2ja8

CPD lesion containing RNA Polymerase II elongation complex D

Method: X-RAY DIFFRACTION

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

DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 DNA 2 RNA 1	DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE × 1 （P08518） DNA-DIRECTED RNA POLYMERASE II 45KDA POLYPEPTIDE × 1 （P16370） DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE × 1 （P20433） DNA-DIRECTED RNA POLYMERASES I, II, AND III 27 KDA POLYPEPTIDE × 1 （P20434） DNA-DIRECTED RNA POLYMERASES I, II, AND III 23 KDA POLYPEPTIDE × 1 （P20435） DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE × 1 （P34087） DNA-DIRECTED RNA POLYMERASES I, II, AND III 14.5 KDA POLYPEPTIDE × 1 （P20436） DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9 × 1 （P27999） DNA-DIRECTED RNA POLYMERASES I/II/III SUBUNIT 10 × 1 （P22139） DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE × 1 （P38902） DNA-DIRECTED RNA POLYMERASES I, II, AND III 7.7 KDA POLYPEPTIDE × 1 （P40422） ;5'-D(TPAPAPGPTPAPCPTPTPGP APGPCPT)-3' ; × 1 5'-R(UPUPCPGPAPCPCPAPGPAPUP)-3' × 1 ;5'-D(APGPCPTPCPAPAPGPTPAP CPTPTPTPTPTTPCPBRUPGPGPTPCPAPTPT)-3' ; × 1 MAGNESIUM ION × 1 ZINC ION × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPB1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1733； UniProt 1–1733

DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE

OrganismNot specified

UniProt P08518

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 DNA 2 RNA 1	DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT × 1 （P04050） DNA-DIRECTED RNA POLYMERASE II 45KDA POLYPEPTIDE × 1 （P16370） DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE × 1 （P20433） DNA-DIRECTED RNA POLYMERASES I, II, AND III 27 KDA POLYPEPTIDE × 1 （P20434） DNA-DIRECTED RNA POLYMERASES I, II, AND III 23 KDA POLYPEPTIDE × 1 （P20435） DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE × 1 （P34087） DNA-DIRECTED RNA POLYMERASES I, II, AND III 14.5 KDA POLYPEPTIDE × 1 （P20436） DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9 × 1 （P27999） DNA-DIRECTED RNA POLYMERASES I/II/III SUBUNIT 10 × 1 （P22139） DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE × 1 （P38902） DNA-DIRECTED RNA POLYMERASES I, II, AND III 7.7 KDA POLYPEPTIDE × 1 （P40422） ;5'-D(TPAPAPGPTPAPCPTPTPGP APGPCPT)-3' ; × 1 5'-R(UPUPCPGPAPCPCPAPGPAPUP)-3' × 1 ;5'-D(APGPCPTPCPAPAPGPTPAP CPTPTPTPTPTTPCPBRUPGPGPTPCPAPTPT)-3' ; × 1 MAGNESIUM ION × 1 ZINC ION × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPB2_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–1224； UniProt 1–1224

DNA-DIRECTED RNA POLYMERASE II 45KDA POLYPEPTIDE

OrganismNot specified

UniProt P16370

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 DNA 2 RNA 1	DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT × 1 （P04050） DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE × 1 （P08518） DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE × 1 （P20433） DNA-DIRECTED RNA POLYMERASES I, II, AND III 27 KDA POLYPEPTIDE × 1 （P20434） DNA-DIRECTED RNA POLYMERASES I, II, AND III 23 KDA POLYPEPTIDE × 1 （P20435） DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE × 1 （P34087） DNA-DIRECTED RNA POLYMERASES I, II, AND III 14.5 KDA POLYPEPTIDE × 1 （P20436） DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9 × 1 （P27999） DNA-DIRECTED RNA POLYMERASES I/II/III SUBUNIT 10 × 1 （P22139） DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE × 1 （P38902） DNA-DIRECTED RNA POLYMERASES I, II, AND III 7.7 KDA POLYPEPTIDE × 1 （P40422） ;5'-D(TPAPAPGPTPAPCPTPTPGP APGPCPT)-3' ; × 1 5'-R(UPUPCPGPAPCPCPAPGPAPUP)-3' × 1 ;5'-D(APGPCPTPCPAPAPGPTPAP CPTPTPTPTPTTPCPBRUPGPGPTPCPAPTPT)-3' ; × 1 MAGNESIUM ION × 1 ZINC ION × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPB3_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–318； UniProt 1–318

DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE

OrganismNot specified

UniProt P20433

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 DNA 2 RNA 1	DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT × 1 （P04050） DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE × 1 （P08518） DNA-DIRECTED RNA POLYMERASE II 45KDA POLYPEPTIDE × 1 （P16370） DNA-DIRECTED RNA POLYMERASES I, II, AND III 27 KDA POLYPEPTIDE × 1 （P20434） DNA-DIRECTED RNA POLYMERASES I, II, AND III 23 KDA POLYPEPTIDE × 1 （P20435） DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE × 1 （P34087） DNA-DIRECTED RNA POLYMERASES I, II, AND III 14.5 KDA POLYPEPTIDE × 1 （P20436） DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9 × 1 （P27999） DNA-DIRECTED RNA POLYMERASES I/II/III SUBUNIT 10 × 1 （P22139） DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE × 1 （P38902） DNA-DIRECTED RNA POLYMERASES I, II, AND III 7.7 KDA POLYPEPTIDE × 1 （P40422） ;5'-D(TPAPAPGPTPAPCPTPTPGP APGPCPT)-3' ; × 1 5'-R(UPUPCPGPAPCPCPAPGPAPUP)-3' × 1 ;5'-D(APGPCPTPCPAPAPGPTPAP CPTPTPTPTPTTPCPBRUPGPGPTPCPAPTPT)-3' ; × 1 MAGNESIUM ION × 1 ZINC ION × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPB4_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–221； UniProt 1–221

DNA-DIRECTED RNA POLYMERASES I, II, AND III 27 KDA POLYPEPTIDE

OrganismNot specified

UniProt P20434

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 DNA 2 RNA 1	DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT × 1 （P04050） DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE × 1 （P08518） DNA-DIRECTED RNA POLYMERASE II 45KDA POLYPEPTIDE × 1 （P16370） DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE × 1 （P20433） DNA-DIRECTED RNA POLYMERASES I, II, AND III 23 KDA POLYPEPTIDE × 1 （P20435） DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE × 1 （P34087） DNA-DIRECTED RNA POLYMERASES I, II, AND III 14.5 KDA POLYPEPTIDE × 1 （P20436） DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9 × 1 （P27999） DNA-DIRECTED RNA POLYMERASES I/II/III SUBUNIT 10 × 1 （P22139） DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE × 1 （P38902） DNA-DIRECTED RNA POLYMERASES I, II, AND III 7.7 KDA POLYPEPTIDE × 1 （P40422） ;5'-D(TPAPAPGPTPAPCPTPTPGP APGPCPT)-3' ; × 1 5'-R(UPUPCPGPAPCPCPAPGPAPUP)-3' × 1 ;5'-D(APGPCPTPCPAPAPGPTPAP CPTPTPTPTPTTPCPBRUPGPGPTPCPAPTPT)-3' ; × 1 MAGNESIUM ION × 1 ZINC ION × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPB5_YEAST
Isoform	—
PDB entities	5
Chains and sequence ranges	Author chain E； PDBConstruct 1–215； UniProt 1–215

DNA-DIRECTED RNA POLYMERASES I, II, AND III 23 KDA POLYPEPTIDE

OrganismNot specified

UniProt P20435

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 DNA 2 RNA 1	DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT × 1 （P04050） DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE × 1 （P08518） DNA-DIRECTED RNA POLYMERASE II 45KDA POLYPEPTIDE × 1 （P16370） DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE × 1 （P20433） DNA-DIRECTED RNA POLYMERASES I, II, AND III 27 KDA POLYPEPTIDE × 1 （P20434） DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE × 1 （P34087） DNA-DIRECTED RNA POLYMERASES I, II, AND III 14.5 KDA POLYPEPTIDE × 1 （P20436） DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9 × 1 （P27999） DNA-DIRECTED RNA POLYMERASES I/II/III SUBUNIT 10 × 1 （P22139） DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE × 1 （P38902） DNA-DIRECTED RNA POLYMERASES I, II, AND III 7.7 KDA POLYPEPTIDE × 1 （P40422） ;5'-D(TPAPAPGPTPAPCPTPTPGP APGPCPT)-3' ; × 1 5'-R(UPUPCPGPAPCPCPAPGPAPUP)-3' × 1 ;5'-D(APGPCPTPCPAPAPGPTPAP CPTPTPTPTPTTPCPBRUPGPGPTPCPAPTPT)-3' ; × 1 MAGNESIUM ION × 1 ZINC ION × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPB6_YEAST
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain F； PDBConstruct 1–155； UniProt 1–155

DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE

OrganismNot specified

UniProt P34087

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 DNA 2 RNA 1	DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT × 1 （P04050） DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE × 1 （P08518） DNA-DIRECTED RNA POLYMERASE II 45KDA POLYPEPTIDE × 1 （P16370） DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE × 1 （P20433） DNA-DIRECTED RNA POLYMERASES I, II, AND III 27 KDA POLYPEPTIDE × 1 （P20434） DNA-DIRECTED RNA POLYMERASES I, II, AND III 23 KDA POLYPEPTIDE × 1 （P20435） DNA-DIRECTED RNA POLYMERASES I, II, AND III 14.5 KDA POLYPEPTIDE × 1 （P20436） DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9 × 1 （P27999） DNA-DIRECTED RNA POLYMERASES I/II/III SUBUNIT 10 × 1 （P22139） DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE × 1 （P38902） DNA-DIRECTED RNA POLYMERASES I, II, AND III 7.7 KDA POLYPEPTIDE × 1 （P40422） ;5'-D(TPAPAPGPTPAPCPTPTPGP APGPCPT)-3' ; × 1 5'-R(UPUPCPGPAPCPCPAPGPAPUP)-3' × 1 ;5'-D(APGPCPTPCPAPAPGPTPAP CPTPTPTPTPTTPCPBRUPGPGPTPCPAPTPT)-3' ; × 1 MAGNESIUM ION × 1 ZINC ION × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPB7_YEAST
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain G； PDBConstruct 1–171； UniProt 1–171

DNA-DIRECTED RNA POLYMERASES I, II, AND III 14.5 KDA POLYPEPTIDE

OrganismNot specified

UniProt P20436

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 DNA 2 RNA 1	DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT × 1 （P04050） DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE × 1 （P08518） DNA-DIRECTED RNA POLYMERASE II 45KDA POLYPEPTIDE × 1 （P16370） DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE × 1 （P20433） DNA-DIRECTED RNA POLYMERASES I, II, AND III 27 KDA POLYPEPTIDE × 1 （P20434） DNA-DIRECTED RNA POLYMERASES I, II, AND III 23 KDA POLYPEPTIDE × 1 （P20435） DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE × 1 （P34087） DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9 × 1 （P27999） DNA-DIRECTED RNA POLYMERASES I/II/III SUBUNIT 10 × 1 （P22139） DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE × 1 （P38902） DNA-DIRECTED RNA POLYMERASES I, II, AND III 7.7 KDA POLYPEPTIDE × 1 （P40422） ;5'-D(TPAPAPGPTPAPCPTPTPGP APGPCPT)-3' ; × 1 5'-R(UPUPCPGPAPCPCPAPGPAPUP)-3' × 1 ;5'-D(APGPCPTPCPAPAPGPTPAP CPTPTPTPTPTTPCPBRUPGPGPTPCPAPTPT)-3' ; × 1 MAGNESIUM ION × 1 ZINC ION × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPB8_YEAST
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain H； PDBConstruct 1–146； UniProt 1–146

DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9

OrganismNot specified

UniProt P27999

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 DNA 2 RNA 1	DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT × 1 （P04050） DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE × 1 （P08518） DNA-DIRECTED RNA POLYMERASE II 45KDA POLYPEPTIDE × 1 （P16370） DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE × 1 （P20433） DNA-DIRECTED RNA POLYMERASES I, II, AND III 27 KDA POLYPEPTIDE × 1 （P20434） DNA-DIRECTED RNA POLYMERASES I, II, AND III 23 KDA POLYPEPTIDE × 1 （P20435） DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE × 1 （P34087） DNA-DIRECTED RNA POLYMERASES I, II, AND III 14.5 KDA POLYPEPTIDE × 1 （P20436） DNA-DIRECTED RNA POLYMERASES I/II/III SUBUNIT 10 × 1 （P22139） DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE × 1 （P38902） DNA-DIRECTED RNA POLYMERASES I, II, AND III 7.7 KDA POLYPEPTIDE × 1 （P40422） ;5'-D(TPAPAPGPTPAPCPTPTPGP APGPCPT)-3' ; × 1 5'-R(UPUPCPGPAPCPCPAPGPAPUP)-3' × 1 ;5'-D(APGPCPTPCPAPAPGPTPAP CPTPTPTPTPTTPCPBRUPGPGPTPCPAPTPT)-3' ; × 1 MAGNESIUM ION × 1 ZINC ION × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPB9_YEAST
Isoform	—
PDB entities	9
Chains and sequence ranges	Author chain I； PDBConstruct 1–122； UniProt 1–122

DNA-DIRECTED RNA POLYMERASES I/II/III SUBUNIT 10

OrganismNot specified

UniProt P22139

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 DNA 2 RNA 1	DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT × 1 （P04050） DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE × 1 （P08518） DNA-DIRECTED RNA POLYMERASE II 45KDA POLYPEPTIDE × 1 （P16370） DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE × 1 （P20433） DNA-DIRECTED RNA POLYMERASES I, II, AND III 27 KDA POLYPEPTIDE × 1 （P20434） DNA-DIRECTED RNA POLYMERASES I, II, AND III 23 KDA POLYPEPTIDE × 1 （P20435） DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE × 1 （P34087） DNA-DIRECTED RNA POLYMERASES I, II, AND III 14.5 KDA POLYPEPTIDE × 1 （P20436） DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9 × 1 （P27999） DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE × 1 （P38902） DNA-DIRECTED RNA POLYMERASES I, II, AND III 7.7 KDA POLYPEPTIDE × 1 （P40422） ;5'-D(TPAPAPGPTPAPCPTPTPGP APGPCPT)-3' ; × 1 5'-R(UPUPCPGPAPCPCPAPGPAPUP)-3' × 1 ;5'-D(APGPCPTPCPAPAPGPTPAP CPTPTPTPTPTTPCPBRUPGPGPTPCPAPTPT)-3' ; × 1 MAGNESIUM ION × 1 ZINC ION × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPB10_YEAST
Isoform	—
PDB entities	10
Chains and sequence ranges	Author chain J； PDBConstruct 1–70； UniProt 1–70

DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE

OrganismNot specified

UniProt P38902

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 DNA 2 RNA 1	DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT × 1 （P04050） DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE × 1 （P08518） DNA-DIRECTED RNA POLYMERASE II 45KDA POLYPEPTIDE × 1 （P16370） DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE × 1 （P20433） DNA-DIRECTED RNA POLYMERASES I, II, AND III 27 KDA POLYPEPTIDE × 1 （P20434） DNA-DIRECTED RNA POLYMERASES I, II, AND III 23 KDA POLYPEPTIDE × 1 （P20435） DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE × 1 （P34087） DNA-DIRECTED RNA POLYMERASES I, II, AND III 14.5 KDA POLYPEPTIDE × 1 （P20436） DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9 × 1 （P27999） DNA-DIRECTED RNA POLYMERASES I/II/III SUBUNIT 10 × 1 （P22139） DNA-DIRECTED RNA POLYMERASES I, II, AND III 7.7 KDA POLYPEPTIDE × 1 （P40422） ;5'-D(TPAPAPGPTPAPCPTPTPGP APGPCPT)-3' ; × 1 5'-R(UPUPCPGPAPCPCPAPGPAPUP)-3' × 1 ;5'-D(APGPCPTPCPAPAPGPTPAP CPTPTPTPTPTTPCPBRUPGPGPTPCPAPTPT)-3' ; × 1 MAGNESIUM ION × 1 ZINC ION × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPB11_YEAST
Isoform	—
PDB entities	11
Chains and sequence ranges	Author chain K； PDBConstruct 1–120； UniProt 1–120

DNA-DIRECTED RNA POLYMERASES I, II, AND III 7.7 KDA POLYPEPTIDE

OrganismNot specified

UniProt P40422

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 12 DNA 2 RNA 1	DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT × 1 （P04050） DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE × 1 （P08518） DNA-DIRECTED RNA POLYMERASE II 45KDA POLYPEPTIDE × 1 （P16370） DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE × 1 （P20433） DNA-DIRECTED RNA POLYMERASES I, II, AND III 27 KDA POLYPEPTIDE × 1 （P20434） DNA-DIRECTED RNA POLYMERASES I, II, AND III 23 KDA POLYPEPTIDE × 1 （P20435） DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE × 1 （P34087） DNA-DIRECTED RNA POLYMERASES I, II, AND III 14.5 KDA POLYPEPTIDE × 1 （P20436） DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9 × 1 （P27999） DNA-DIRECTED RNA POLYMERASES I/II/III SUBUNIT 10 × 1 （P22139） DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE × 1 （P38902） ;5'-D(TPAPAPGPTPAPCPTPTPGP APGPCPT)-3' ; × 1 5'-R(UPUPCPGPAPCPCPAPGPAPUP)-3' × 1 ;5'-D(APGPCPTPCPAPAPGPTPAP CPTPTPTPTPTTPCPBRUPGPGPTPCPAPTPT)-3' ; × 1 MAGNESIUM ION × 1 ZINC ION × 8	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	RPC10_YEAST
Isoform	—
PDB entities	12
Chains and sequence ranges	Author chain L； PDBConstruct 1–70； UniProt 1–70

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2ja8
Deposition date deposition_date	2006-11-23
Structure title title	CPD lesion containing RNA Polymerase II elongation complex D
Keywords keywords	;DNA-DIRECTED RNA POLYMERASE, LESION RECOGNITION, TRANSFERASE/DNA/RNA, DNA DAMAGE, ZINC-FINGER, DNA-BINDING, PHOTOLESION, PHOSPHORYLATION, MISINCORPORATION, RNA POLYMERASE II, TRANSCRIPTION-COUPLED REPAIR, CYCLOBUTANE PYRIMIDINE DIMER TCR, CPD, ARREST, STALLING, DNA LESION, METAL-BINDING, NUCLEAR PROTEIN, TRANSCRIPTION BUBBLE, NUCLEOTIDYLTRANSFERASE, DAMAGE RECOGNITION, ELONGATION COMPLEX, TRANSFERASE, THYMINE DIMER, TRANSCRIPTION ;; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

2ja8__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2ja8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ja8__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	50.60 Å
Rg (electron density)	50.42 Å
Total Rg	50.60 Å
Atom count	32000
Residues	3963
Excluded volume	568680 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ja8__assembly_1__model_1`	pentadecameric （15）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (17)

Entity 1 Entity 1 polymer

Description description	DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT
Molecular weight formula_weight	191821.6 kDa
EC 编号 ec_number	2.7.7.6
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	32000

MVGQQYSSAPLRTVKEVQFGLFSPEEVRAISVAKIRFPETMDETQTRAKIGGLNDPRLGSIDRNLKCQTCQEGMNECPGHFGHIDLAKPVFHVGFIAKIKKVCECVCMHCGKLLLDEHNELMRQALAIKDSKKRFAAIWTLCKTKMVCETDVPSEDDPTQLVSRGGCGNTQPTIRKDGLKLVGSWKKDRATGDADEPELRVLSTEEILNIFKHISVKDFTSLGFNEVFSRPEWMILTCLPVPPPPVRPSISFNESQRGEDDLTFKLADILKANISLETLEHNGAPHHAIEEAESLLQFHVATYMDNDIAGQPQALQKSGRPVKSIRARLKGKEGRIRGNLMGKRVDFSARTVISGDPNLELDQVGVPKSIAKTLTYPEVVTPYNIDRLTQLVRNGPNEHPGAKYVIRDSGDRIDLRYSKRAGDIQLQYGWKVERHIMDNDPVLFNRQPSLHKMSMMAHRVKVIPYSTFRLNLSVTSPYNADFDGDEMNLHVPQSEETRAELSQLCAVPLQIVSPQSNKPCMGIVQDTLCGIRKLTLRDTFIELDQVLNMLYWVPDWDGVIPTPAIIKPKPLWSGKQILSVAIPNGIHLQRFDEGTTLLSPKDNGMLIIDGQIIFGVVEKKTVGSSNGGLIHVVTREKGPQVCAKLFGNIQKVVNFWLLHNGFSTGIGDTIADGPTMREITETIAEAKKKVLDVTKEAQANLLTAKHGMTLRESFEDNVVRFLNEARDKAGRLAEVNLKDLNNVKQMVMAGSKGSFINIAQMSACVGQQSVEGKRIAFGFVDRTLPHFSKDDYSPESKGFVENSYLRGLTPQEFFFHAMGGREGLIDTAVKTAETGYIQRRLVKALEDIMVHYDNTTRNSLGNVIQFIYGEDGMDAAHIEKQSLDTIGGSDAAFEKRYRVDLLNTDHTLDPSLLESGSEILGDLKLQVLLDEEYKQLVKDRKFLREVFVDGEANWPLPVNIRRIIQNAQQTFHIDHTKPSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSVVHPGEMVGVLAAQSIGEPATQMTLNTFHFAGVASKKVTSGVPRLKEILNVAKNMKTPSLTVYLEPGHAADQEQAKLIRSAIEHTTLKSVTIASEIYYDPDPRSTVIPEDEEIIQLHFSLLDEEAEQSFDQQSPWLLRLELDRAAMNDKDLTMGQVGERIKQTFKNDLFVIWSEDNDEKLIIRCRVVRPKSLDAETEAEEDHMLKKIENTMLENITLRGVENIERVVMMKYDRKVPSPTGEYVKEPEWVLETDGVNLSEVMTVPGIDPTRIYTNSFIDIMEVLGIEAGRAALYKEVYNVIASDGSYVNYRHMALLVDVMTTQGGLTSVTRHGFNRSNTGALMRCSFEETVEILFEAGASAELDDCRGVSENVILGQMAPIGTGAFDVMIDEESLVKYMPEQKITEIEDGQDGGVTPYSNESGLVNADLDVKDELMFSPLVDSGSNDAMAGGFTAYGGADYGEATSPFGAYGEAPTSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKHNENENSR

Entity 2 Entity 2 polymer

Description description	DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE
Molecular weight formula_weight	138937.3 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSDLANSEKYYDEDPYGFEDESAPITAEDSWAVISAFFREKGLVSQQLDSFNQFVDYTLQDIICEDSTLILEQLAQHTTESDNISRKYEISFGKIYVTKPMVNESDGVTHALYPQEARLRNLTYSSGLFVDVKKRTYEAIDVPGRELKYELIAEESEDDSESGKVFIGRLPIMLRSKNCYLSEATESDLYKLKECPFDMGGYFIINGSEKVLIAQERSAGNIVQVFKKAAPSPISHVAEIRSALEKGSRFISTLQVKLYGREGSSARTIKATLPYIKQDIPIVIIFRALGIIPDGEILEHICYDVNDWQMLEMLKPCVEDGFVIQDRETALDFIGRRGTALGIKKEKRIQYAKDILQKEFLPHITQLEGFESRKAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLDLAGPLLAQLFKTLFKKLTKDIFRYMQRTVEEAHDFNMKLAINAKTITSGLKYALATGNWGEQKKAMSSRAGVSQVLNRYTYSSTLSHLRRTNTPIGRDGKLAKPRQLHNTHWGLVCPAETPEGQACGLVKNLSLMSCISVGTDPMPIITFLSEWGMEPLEDYVPHQSPDATRVFVNGVWHGVHRNPARLMETLRTLRRKGDINPEVSMIRDIREKELKIFTDAGRVYRPLFIVEDDESLGHKELKVRKGHIAKLMATEYQDIEGGFEDVEEYTWSSLLNEGLVEYIDAEEEESILIAMQPEDLEPAEANEENDLDVDPAKRIRVSHHATTFTHCEIHPSMILGVAASIIPFPDHNQSPRNTYQSAMGKQAMGVFLTNYNVRMDTMANILYYPQKPLGTTRAMEYLKFRELPAGQNAIVAIACYSGYNQEDSMIMNQSSIDRGLFRSLFFRSYMDQEKKYGMSITETFEKPQRTNTLRMKHGTYDKLDDDGLIAPGVRVSGEDVIIGKTTPISPDEEELGQRTAYHSKRDASTPLRSTENGIVDQVLVTTNQDGLKFVKVRVRTTKIPQIGDKFASRHGQKGTIGITYRREDMPFTAEGIVPDLIINPHAIPSRMTVAHLIECLLSKVAALSGNEGDASPFTDITVEGISKLLREHGYQSRGFEVMYNGHTGKKLMAQIFFGPTYYQRLRHMVDDKIHARARGPMQVLTRQPVEGRSRDGGLRFGEMERDCMIAHGAASFLKERLMEASDAFRVHICGICGLMTVIAKLNHNQFECKGCDNKIDIYQIHIPYAAKLLFQELMAMNITPRLYTDRSRDF

Entity 3 Entity 3 polymer

Description description	DNA-DIRECTED RNA POLYMERASE II 45KDA POLYPEPTIDE
Molecular weight formula_weight	35330.5 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MSEEGPQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIPTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEYSRDCFCEDHCDKCSVVLTLQAFGESESTTNVYSKDLVIVSNLMGRNIGHPIIQDKEGNGVLICKLRKGQELKLTCVAKKGIAKEHAKWGPAAAIEFEYDPWNKLKHTDYWYEQDSAKEWPQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQMDQDKVNFASGDNNTASNMLGSNEDVMMTGAEQDPYSNASQMGNTGSGGYDNAW

Entity 4 Entity 4 polymer

Description description	DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE
Molecular weight formula_weight	25451.2 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MNVSTSTFQTRRRRLKKVEEEENAATLQLGQEFQLKQINHQGEEEELIALNLSEARLVIKEALVERRRAFKRSQKKHKKKHLKHENANDETTAVEDEDDDLDEDDVNADDDDFMHSETREKELESIDVLLEQTTGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQLLKSTGLHPFEVAQLGSLACDTADEAKTLIPSLNNKISDDELERILKELSNLETLY

Entity 5 Entity 5 polymer

Description description	DNA-DIRECTED RNA POLYMERASES I, II, AND III 27 KDA POLYPEPTIDE
Molecular weight formula_weight	25117.1 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E

MDQENERNISRLWRAFRTVKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMSFQANPTEESISKFPDMGSLWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMKLVPSIPPATIETFNEAALVVNITHHELVPKHIRLSSDEKRELLKRYRLKESQLPRIQRADPVALYLGLKRGEVVKIIRKSETSGRYASYRICM

Entity 6 Entity 6 polymer

Description description	DNA-DIRECTED RNA POLYMERASES I, II, AND III 23 KDA POLYPEPTIDE
Molecular weight formula_weight	17931.8 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F

MSDYEEAFNDGNENFEDFDVEHFSDEETYEEKPQFKDGETTDANGKTIVTGGNGPEDFQQHEQIRRKTLKEKAIPKDQRATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYLPDGSFEDWSVEELIVDL

Entity 7 Entity 7 polymer

Description description	DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE
Molecular weight formula_weight	19081.1 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G

MFFIKDLSLNITLHPSFFGPRMKQYLKTKLLEEVEGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKSRIRVKIEGCISQVSSIHAIGSIKEDYLGAI

Entity 8 Entity 8 polymer

Description description	DNA-DIRECTED RNA POLYMERASES I, II, AND III 14.5 KDA POLYPEPTIDE
Molecular weight formula_weight	16525.4 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

MSNTLFDDIFQVSEVDPGRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTVTIASSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYKFEEVSKDLIAVYYSFGGLLMRLEGNYRNLNNLKQENAYLLIRR

Entity 9 Entity 9 polymer

Description description	DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9
Molecular weight formula_weight	14308.2 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

MTTFRFCRDCNNMLYPREDKENNRLLFECRTCSYVEEAGSPLVYRHELITNIGETAGVVQDIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSHIFTSDQKNKRTQFS

Entity 10 Entity 10 polymer

Description description	DNA-DIRECTED RNA POLYMERASES I/II/III SUBUNIT 10
Molecular weight formula_weight	8290.7 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	J

MIVPVRCFSCGKVVGDKWESYLNLLQEDELDEGTALSRLGLKRYCCRRMILTHVDLIEKFLRYNPLEKRD

Entity 11 Entity 11 polymer

Description description	DNA-DIRECTED RNA POLYMERASE II 13.6 KDA POLYPEPTIDE
Molecular weight formula_weight	13633.5 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	K

MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAAYKVEHPFFARFKLRIQTTEGYDPKDALKNACNSIINKLGALKTNFETEWNLQTLAADDAF

Entity 12 Entity 12 polymer

Description description	DNA-DIRECTED RNA POLYMERASES I, II, AND III 7.7 KDA POLYPEPTIDE
Molecular weight formula_weight	7730.0 kDa
EC 编号 ec_number	2.7.7.6
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

MSREGFQIPTNLDAAAAGTSQARTATLKYICAECSSKLSLSRTDAVRCKDCGHRILLKARTKRLVQFEAR

Entity 13 Entity 13 polymer

Description description	;5'-D(TPAPAPGPTPAPCPTPTPGP APGPCPT)-3' ;
Molecular weight formula_weight	4294.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	N

TAAGTACTTGAGCT

Entity 14 Entity 14 polymer

Description description	5'-R(UPUPCPGPAPCPCPAPGPAP*UP)-3'
Molecular weight formula_weight	3467.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	P

UUCGACCAGAU

Entity 15 Entity 15 polymer

Description description	;5'-D(APGPCPTPCPAPAPGPTPAP CPTPTPTPTPTTPCPBRUPGPGPTPCPAPTP*T)-3' ;
Molecular weight formula_weight	7949.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	T

AGCTCAAGTACTTTTNCUGGTCATT

Entity 16 Entity 16 non-polymer

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

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

▼

6. Fold Classification (SCOP + CATH) 40 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d2ja8a1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.29 — beta and beta-prime subunits of DNA dependent RNA-polymerase
Superfamily Superfamily superfamily	e.29.1 — beta and beta-prime subunits of DNA dependent RNA-polymerase
Family Family family	e.29.1.2 — RNA-polymerase beta-prime

Domain ID domain_id	d2ja8b1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.29 — beta and beta-prime subunits of DNA dependent RNA-polymerase
Superfamily Superfamily superfamily	e.29.1 — beta and beta-prime subunits of DNA dependent RNA-polymerase
Family Family family	e.29.1.1 — RNA-polymerase beta

Domain ID domain_id	d2ja8c1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.74 — DCoH-like
Superfamily Superfamily superfamily	d.74.3 — RBP11-like subunits of RNA polymerase
Family Family family	d.74.3.1 — RNA polymerase alpha subunit dimerisation domain

Domain ID domain_id	d2ja8c2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.181 — Insert subdomain of RNA polymerase alpha subunit
Superfamily Superfamily superfamily	d.181.1 — Insert subdomain of RNA polymerase alpha subunit
Family Family family	d.181.1.1 — Insert subdomain of RNA polymerase alpha subunit

Domain ID domain_id	d2ja8d1
Class class	i — Low resolution protein structures
Fold Fold fold	i.8 — RNA polymerase
Superfamily Superfamily superfamily	i.8.1 — RNA polymerase
Family Family family	i.8.1.1 — RNA polymerase

Domain ID domain_id	d2ja8e1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.52 — Restriction endonuclease-like
Superfamily Superfamily superfamily	c.52.3 — Eukaryotic RPB5 N-terminal domain
Family Family family	c.52.3.1 — Eukaryotic RPB5 N-terminal domain

Domain ID domain_id	d2ja8e2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.78 — RPB5-like RNA polymerase subunit
Superfamily Superfamily superfamily	d.78.1 — RPB5-like RNA polymerase subunit
Family Family family	d.78.1.1 — RPB5

Domain ID domain_id	d2ja8f1
Class class	a — All alpha proteins
Fold Fold fold	a.143 — RPB6/omega subunit-like
Superfamily Superfamily superfamily	a.143.1 — RPB6/omega subunit-like
Family Family family	a.143.1.2 — RPB6

Domain ID domain_id	d2ja8g1
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.5 — Cold shock DNA-binding domain-like

Domain ID domain_id	d2ja8g2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.230 — Dodecin subunit-like
Superfamily Superfamily superfamily	d.230.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE)
Family Family family	d.230.1.1 — N-terminal, heterodimerisation domain of RBP7 (RpoE)

Domain ID domain_id	d2ja8h1
Class class	b — All beta proteins
Fold Fold fold	b.40 — OB-fold
Superfamily Superfamily superfamily	b.40.4 — Nucleic acid-binding proteins
Family Family family	b.40.4.8 — RNA polymerase subunit RBP8

Domain ID domain_id	d2ja8i1
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.3 — Zinc beta-ribbon
Family Family family	g.41.3.1 — Transcriptional factor domain

Domain ID domain_id	d2ja8i2
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.3 — Zinc beta-ribbon
Family Family family	g.41.3.1 — Transcriptional factor domain

Domain ID domain_id	d2ja8j1
Class class	a — All alpha proteins
Fold Fold fold	a.4 — DNA/RNA-binding 3-helical bundle
Superfamily Superfamily superfamily	a.4.11 — RNA polymerase subunit RPB10
Family Family family	a.4.11.1 — RNA polymerase subunit RPB10

Domain ID domain_id	d2ja8k1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.74 — DCoH-like
Superfamily Superfamily superfamily	d.74.3 — RBP11-like subunits of RNA polymerase
Family Family family	d.74.3.2 — RBP11/RpoL

Domain ID domain_id	d2ja8l1
Class class	g — Small proteins
Fold Fold fold	g.41 — Rubredoxin-like
Superfamily Superfamily superfamily	g.41.9 — RNA polymerase subunits
Family Family family	g.41.9.2 — RBP12 subunit of RNA polymerase II

CATH v4.4 (24 domains)

Domain ID domain_id	2ja8A03
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	40 — Barwin-like endoglucanases
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2ja8A04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	180 — RNA polymerase ii

Domain ID domain_id	2ja8A05
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	274 — Enzyme I; Chain A, domain 2
Homologous superfamily homologous superfamily	100 — RNA polymerase Rpb1, domain 3

Domain ID domain_id	2ja8A06
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	132 — Topoisomerase I; Chain A, domain 4
Homologous superfamily homologous superfamily	30 — RNA polymerase Rpb1 funnel domain

Domain ID domain_id	2ja8A09
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	2ja8B04
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1110 — Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3
Homologous superfamily homologous superfamily	10 — RNA polymerase Rpb2, domain 2

Domain ID domain_id	2ja8B05
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1070 — Hypothetical Protein Ta0175; Chain: A, domain 2
Homologous superfamily homologous superfamily	20 —

Domain ID domain_id	2ja8B06
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	270 — Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6
Homologous superfamily homologous superfamily	10 — DNA-directed RNA polymerase, subunit 2, domain 6

Domain ID domain_id	2ja8B07
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	150 — RNA polymerase II, Rpb2 subunit, wall domain

Domain ID domain_id	2ja8B08
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1800 — DCoH-like
Homologous superfamily homologous superfamily	10 — RNA polymerase alpha subunit dimerisation domain

Domain ID domain_id	2ja8C01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	10 — RNA polymerase, RBP11-like subunit

Domain ID domain_id	2ja8C02
Class class	2 — Mainly Beta
Architecture architecture	170 — Beta Complex
Topology topology	120 — RNA Polymerase Alpha Subunit; Chain A, domain 2
Homologous superfamily homologous superfamily	12 — DNA-directed RNA polymerase, insert domain

Domain ID domain_id	2ja8D02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1250 — Growth Hormone; Chain: A;
Homologous superfamily homologous superfamily	40 — RNA Polymerase II, Rpb4 subunit

Domain ID domain_id	2ja8E01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1340 — Dna-directed Rna Polymerases I, Ii, And Iii 27 Kd Polypeptide; Chain: A; domain 1
Homologous superfamily homologous superfamily	10 — RNA polymerase, Rpb5, N-terminal domain

Domain ID domain_id	2ja8E02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	940 — Eukaryotic RPB6 RNA polymerase subunit
Homologous superfamily homologous superfamily	20 — RPB5-like RNA polymerase subunit

Domain ID domain_id	2ja8F00
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	940 — Eukaryotic RPB6 RNA polymerase subunit
Homologous superfamily homologous superfamily	10 — RNA polymerase subunit, RPB6/omega

Domain ID domain_id	2ja8G01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily	120 — RNA polymerase Rpb7-like, N-terminal domain

Domain ID domain_id	2ja8G02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	2ja8H00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	140 — Nucleic acid-binding proteins

Domain ID domain_id	2ja8I01
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2ja8I02
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	25 — N-terminal domain of TfIIb
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	2ja8J00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	60 — Homeodomain-like

Domain ID domain_id	2ja8K00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1360 — Gyrase A; domain 2
Homologous superfamily homologous superfamily	10 — RNA polymerase, RBP11-like subunit

Domain ID domain_id	2ja8L00
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	28 — Rubrerythrin, domain 2
Homologous superfamily homologous superfamily	30 — RNA polymerase ii, chain L

▶

Unit-cell length a length_a	222.642 Å
Unit-cell length b length_b	392.845 Å
Unit-cell length c length_c	282.894 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	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	3.800 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2686
R_work r_work	0.2686
R_free r_free	0.2876

CPD lesion containing RNA Polymerase II elongation complex D

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

DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNIT

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA-DIRECTED RNA POLYMERASE II 140 KDA POLYPEPTIDE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA-DIRECTED RNA POLYMERASE II 45KDA POLYPEPTIDE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA-DIRECTED RNA POLYMERASE II 32KDA POLYPEPTIDE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA-DIRECTED RNA POLYMERASES I, II, AND III 27 KDA POLYPEPTIDE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA-DIRECTED RNA POLYMERASES I, II, AND III 23 KDA POLYPEPTIDE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA-DIRECTED RNA POLYMERASE II 19KDA POLYPEPTIDE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA-DIRECTED RNA POLYMERASES I, II, AND III 14.5 KDA POLYPEPTIDE

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA-DIRECTED RNA POLYMERASE II SUBUNIT 9

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

DNA-DIRECTED RNA POLYMERASES I/II/III SUBUNIT 10

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer