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9ia7

NMR solution structure of RPRD2 CTD-interacting domain and pT4 RNAPII CTD peptide.

Method: SOLUTION NMR Dmax: 45.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Regulation of nuclear pre-mRNA domain-containing protein 2

Homo sapiens

UniProt Q5VT52

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 16–155 Not recorded DNA-directed RNA polymerase II subunit RPB1 × 1 （P24928） SOLUTION NMR NMR measurement conditions：pH 8；293.15 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition：0.5 mM [U-100% 13C; U-100% 15N] RPRD2 CID, 1.5 mM pT4 CTD, 90% H2O/10% D2O | 90% H2O/10% D2O Resolution not provided

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 9IA7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4FLB CID of human RPRD2 Deposited 2012-06-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 19–149（131 aa）
Not recorded SO4 SULFATE ION × 4 PR PRASEODYMIUM ION × 4 UNX UNKNOWN LIGAND × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；291 K；25% PEG-3350, 0.2M ammounium sulfate, 0.1M sodium cacodylate, praseodymium(III) acetate, pH 5.5, vapor diffusion, temperature 291K
Resolution 1.80 Å R-free 0.216
9HM8 NMR solution structure of RPRD2 CTD-interacting domain and pS2,7 RNAPII CTD peptide. Deposited 2024-12-07 Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 16–155（140 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 8；293.15 K；Ionic strength (raw mmCIF value) 100；Pressure 1
NMR sample composition 0.4 mM [U-100% 13C; U-100% 15N] RPRD2 CID, 1 mM pS2pS7 CTD, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPRD2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–141； UniProt 16–155

DNA-directed RNA polymerase II subunit RPB1

OrganismNot specified

UniProt P24928

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1612–1623 Non-standard monomer：Yes (specific site not provided by mmCIF) Regulation of nuclear pre-mRNA domain-containing protein 2 × 1 （Q5VT52） SOLUTION NMR NMR measurement conditions：pH 8；293.15 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition：0.5 mM [U-100% 13C; U-100% 15N] RPRD2 CID, 1.5 mM pT4 CTD, 90% H2O/10% D2O | 90% H2O/10% D2O Resolution not provided

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 9IA7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2GHQ CTD-specific phosphatase Scp1 in complex with peptide C-terminal domain of RNA polymerase II Deposited 2006-03-27 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1795–1803（9 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；(1)0.5M Ammonium sulfate, 0.2M Lithium sulfate, 100mM HEPES 7.5 (2) 1M sodium tartrate, 100mM Tris pH 8.5 , pH 7.5 - 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.05 Å R-free 0.248
2GHQ CTD-specific phosphatase Scp1 in complex with peptide C-terminal domain of RNA polymerase II Deposited 2006-03-27 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1795–1803（9 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；(1)0.5M Ammonium sulfate, 0.2M Lithium sulfate, 100mM HEPES 7.5 (2) 1M sodium tartrate, 100mM Tris pH 8.5 , pH 7.5 - 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 2.05 Å R-free 0.248
2GHT CTD-specific phosphatase Scp1 in complex with peptide from C-terminal domain of RNA polymerase II Deposited 2006-03-27 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1796–1803（8 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；(1) 0.5M Ammonium sulfate, 0.2M Lithium sulfate, 100mM HEPES 7.5 (2) 2M sodium tartrate, 100mM Tris pH 8.5, pH 7.5 - 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.80 Å R-free 0.232
2GHT CTD-specific phosphatase Scp1 in complex with peptide from C-terminal domain of RNA polymerase II Deposited 2006-03-27 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1796–1803（8 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；(1) 0.5M Ammonium sulfate, 0.2M Lithium sulfate, 100mM HEPES 7.5 (2) 2M sodium tartrate, 100mM Tris pH 8.5, pH 7.5 - 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.80 Å R-free 0.232
2LTO TDRD3 complex Deposited 2012-05-30 Different construct Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1804–1816（13 aa） Fragment：UNP residues 1804-1816
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 8；293.15 K；Ionic strength (raw mmCIF value) 150；Pressure ambient
NMR sample composition 1.7 mM [U-99% 13C; U-99% 15N] protein_1, 50 mM sodium phosphate, 10 mM beta-mercaptoethanol, 150 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
4JXT CID of human RPRD1A in complex with a phosphorylated peptide from RPB1-CTD Deposited 2013-03-28 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1612–1630（19 aa） Fragment：UNP residues 1612-1630
Non-standard monomer：Yes (specific site not provided by mmCIF) UNX UNKNOWN LIGAND × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；20% PEG-4000, 10% isopropanol, 0.1M HEPES., pH 7.5, vapor diffusion, temperature 291K
Resolution 1.90 Å R-free 0.237
5IY6 Human holo-PIC in the closed state Deposited 2016-03-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain A 1–1970（1970 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.20 Å
5IY7 Human holo-PIC in the open state Deposited 2016-03-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain A 1–1970（1970 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 8.60 Å
5IY8 Human holo-PIC in the initial transcribing state Deposited 2016-03-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain A 1–1970（1970 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 7.90 Å
5IY9 Human holo-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric
Chain A 1–1970（1970 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 6.30 Å
5IYA Human core-PIC in the closed state Deposited 2016-03-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain A 1–1970（1970 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 5.40 Å
5IYB Human core-PIC in the open state Deposited 2016-03-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain A 1–1970（1970 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5IYC Human core-PIC in the initial transcribing state Deposited 2016-03-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric
Chain A 1–1970（1970 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
5IYD Human core-PIC in the initial transcribing state (no IIS) Deposited 2016-03-24 Different construct Different mutation/modification 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 1–1970（1970 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 11 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds before plunging into liquid ethane (FEI VITROBOT MARK IV).
Resolution 3.90 Å
6DRD RNA Pol II(G) Deposited 2018-06-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain A 1–1970（1970 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6G0R Crystal Structure of the first bromodomain of human BRD4 in complex with an acetylated POLR2A peptide (K775ac/K778ac) Deposited 2018-03-19 Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 772–782（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；20.0 % PEG 6K 10.0 % EtGly 0.1 M HEPES pH 7.0 0.1 M MgCl2
Resolution 1.25 Å R-free 0.175
6O9L Human holo-PIC in the closed state Deposited 2019-03-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 31 PDB declaration: 33-meric
Chain A 1–1970（1970 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.20 Å
6XRE Structure of the p53/RNA polymerase II assembly Deposited 2020-07-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain A 1–1970（1970 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE；The assembled p53/Pol II co-complex was applied directly on the grid for 10 sec followed by 5.5 sec of blotting. The sample grid was then washed with 3.5% trehalose in 0.1 M KCl/HEM buffer (20 mM HEPES, 0.2 mM EDTA, 2 mM MgCl2 at pH 7.9) for 10 sec, blotted for 5.5 sec, and finally frozen in liquid ethane.
Resolution 4.60 Å
7EGB TFIID-based holo PIC on SCP promoter Deposited 2021-03-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain o 1–1970（1970 aa）
Not recorded ZN ZINC ION × 17 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7EGC p53-bound TFIID-based holo PIC on HDM2 promoter Deposited 2021-03-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain o 1–1970（1970 aa）
Not recorded ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
7LBM Structure of the human Mediator-bound transcription pre-initiation complex Deposited 2021-01-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain A 1–1970（1970 aa）
Not recorded MG MAGNESIUM ION × 2 ZN ZINC ION × 16 SF4 IRON/SULFUR CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
7YCX The structure of INTAC-PEC complex Deposited 2022-07-02 Different construct Different mutation/modification 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 1 1–1699（1699 aa）
Chain 1 1704–1856（153 aa）
Chain 1 1865–1970（106 aa）
Not recorded ZN ZINC ION × 10 MN MANGANESE (II) ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.18 Å
8XRJ RNA polymerase II elongation complex with upstream nucleosome extracted from human nuclei Deposited 2024-01-07 Different construct Different mutation/modification 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 1–1970（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
Resolution 3.60 Å
8XRM RNA polymerase II elongation complex with DSIF, SPT6, and ELOF1 transcribing genomic DNA extracted from human nuclei Deposited 2024-01-07 Different construct Different mutation/modification 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: 19-meric
Chain A 1–1970（1970 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 3.13 Å
8XSO RNA polymerase II elongation complex transcribing genomic DNA extracted from human nuclei Deposited 2024-01-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: 15-meric
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
Resolution 2.70 Å
8XVS RNA polymerase II elongation complex with downstream nucleosome extracted from human nuclei Deposited 2024-01-15 Different construct Different mutation/modification 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 1–1970（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
Resolution 4.10 Å
9B9L RPRD1B C-terminal interacting domain bound to a pThr4 CTD peptide Deposited 2024-04-02 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1616–1630（15 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Co-crystallization of CID with CTD peptide occurred in a reservoir solution of 20-32% PEG3350 and 0.1M lithium sulfate. 1:3 molar ratio of protein to peptide was used
Resolution 2.50 Å R-free 0.347
9EHZ Cryo-EM structure of Human RNA polymerase II Elongation Complex in an Intermediate Translocation State Deposited 2024-11-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: pentadecameric
Chain A 1–1970（1970 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9EI1 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the absence of nucleotide Deposited 2024-11-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9EI2 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to an apo RECQL5 helicase (RECQL5 IRI Module focused-classified) Deposited 2024-11-25 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1970（1970 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9EI3 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of AMPPNP Deposited 2024-11-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9EI4 Cryo-EM structure of Human RNA polymerase II Elongation Complex bound to the RECQL5 helicase in the presence of ADP Deposited 2024-11-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9HM8 NMR solution structure of RPRD2 CTD-interacting domain and pS2,7 RNAPII CTD peptide. Deposited 2024-12-07 Different construct Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1612–1622（11 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 8；293.15 K；Ionic strength (raw mmCIF value) 100；Pressure 1
NMR sample composition 0.4 mM [U-100% 13C; U-100% 15N] RPRD2 CID, 1 mM pS2pS7 CTD, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
9QPX BRCA1 BRCT tandem repeat with RNA polymerase II pSer5-CTD peptide Deposited 2025-03-30 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1615–1628（14 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；0.1M PCB buffer (sodium propionate, sodium cacodylate, BIS-TRIS propane in the molar ratios 2:1:2) pH 6, 25%PEG 1500
Resolution 3.00 Å R-free 0.312
9QPX BRCA1 BRCT tandem repeat with RNA polymerase II pSer5-CTD peptide Deposited 2025-03-30 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1615–1628（14 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；0.1M PCB buffer (sodium propionate, sodium cacodylate, BIS-TRIS propane in the molar ratios 2:1:2) pH 6, 25%PEG 1500
Resolution 3.00 Å R-free 0.312
9QPX BRCA1 BRCT tandem repeat with RNA polymerase II pSer5-CTD peptide Deposited 2025-03-30 Different construct Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 1615–1628（14 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；0.1M PCB buffer (sodium propionate, sodium cacodylate, BIS-TRIS propane in the molar ratios 2:1:2) pH 6, 25%PEG 1500
Resolution 3.00 Å R-free 0.312
9VD9 Cryo-EM structure of the human DSS1-INTAC-PEC complex Deposited 2025-06-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 35 PDB declaration: 38-meric
Chain 1 1–1970（1970 aa）
Chain m 1618–1631（14 aa）
Not recorded ZN ZINC ION × 10 MN MANGANESE (II) ION × 2 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å

33 other PDB entries and 37 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RPB1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–12； UniProt 1612–1623

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 9ia7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9ia7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9ia7
Deposition date deposition_date2025-02-07
最后修订 last_revision2026-02-18
Structure title titleNMR solution structure of RPRD2 CTD-interacting domain and pT4 RNAPII CTD peptide.
Keywords keywordsRPRD2, CID, RNAPII CTD, Complex, PROTEIN BINDING, Threonine, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier14.88 Å
Radius of gyration Rg (electron density) rg_electron14.49 Å
Forward intensity I(0) i01481040000.00
Molecular weight molecular_weight325970.0 kDa
Excluded volume excluded_volume407300 ų
Envelope volume envelope_volume34343 ų
Hydration-shell volume shell_volume17230 ų
Envelope diameter envelope_diameter53.1 Å
Shell Rg shell_rg22.91 Å
Envelope Rg envelope_rg16.75 Å
Shape Rg shape_rg14.44 Å
Total Rg total_rg14.76 Å
Total atoms total_atoms45560
Residues n_residues2800
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 dmax45.0 Å
Rg (real space) rg_real14.75 Å
Rg uncertainty (real space) rg_real_error0.21 Å
I(0) (real space) i0_real1.4810e+09
I(0) uncertainty (real space) i0_real_error1.6160e+07
Rg (reciprocal space) rg_reciprocal14.76 Å
I(0) (reciprocal space) i0_reciprocal1481000000.0000
Solution quality estimate total_estimate0.8186
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.5 Å
Skewness Skewness skewness0.021
Kurtosis Kurtosis kurtosis-0.399
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha455800.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.889; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.975; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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9. Files and Curves (10)