adjusted at 25 degrees Celsius cryo-EM vitrification conditions Cryogen ETHANE；Sample (four microliters) was applied to glow-discharged Quantifoil R 2/1 holey carbon grids, which were then blotted for 8.5s and plunge-frozen in liquid ethane.	Resolution 3.70 Å
8QQ2 RNAPII elongation complex bound to RECQ5 Deposited 2023-10-03	Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain D 1–142（142 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-PROPANE	Resolution 4.20 Å
8QW8 In condensate RNAPII elongation complex bound to RECQ5 Deposited 2023-10-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain D 1–142（142 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.70 Å
8QW9 RNAPII elongation complex bound to RECQ5_R502E Deposited 2023-10-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain D 1–142（142 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.30 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPB4_BOVIN
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–142； UniProt 1–142

DNA-directed RNA polymerases I, II, and III subunit RPABC1

OrganismNot specified

UniProt Q2T9T3

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 × 13 DNA 2 RNA 1 PDB declaration: hexadecameric（16） Consistent with all polymer counts	Chain E； UniProt 1–210	Not recorded	DNA-directed RNA polymerase II subunit RPB1 × 1 （G3MZY8） DNA-directed RNA polymerase II subunit RPB2 × 1 （A5PJW8） DNA-directed RNA polymerase II subunit RPB3 × 1 （Q3T0Q3） DNA-directed RNA polymerase II subunit RPB4 × 1 （Q1JQ91） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （F2Z4C9） DNA-directed RNA polymerase II subunit RPB7 × 1 （Q5E9B8） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （F2Z4H3） DNA-directed RNA polymerase II subunit RPB9 × 1 （Q32P73） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q32P78） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q32P79） DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 （Q3ZBC0） Actinomycin D × 1 DNA (NTS, non-template strand) × 1 RNA × 1 DNA (TS, template strand) × 1 ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.53 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9XGK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5FLM Structure of transcribing mammalian RNA polymerase II Deposited 2015-10-26	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric	Chain E 1–210（210 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer 150 MM NACL, 5 MM HEPES, 0.01 MM ZNCL2, 10 MM DTT；pH 7.25；150 MM NACL, 5 MM HEPES, 0.01 MM ZNCL2, 10 MM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
5OIK Structure of an RNA polymerase II-DSIF transcription elongation complex Deposited 2017-07-18	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain E 1–210（210 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.25；pH was adjusted at 25 degrees Celsius cryo-EM vitrification conditions Cryogen ETHANE；Sample (four microliters) was applied to glow-discharged Quantifoil R 2/1 holey carbon grids, which were then blotted for 8.5s and plunge-frozen in liquid ethane.	Resolution 3.70 Å
8QQ2 RNAPII elongation complex bound to RECQ5 Deposited 2023-10-03	Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain E 1–210（210 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-PROPANE	Resolution 4.20 Å
8QW8 In condensate RNAPII elongation complex bound to RECQ5 Deposited 2023-10-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain E 1–210（210 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.70 Å
8QW9 RNAPII elongation complex bound to RECQ5_R502E Deposited 2023-10-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain E 1–210（210 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.30 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPAB1_BOVIN
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–210； UniProt 1–210

DNA-directed RNA polymerases I, II, and III subunit RPABC2

OrganismNot specified

UniProt F2Z4C9

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 × 13 DNA 2 RNA 1 PDB declaration: hexadecameric（16） Consistent with all polymer counts	Chain F； UniProt 1–127	Not recorded	DNA-directed RNA polymerase II subunit RPB1 × 1 （G3MZY8） DNA-directed RNA polymerase II subunit RPB2 × 1 （A5PJW8） DNA-directed RNA polymerase II subunit RPB3 × 1 （Q3T0Q3） DNA-directed RNA polymerase II subunit RPB4 × 1 （Q1JQ91） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （Q2T9T3） DNA-directed RNA polymerase II subunit RPB7 × 1 （Q5E9B8） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （F2Z4H3） DNA-directed RNA polymerase II subunit RPB9 × 1 （Q32P73） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q32P78） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q32P79） DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 （Q3ZBC0） Actinomycin D × 1 DNA (NTS, non-template strand) × 1 RNA × 1 DNA (TS, template strand) × 1 ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.53 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9XGK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5OIK Structure of an RNA polymerase II-DSIF transcription elongation complex Deposited 2017-07-18	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain F 1–127（127 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.25；pH was adjusted at 25 degrees Celsius cryo-EM vitrification conditions Cryogen ETHANE；Sample (four microliters) was applied to glow-discharged Quantifoil R 2/1 holey carbon grids, which were then blotted for 8.5s and plunge-frozen in liquid ethane.	Resolution 3.70 Å

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

View Construct and Data Evidence

UniProt name	F2Z4C9_BOVIN
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain F； PDBConstruct 1–127； UniProt 1–127

DNA-directed RNA polymerase II subunit RPB7

OrganismNot specified

UniProt Q5E9B8

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 × 13 DNA 2 RNA 1 PDB declaration: hexadecameric（16） Consistent with all polymer counts	Chain G； UniProt 1–172	Not recorded	DNA-directed RNA polymerase II subunit RPB1 × 1 （G3MZY8） DNA-directed RNA polymerase II subunit RPB2 × 1 （A5PJW8） DNA-directed RNA polymerase II subunit RPB3 × 1 （Q3T0Q3） DNA-directed RNA polymerase II subunit RPB4 × 1 （Q1JQ91） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （Q2T9T3） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （F2Z4C9） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （F2Z4H3） DNA-directed RNA polymerase II subunit RPB9 × 1 （Q32P73） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q32P78） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q32P79） DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 （Q3ZBC0） Actinomycin D × 1 DNA (NTS, non-template strand) × 1 RNA × 1 DNA (TS, template strand) × 1 ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.53 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9XGK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5FLM Structure of transcribing mammalian RNA polymerase II Deposited 2015-10-26	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric	Chain G 1–172（172 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer 150 MM NACL, 5 MM HEPES, 0.01 MM ZNCL2, 10 MM DTT；pH 7.25；150 MM NACL, 5 MM HEPES, 0.01 MM ZNCL2, 10 MM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
5OIK Structure of an RNA polymerase II-DSIF transcription elongation complex Deposited 2017-07-18	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain G 1–172（172 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.25；pH was adjusted at 25 degrees Celsius cryo-EM vitrification conditions Cryogen ETHANE；Sample (four microliters) was applied to glow-discharged Quantifoil R 2/1 holey carbon grids, which were then blotted for 8.5s and plunge-frozen in liquid ethane.	Resolution 3.70 Å
8QQ2 RNAPII elongation complex bound to RECQ5 Deposited 2023-10-03	Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain G 1–172（172 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-PROPANE	Resolution 4.20 Å
8QW8 In condensate RNAPII elongation complex bound to RECQ5 Deposited 2023-10-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain G 1–172（172 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.70 Å
8QW9 RNAPII elongation complex bound to RECQ5_R502E Deposited 2023-10-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain G 1–172（172 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.30 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPB7_BOVIN
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain G； PDBConstruct 1–172； UniProt 1–172

DNA-directed RNA polymerases I, II, and III subunit RPABC3

OrganismNot specified

UniProt F2Z4H3

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 × 13 DNA 2 RNA 1 PDB declaration: hexadecameric（16） Consistent with all polymer counts	Chain H； UniProt 1–150	Not recorded	DNA-directed RNA polymerase II subunit RPB1 × 1 （G3MZY8） DNA-directed RNA polymerase II subunit RPB2 × 1 （A5PJW8） DNA-directed RNA polymerase II subunit RPB3 × 1 （Q3T0Q3） DNA-directed RNA polymerase II subunit RPB4 × 1 （Q1JQ91） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （Q2T9T3） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （F2Z4C9） DNA-directed RNA polymerase II subunit RPB7 × 1 （Q5E9B8） DNA-directed RNA polymerase II subunit RPB9 × 1 （Q32P73） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q32P78） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q32P79） DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 （Q3ZBC0） Actinomycin D × 1 DNA (NTS, non-template strand) × 1 RNA × 1 DNA (TS, template strand) × 1 ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.53 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9XGK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5FLM Structure of transcribing mammalian RNA polymerase II Deposited 2015-10-26	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric	Chain H 1–150（150 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer 150 MM NACL, 5 MM HEPES, 0.01 MM ZNCL2, 10 MM DTT；pH 7.25；150 MM NACL, 5 MM HEPES, 0.01 MM ZNCL2, 10 MM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
5OIK Structure of an RNA polymerase II-DSIF transcription elongation complex Deposited 2017-07-18	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain H 1–150（150 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.25；pH was adjusted at 25 degrees Celsius cryo-EM vitrification conditions Cryogen ETHANE；Sample (four microliters) was applied to glow-discharged Quantifoil R 2/1 holey carbon grids, which were then blotted for 8.5s and plunge-frozen in liquid ethane.	Resolution 3.70 Å
8QQ2 RNAPII elongation complex bound to RECQ5 Deposited 2023-10-03	Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain H 1–150（150 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-PROPANE	Resolution 4.20 Å
8QW8 In condensate RNAPII elongation complex bound to RECQ5 Deposited 2023-10-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain H 1–150（150 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.70 Å
8QW9 RNAPII elongation complex bound to RECQ5_R502E Deposited 2023-10-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain H 1–150（150 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.30 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPAB3_BOVIN
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain H； PDBConstruct 1–150； UniProt 1–150

DNA-directed RNA polymerase II subunit RPB9

OrganismNot specified

UniProt Q32P73

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 × 13 DNA 2 RNA 1 PDB declaration: hexadecameric（16） Consistent with all polymer counts	Chain I； UniProt 1–125	Not recorded	DNA-directed RNA polymerase II subunit RPB1 × 1 （G3MZY8） DNA-directed RNA polymerase II subunit RPB2 × 1 （A5PJW8） DNA-directed RNA polymerase II subunit RPB3 × 1 （Q3T0Q3） DNA-directed RNA polymerase II subunit RPB4 × 1 （Q1JQ91） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （Q2T9T3） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （F2Z4C9） DNA-directed RNA polymerase II subunit RPB7 × 1 （Q5E9B8） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （F2Z4H3） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q32P78） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q32P79） DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 （Q3ZBC0） Actinomycin D × 1 DNA (NTS, non-template strand) × 1 RNA × 1 DNA (TS, template strand) × 1 ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.53 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9XGK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5FLM Structure of transcribing mammalian RNA polymerase II Deposited 2015-10-26	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric	Chain I 1–125（125 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer 150 MM NACL, 5 MM HEPES, 0.01 MM ZNCL2, 10 MM DTT；pH 7.25；150 MM NACL, 5 MM HEPES, 0.01 MM ZNCL2, 10 MM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
5OIK Structure of an RNA polymerase II-DSIF transcription elongation complex Deposited 2017-07-18	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain I 1–125（125 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.25；pH was adjusted at 25 degrees Celsius cryo-EM vitrification conditions Cryogen ETHANE；Sample (four microliters) was applied to glow-discharged Quantifoil R 2/1 holey carbon grids, which were then blotted for 8.5s and plunge-frozen in liquid ethane.	Resolution 3.70 Å
8QQ2 RNAPII elongation complex bound to RECQ5 Deposited 2023-10-03	Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain I 1–125（125 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-PROPANE	Resolution 4.20 Å
8QW8 In condensate RNAPII elongation complex bound to RECQ5 Deposited 2023-10-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain I 1–125（125 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.70 Å
8QW9 RNAPII elongation complex bound to RECQ5_R502E Deposited 2023-10-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain I 1–125（125 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.30 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPB9_BOVIN
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain I； PDBConstruct 1–125； UniProt 1–125

DNA-directed RNA polymerases I, II, and III subunit RPABC5

OrganismNot specified

UniProt Q32P78

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 × 13 DNA 2 RNA 1 PDB declaration: hexadecameric（16） Consistent with all polymer counts	Chain J； UniProt 1–67	Not recorded	DNA-directed RNA polymerase II subunit RPB1 × 1 （G3MZY8） DNA-directed RNA polymerase II subunit RPB2 × 1 （A5PJW8） DNA-directed RNA polymerase II subunit RPB3 × 1 （Q3T0Q3） DNA-directed RNA polymerase II subunit RPB4 × 1 （Q1JQ91） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （Q2T9T3） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （F2Z4C9） DNA-directed RNA polymerase II subunit RPB7 × 1 （Q5E9B8） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （F2Z4H3） DNA-directed RNA polymerase II subunit RPB9 × 1 （Q32P73） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q32P79） DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 （Q3ZBC0） Actinomycin D × 1 DNA (NTS, non-template strand) × 1 RNA × 1 DNA (TS, template strand) × 1 ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.53 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9XGK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5FLM Structure of transcribing mammalian RNA polymerase II Deposited 2015-10-26	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric	Chain J 1–67（67 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer 150 MM NACL, 5 MM HEPES, 0.01 MM ZNCL2, 10 MM DTT；pH 7.25；150 MM NACL, 5 MM HEPES, 0.01 MM ZNCL2, 10 MM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
5OIK Structure of an RNA polymerase II-DSIF transcription elongation complex Deposited 2017-07-18	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain J 1–67（67 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.25；pH was adjusted at 25 degrees Celsius cryo-EM vitrification conditions Cryogen ETHANE；Sample (four microliters) was applied to glow-discharged Quantifoil R 2/1 holey carbon grids, which were then blotted for 8.5s and plunge-frozen in liquid ethane.	Resolution 3.70 Å
8QQ2 RNAPII elongation complex bound to RECQ5 Deposited 2023-10-03	Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain J 1–67（67 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-PROPANE	Resolution 4.20 Å
8QW8 In condensate RNAPII elongation complex bound to RECQ5 Deposited 2023-10-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain J 1–67（67 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.70 Å
8QW9 RNAPII elongation complex bound to RECQ5_R502E Deposited 2023-10-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain J 1–67（67 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.30 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPAB5_BOVIN
Isoform	—
PDB entities	10
Chains and sequence ranges	Author chain J； PDBConstruct 1–67； UniProt 1–67

DNA-directed RNA polymerase II subunit RPB11

OrganismNot specified

UniProt Q32P79

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 × 13 DNA 2 RNA 1 PDB declaration: hexadecameric（16） Consistent with all polymer counts	Chain K； UniProt 1–117	Not recorded	DNA-directed RNA polymerase II subunit RPB1 × 1 （G3MZY8） DNA-directed RNA polymerase II subunit RPB2 × 1 （A5PJW8） DNA-directed RNA polymerase II subunit RPB3 × 1 （Q3T0Q3） DNA-directed RNA polymerase II subunit RPB4 × 1 （Q1JQ91） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （Q2T9T3） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （F2Z4C9） DNA-directed RNA polymerase II subunit RPB7 × 1 （Q5E9B8） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （F2Z4H3） DNA-directed RNA polymerase II subunit RPB9 × 1 （Q32P73） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q32P78） DNA-directed RNA polymerases I, II, and III subunit RPABC4 × 1 （Q3ZBC0） Actinomycin D × 1 DNA (NTS, non-template strand) × 1 RNA × 1 DNA (TS, template strand) × 1 ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.53 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9XGK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5FLM Structure of transcribing mammalian RNA polymerase II Deposited 2015-10-26	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric	Chain K 1–117（117 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer 150 MM NACL, 5 MM HEPES, 0.01 MM ZNCL2, 10 MM DTT；pH 7.25；150 MM NACL, 5 MM HEPES, 0.01 MM ZNCL2, 10 MM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
5OIK Structure of an RNA polymerase II-DSIF transcription elongation complex Deposited 2017-07-18	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain K 1–117（117 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.25；pH was adjusted at 25 degrees Celsius cryo-EM vitrification conditions Cryogen ETHANE；Sample (four microliters) was applied to glow-discharged Quantifoil R 2/1 holey carbon grids, which were then blotted for 8.5s and plunge-frozen in liquid ethane.	Resolution 3.70 Å
8QQ2 RNAPII elongation complex bound to RECQ5 Deposited 2023-10-03	Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain K 1–117（117 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-PROPANE	Resolution 4.20 Å
8QW8 In condensate RNAPII elongation complex bound to RECQ5 Deposited 2023-10-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain K 1–117（117 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.70 Å
8QW9 RNAPII elongation complex bound to RECQ5_R502E Deposited 2023-10-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain K 1–117（117 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.30 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPB11_BOVIN
Isoform	—
PDB entities	11
Chains and sequence ranges	Author chain K； PDBConstruct 1–117； UniProt 1–117

DNA-directed RNA polymerases I, II, and III subunit RPABC4

OrganismNot specified

UniProt Q3ZBC0

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 × 13 DNA 2 RNA 1 PDB declaration: hexadecameric（16） Consistent with all polymer counts	Chain L； UniProt 1–58	Not recorded	DNA-directed RNA polymerase II subunit RPB1 × 1 （G3MZY8） DNA-directed RNA polymerase II subunit RPB2 × 1 （A5PJW8） DNA-directed RNA polymerase II subunit RPB3 × 1 （Q3T0Q3） DNA-directed RNA polymerase II subunit RPB4 × 1 （Q1JQ91） DNA-directed RNA polymerases I, II, and III subunit RPABC1 × 1 （Q2T9T3） DNA-directed RNA polymerases I, II, and III subunit RPABC2 × 1 （F2Z4C9） DNA-directed RNA polymerase II subunit RPB7 × 1 （Q5E9B8） DNA-directed RNA polymerases I, II, and III subunit RPABC3 × 1 （F2Z4H3） DNA-directed RNA polymerase II subunit RPB9 × 1 （Q32P73） DNA-directed RNA polymerases I, II, and III subunit RPABC5 × 1 （Q32P78） DNA-directed RNA polymerase II subunit RPB11 × 1 （Q32P79） Actinomycin D × 1 DNA (NTS, non-template strand) × 1 RNA × 1 DNA (TS, template strand) × 1 ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.53 Å

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 9XGK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5FLM Structure of transcribing mammalian RNA polymerase II Deposited 2015-10-26	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric	Chain L 1–58（58 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer 150 MM NACL, 5 MM HEPES, 0.01 MM ZNCL2, 10 MM DTT；pH 7.25；150 MM NACL, 5 MM HEPES, 0.01 MM ZNCL2, 10 MM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
5OIK Structure of an RNA polymerase II-DSIF transcription elongation complex Deposited 2017-07-18	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain L 1–58（58 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.25；pH was adjusted at 25 degrees Celsius cryo-EM vitrification conditions Cryogen ETHANE；Sample (four microliters) was applied to glow-discharged Quantifoil R 2/1 holey carbon grids, which were then blotted for 8.5s and plunge-frozen in liquid ethane.	Resolution 3.70 Å
8QQ2 RNAPII elongation complex bound to RECQ5 Deposited 2023-10-03	Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain L 1–58（58 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-PROPANE	Resolution 4.20 Å
8QW8 In condensate RNAPII elongation complex bound to RECQ5 Deposited 2023-10-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain L 1–58（58 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 7.70 Å
8QW9 RNAPII elongation complex bound to RECQ5_R502E Deposited 2023-10-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 13 PDB declaration: hexadecameric	Chain L 1–58（58 aa）	Not recorded	ZN ZINC ION × 7 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 4.30 Å

5 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	RPAB4_BOVIN
Isoform	—
PDB entities	12
Chains and sequence ranges	Author chain L； PDBConstruct 1–58； UniProt 1–58

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	9xgk
Deposition date deposition_date	2025-10-30
Structure title title	Structure of mammalian RNA polymerase II stalled by Actinomycin D at the N-1 position.
Keywords keywords	mammalian RNA polymerase II, Actinomycin D, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	49.84 Å
Radius of gyration Rg (electron density) rg_electron	49.41 Å
Forward intensity I(0) i0	3253890000.00
Molecular weight molecular_weight	463880.0 kDa
Excluded volume excluded_volume	574960 Å³
Envelope volume envelope_volume	783990 Å³
Hydration-shell volume shell_volume	123760 Å³
Envelope diameter envelope_diameter	164.1 Å
Shell Rg shell_rg	58.92 Å
Envelope Rg envelope_rg	49.42 Å
Shape Rg shape_rg	49.44 Å
Total Rg total_rg	49.59 Å
Total atoms total_atoms	32455
Residues n_residues	3963
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	160.8 Å
Rg (real space) rg_real	49.52 Å
Rg uncertainty (real space) rg_real_error	1.02 Å
I(0) (real space) i0_real	3.2540e+09
I(0) uncertainty (real space) i0_real_error	5.5490e+07
Rg (reciprocal space) rg_reciprocal	49.83 Å
I(0) (reciprocal space) i0_reciprocal	3255000000.0000
Solution quality estimate total_estimate	0.8780
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	60.3 Å
Skewness Skewness skewness	0.201
Kurtosis Kurtosis kurtosis	-0.400
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	650200000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.859; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.970; Smooth: 0.861

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5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (18)

Entity 1 Entity 1 polymer

Description description	DNA-directed RNA polymerase II subunit RPB1
Molecular weight formula_weight	217436.1 kDa
EC 编号 ec_number	2.7.7.6,3.1.13.-,2.7.7.48
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	32455

MHGGGPPSGDSACPLRTIKRVQFGVLSPDELKRMSVTEGGIKYPETTEGGRPKLGGLMDPRQGVIERTGRCQTCAGNMTECPGHFGHIELAKPVFHVGFLVKTMKVLRCVCFFCSKLLVDSNNPKIKDILAKSKGQPKKRLTHVYDLCKGKNICEGGEEMDNKFGVEQPEGDEDLTKEKGHGGCGRYQPRIRRSGLELYAEWKHVNEDSQEKKILLSPERVHEIFKRISDEECFVLGMEPRYARPEWMIVTVLPVPPLSVRPAVVMQGSARNQDDLTHKLADIVKINNQLRRNEQNGAAAHVIAEDVKLLQFHVATMVDNELPGLPRAMQKSGRPLKSLKQRLKGKEGRVRGNLMGKRVDFSARTVITPDPNLSIDQVGVPRSIAANMTFAEIVTPFNIDRLQELVRRGNSQYPGAKYIIRDNGDRIDLRFHPKPSDLHLQTGYKVERHMCDGDIVIFNRQPTLHKMSMMGHRVRILPWSTFRLNLSVTTPYNADFDGDEMNLHLPQSLETRAEIQELAMVPRMIVTPQSNRPVMGIVQDTLTAVRKFTKRDVFLERGEVMNLLMFLSTWDGKVPQPAILKPRPLWTGKQIFSLIIPGHINCIRTHSTHPDDEDSGPYKHISPGDTKVVVENGELIMGILCKKSLGTSAGSLVHISYLEMGHDITRLFYSNIQTVINNWLLIEGHTIGIGDSIADSKTYQDIQNTIKKAKQDVIEVIEKAHNNELEPTPGNTLRQTFENQVNRILNDARDKTGSSAQKSLSEYNNFKSMVVSGAKGSKINISQVIAVVGQQNVEGKRIPFGFKHRTLPHFIKDDYGPESRGFVENSYLAGLTPTEFFFHAMGGREGLIDTAVKTAETGYIQRRLIKSMESVMVKYDATVRNSINQVVQLRYGEDGLAGESVEFQNLATLKPSNKAFEKKFRFDYTNERALRRTLQEDLVKDVLSNAHIQNELEREFERMREDREVLRVIFPTGDSKVVLPCNLLRMIWNAQKIFHINPRLPSDLHPIKVVEGVKELSKKLVIVNGDDPLSRQAQENATLLFNIHLRSTLCSRRMAEEFRLSGEAFDWLLGEIESKFNQAIAHPGEMVGALAAQSLGEPATQMTLNTFHYAGVSAKNVTLGVPRLKELINISKKPKTPSLTVFLLGQSARDAERAKDILCRLEHTTLRKVTANTAIYYDPNPQSTVVAEDQEWVNVYYEMPDFDVARISPWLLRVELDRKHMTDRKLTMEQIAEKINAGFGDDLNCIFNDDNAEKLVLRIRIMNSDENKMQEEEEVVDKMDDDVFLRCIESNMLTDMTLQGIEQISKVYMHLPQTDNKKKIIITEDGEFKALQEWILETDGVSLMRVLSEKDVDPVRTTSNDIVEIFTVLGIEAVRKALERELYHVISFDGSYVNYRHLALLCDTMTCRGHLMAITRHGVNRQDTGPLMKCSFEETVDVLMEAAAHGESDPMKGVSENIMLGQLAPAGTGCFDLLLDAEKCKYGMEIPTNIPGLGAAGPTGMFFGSAPSPMGGISPAMTPWNQGATPAYGAWSPSVGSGMTPGAAGFSPSAASDASGFSPGYSPAWSPTPGSPGSPGPSSPYIPSPGGAMSPSYSPTSPAYEPRSPGGYTPQSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPNYTPTSPSYSPTSPSYSPTSPNYTPTSPNYSPTSPSYSPTSPSYSPTSPSYSPSSPRYTPQSPTYTPSSPSYSPSSPSYSPTSPKYTPTSPSYSPSSPEYTPTSPKYSPTSPKYSPTSPKYSPTSPTYSPTTPKYSPTSPTYSPTSPVYTPTSPKYSPTSPTYSPTSPKYSPTSPTYSPTSPKGSTYSPTSPGYSPTSPTYSLTSPAISPDDSDDEN

Entity 2 Entity 2 polymer

Description description	DNA-directed RNA polymerase II subunit RPB2
Molecular weight formula_weight	134041.4 kDa
EC 编号 ec_number	2.7.7.6,3.1.13.-,2.7.7.48
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MYDADEDMQYDEDDDEITPDLWQEACWIVISSYFDEKGLVRQQLDSFDEFIQMSVQRIVEDAPPIDLQAEAQHASGEVEEPPRYLLKFEQIYLSKPTHWERDGAPSPMMPNEARLRNLTYSAPLYVDITKTVIKEGEEQLQTQHQKTFIGKIPIMLRSTYCLLNGLTDRDLCELNECPLDPGGYFIINGSEKVLIAQEKMATNTVYVFAKKDSKYAYTGECRSCLENSSRPTSTIWVSMLARGGQGAKKSAIGQRIVATLPYIKQEVPIIIVFRALGFVSDRDILEHIIYDFEDPEMMEMVKPSLDEAFVIQEQNVALNFIGSRGAKPGVTKEKRIKYAKEVLQKEMLPHVGVSDFCETKKAYFLGYMVHRLLLAALGRRELDDRDHYGNKRLDLAGPLLAFLFRGMFKNLLKEVRIYAQKFIDRGKDFNLELAIKTRIISDGLKYSLATGNWGDQKKAHQARAGVSQVLNRLTFASTLSHLRRLNSPIGRDGKLAKPRQLHNTLWGMVCPAETPEGHAVGLVKNLALMAYISVGSQPSPILEFLEEWSMENLEEISPAAIADATKIFVNGCWVGIHKDPEQLMNTLRKLRRQMDIIVSEVSMIRDIREREIRIYTDAGRICRPLLIVEKQKLLLKKRHIDQLKEREYNNYSWQDLVASGVVEYIDTLEEETVMLAMTPDDLQEKEVAYCSTYTHCEIHPSMILGVCASIIPFPDHNQSPRNTYQSAMGKQAMGVYITNFHVRMDTLAHVLYYPQKPLVTTRSMEYLRFRELPAGINSIVAIASYTGYNQEDSVIMNRSAVDRGFFRSVFYRSYKEQESKKGFDQEEVFEKPTRETCQGMRHAIYDKLDDDGLIAPGVRVSGDDVIIGKTVTLPENEDELEGTNRRYTKRDCSTFLRTSETGIVDQVMVTLNQEGYKFCKIRVRSVRIPQIGDKFASRHGQKGTCGIQYRQEDMPFTCEGITPDIIINPHAIPSRMTIGHLIECLQGKVSANKGEIGDATPFNDAVNVQKISNLLSDYGYHLRGNEVLYNGFTGRKITSQIFIGPTYYQRLKHMVDDKIHSRARGPIQILNRQPMEGRSRDGGLRFGEMERDCQIAHGAAQFLRERLFEASDPYQVHVCNLCGIMAIANTRTHTYECRGCRNKTQISLVRMPYACKLLFQELMSMSIAPRMMSV

Entity 3 Entity 3 polymer

Description description	DNA-directed RNA polymerase II subunit RPB3
Molecular weight formula_weight	31466.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MPYANQPTVRITELTDENVKFIIENTDLAVANSIRRVFIAEVPIIAIDWVQIDANSSVLHDEFIAHRLGLIPLTSDDIVDKLQYSRDCTCEEFCPECSVEFTLDVRCNEDQTRHVTSRDLISNSPRVIPVTSRNRDNDPNDYVEQDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVAFEYDPDNALRHTVYPKPEEWPKSEYSELDEDESQAPYDPNGKPERFYYNVESCGSLRPETIVLSALSGLKKKLSDLQTQLSHEIQSDVLTIN

Entity 4 Entity 4 polymer

Description description	DNA-directed RNA polymerase II subunit RPB4
Molecular weight formula_weight	16347.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MAAGGSDPRSGDVEEDASQLIFPKEFETAETLLNSEVHMLLEHRKQQNESAEDEQELSEVFMKTLNYTARFSRFKNRETIASVRSLLLQKKLHKFELACLANLCPETAEESKALIPSLEGRFEDEELQQILDDIQTKRSFQY

Entity 5 Entity 5 polymer

Description description	DNA-directed RNA polymerases I, II, and III subunit RPABC1
Molecular weight formula_weight	24514.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MDDEEETYRLWKIRKTIMQLCHDRGYLVTQDGLDQTLEEFKAQFGGKPSEGRPRRTDLTVLVAHNDDPTDQMFVFFPEEPKVGIKTIKVYCQRMQEENITRALIVVQQGMTPSAKQSLVDMAPKYILEQFLQQELLINITEHELVPEHVVMTKEEVTELLARYKLRENQLPRIQAGDPVARYFGIKRGQVVKIIRPSETAGRYITYRLVQ

Entity 6 Entity 6 polymer

Description description	DNA-directed RNA polymerases I, II, and III subunit RPABC2
Molecular weight formula_weight	14491.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MSDNEDNFDGDDFDDVEEDEGLDDLENAEEEGQENVEILPSGERPQANQKRITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYLPDGSYEDWGVDELIITD

Entity 7 Entity 7 polymer

Description description	DNA-directed RNA polymerase II subunit RPB7
Molecular weight formula_weight	19314.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MFYHISLEHEILLHPRYFGPNLLNTVKQKLFTEVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRVDKNDIFAIGSLMDDYLGLVS

Entity 8 Entity 8 polymer

Description description	DNA-directed RNA polymerases I, II, and III subunit RPABC3
Molecular weight formula_weight	17162.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MAGILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVIASTLYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAYVSYGGLLMRLQGDANNLHGFEVDSRVYLLMKKLAF

Entity 9 Entity 9 polymer

Description description	DNA-directed RNA polymerase II subunit RPB9
Molecular weight formula_weight	14507.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MEPDGTYEPGIVGIRFCQECNNMLYPKEDKENRILLYACRNCDYQQEADNSCIYVNKITHEVDELTQIIADVSQDPTLPRTEDHPCQKCGHKEAVFFQSHSARAEDAMRLYYVCTAPHCGHRWTE

Entity 10 Entity 10 polymer

Description description	DNA-directed RNA polymerases I, II, and III subunit RPABC5
Molecular weight formula_weight	7655.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

MIIPVRCFTCGKIVGNKWEAYLGLLQAEYTEGDALDALGLKRYCCRRMLLAHVDLIEKLLNYAPLEK

Entity 11 Entity 11 polymer

Description description	DNA-directed RNA polymerase II subunit RPB11
Molecular weight formula_weight	13310.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MNAPPAFESFLLFEGEKKITINKDTKVPNACLFTINKEDHTLGNIIKSQLLKDPQVLFAGYKVPHPLEHKIIIRVQTTPDYSPQEAFTNAITDLISELSLLEERFRVAIKDKQEGIE

Entity 12 Entity 12 polymer

Description description	DNA-directed RNA polymerases I, II, and III subunit RPABC4
Molecular weight formula_weight	7018.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MDTQKDVQPPKQQPMIYICGECHTENEIKSRDPIRCRECGYRIMYKKRTKRLVVFDAR

Entity 13 Entity 13 polymer

Description description	Actinomycin D
Molecular weight formula_weight	1291.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	M

TVPGVXTVPGV

Entity 14 Entity 14 polymer

Description description	DNA (NTS, non-template strand)
Molecular weight formula_weight	14697.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	N

CTAGTTGATCTCATATTGATTTTTCCTTTTGCAAAATGACAAAGTCCA

Entity 15 Entity 15 polymer

Description description	RNA
Molecular weight formula_weight	4100.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	P

CCCUAAGAGUACC

Entity 16 Entity 16 polymer

Description description	DNA (TS, template strand)
Molecular weight formula_weight	15082.7 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T

TGGACTTTGTCATTTTGCAGGTACTCTTATTCAATATGAGATCAACTAG

Entity 17 Entity 17 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 18 Entity 18 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.530 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.53 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	83354

fit	/app/data/saxs_computation/xg/9xgk/9xgk.fit
pddf	/app/data/pr_computation/xg/9xgk/9xgk.pr.out
profile	/app/data/saxs_computation/xg/9xgk/9xgk.dat

Structure of mammalian RNA polymerase II stalled by Actinomycin D at the N-1 position.

1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed RNA polymerase II subunit RPB1

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerase II subunit RPB2

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerase II subunit RPB3

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerase II subunit RPB4

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerases I, II, and III subunit RPABC1

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerases I, II, and III subunit RPABC2

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerase II subunit RPB7

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerases I, II, and III subunit RPABC3

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerase II subunit RPB9

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerases I, II, and III subunit RPABC5

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerase II subunit RPB11

State in the Current Structure

Other States of the Same Protein in the Database

DNA-directed RNA polymerases I, II, and III subunit RPABC4

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (18)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 polymer

Polymer Polymer

Entity 8 Entity 8 polymer

Polymer Polymer

Entity 9 Entity 9 polymer

Polymer Polymer

Entity 10 Entity 10 polymer

Polymer Polymer

Entity 11 Entity 11 polymer

Polymer Polymer

Entity 12 Entity 12 polymer

Polymer Polymer

Entity 13 Entity 13 polymer

Polymer Polymer

Entity 14 Entity 14 polymer

Polymer Polymer

Entity 15 Entity 15 polymer

Polymer Polymer

Entity 16 Entity 16 polymer