8B3F | pdb_00008b3f

Pol II-CSB-CSA-DDB1-ELOF1

PDB DOI: https://doi.org/10.2210/pdb8B3F/pdb
EM Map EMD-15826: EMDB EMDataResource
NAKB: 8B3F

Classification: TRANSCRIPTION
Organism(s): Sus scrofa domesticus, Homo sapiens
Expression System: Escherichia coli, Trichoplusia ni
Mutation(s): No

Deposited: 2022-09-16 Released: 2023-09-27
Deposition Author(s): Kokic, G., Cramer, P.
Funding Organization(s): German Research Foundation (DFG), European Research Council (ERC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Pol II-CSB-CSA-DDB1-ELOF1 structure.

Kokic, G., Cramer, P.

To be published.

Macromolecule Content

Total Structure Weight: 901.9 kDa
Atom Count: 46,917
Modeled Residue Count: 5,728
Deposited Residue Count: 7,809
Unique protein chains: 16
Unique nucleic acid chains: 3

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit	A	1,970	Sus scrofa domesticus	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for A0A8D1DPV6 (Sus scrofa) Explore A0A8D1DPV6 Go to UniProtKB: A0A8D1DPV6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8D1DPV6
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	B	1,167	Sus scrofa domesticus	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for I3LGP4 (Sus scrofa) Explore I3LGP4 Go to UniProtKB: I3LGP4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I3LGP4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB3	C	275	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for I3LCH3 (Sus scrofa) Explore I3LCH3 Go to UniProtKB: I3LCH3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I3LCH3
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase II subunit D	D	142	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for A0A4X1VM56 (Sus scrofa) Explore A0A4X1VM56 Go to UniProtKB: A0A4X1VM56
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A4X1VM56
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit E	E	210	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for I3LSI7 (Sus scrofa) Explore I3LSI7 Go to UniProtKB: I3LSI7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I3LSI7
Sequence Annotations Expand
Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit F	F	127	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for A0A4X1VEK9 (Sus scrofa) Explore A0A4X1VEK9 Go to UniProtKB: A0A4X1VEK9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A4X1VEK9
Sequence Annotations Expand
Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB7	G	172	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for A0A4X1VKG7 (Sus scrofa) Explore A0A4X1VKG7 Go to UniProtKB: A0A4X1VKG7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A4X1VKG7
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC3	H	150	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for I3LCB2 (Sus scrofa) Explore I3LCB2 Go to UniProtKB: I3LCB2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	I3LCB2
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB9	I	125	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for P60899 (Sus scrofa) Explore P60899 Go to UniProtKB: P60899
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60899
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC5	J	67	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for A0A8W4F9W9 (Sus scrofa) Explore A0A8W4F9W9 Go to UniProtKB: A0A8W4F9W9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8W4F9W9
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA_pol_L_2 domain-containing protein	K	117	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for F1RKE4 (Sus scrofa) Explore F1RKE4 Go to UniProtKB: F1RKE4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	F1RKE4
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase II subunit K	L	58	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for A0A4X1TRS6 (Sus scrofa) Explore A0A4X1TRS6 Go to UniProtKB: A0A4X1TRS6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A4X1TRS6
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription elongation factor 1 homolog	M	83	Homo sapiens	Mutation(s): 0 Gene Names: ELOF1, hCG_29982
UniProt
Find proteins for A0A8D1B522 (Sus scrofa) Explore A0A8D1B522 Go to UniProtKB: A0A8D1B522
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8D1B522
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA excision repair protein ERCC-8	Q [auth a]	396	Homo sapiens	Mutation(s): 0 Gene Names: ERCC8, CKN1, CSA
UniProt & NIH Common Fund Data Resources
Find proteins for Q13216 (Homo sapiens) Explore Q13216 Go to UniProtKB: Q13216
PHAROS: Q13216 GTEx: ENSG00000049167
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q13216
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA excision repair protein ERCC-6	R [auth b]	1,496	Homo sapiens	Mutation(s): 0 Gene Names: ERCC6, CSB EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q03468 (Homo sapiens) Explore Q03468 Go to UniProtKB: Q03468
PHAROS: Q03468 GTEx: ENSG00000225830
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q03468
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Reference Sequence

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA damage-binding protein 1	S [auth d]	1,140	Homo sapiens	Mutation(s): 0 Gene Names: DDB1, XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens) Explore Q16531 Go to UniProtKB: Q16531
PHAROS: Q16531 GTEx: ENSG00000167986
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q16531
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 14
NTS	N	52	Homo sapiens
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 15
RNA	O [auth P]	10	Homo sapiens
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 16
TS	P [auth T]	52	Homo sapiens
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Z [auth I] SDF format, chain Y [auth I] SDF format, chain X [auth C] SDF format, chain W [auth B] SDF format, chain U [auth A] SDF format, chain T [auth A] SDF format, chain CA [auth M] SDF format, chain BA [auth L] SDF format, chain AA [auth J] MOL2 format, chain Z [auth I] MOL2 format, chain Y [auth I] MOL2 format, chain X [auth C] MOL2 format, chain W [auth B] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain CA [auth M] MOL2 format, chain BA [auth L] MOL2 format, chain AA [auth J] mmCIF format, chain Z [auth I] mmCIF format, chain Y [auth I] mmCIF format, chain X [auth C] mmCIF format, chain W [auth B] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A] mmCIF format, chain CA [auth M] mmCIF format, chain BA [auth L] mmCIF format, chain AA [auth J]	AA [auth J] BA [auth L] CA [auth M] T [auth A] U [auth A] AA [auth J], BA [auth L], CA [auth M], T [auth A], U [auth A], W [auth B], X [auth C], Y [auth I], Z [auth I]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth J] Focus chain BA [auth L] Focus chain CA [auth M] Focus chain T [auth A] Focus chain U [auth A] Focus chain W [auth B] Focus chain X [auth C] Focus chain Y [auth I] Focus chain Z [auth I] Interactions & Density Focus chain AA [auth J] Focus chain BA [auth L] Focus chain CA [auth M] Focus chain T [auth A] Focus chain U [auth A] Focus chain W [auth B] Focus chain X [auth C] Focus chain Y [auth I] Focus chain Z [auth I]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain V [auth A] MOL2 format, chain V [auth A] mmCIF format, chain V [auth A]	V [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain V [auth A] Interactions & Density Focus chain V [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-09-27

Deposition Author(s):

Kokic, G.

Cramer, P.

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	EXC 2067/1-390729940
European Research Council (ERC)	European Union	Advanced Investigator Grant CHROMATRANS (grant agreement No. 882357)

Revision History (Full details and data files)

Version 1.0: 2023-09-27
Type: Initial release
Version 1.1: 2025-07-02
Changes: Data collection, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

8B3F | pdb_00008b3f

Pol II-CSB-CSA-DDB1-ELOF1

Literature

Pol II-CSB-CSA-DDB1-ELOF1 structure.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt

Entity Groups

Sequence Annotations

Entity ID: 17

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 18

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 19

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 14

Sequence Annotations

Entity ID: 15

Sequence Annotations

Entity ID: 16

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation