9W8S | pdb_00009w8s

Structure of mammalian RNA polymerase II stalled by a cisplatin-induced inter-strand crosslink lesion at the +2 position.

PDB DOI: https://doi.org/10.2210/pdb9W8S/pdb
EM Map EMD-65750: EMDB EMDataResource
NAKB: 9W8S

Classification: TRANSCRIPTION
Organism(s): Sus scrofa, synthetic construct
Mutation(s): No

Deposited: 2025-08-08 Released: 2026-06-24
Deposition Author(s): Xu, J., Zhu, L.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.04 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

Structure of mammalian RNA polymerase II stalled by a cisplatin-induced inter-strand crosslink lesion at the +2 position.

Xu, J., Zhu, L.

To be published.

Macromolecule Content

Total Structure Weight: 537.1 kDa
Atom Count: 32,013
Modeled Residue Count: 3,941
Deposited Residue Count: 4,643
Unique protein chains: 12
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 II subunit RPB1	A	1,970	Sus scrofa	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	B	1,174	Sus scrofa	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	271	Sus scrofa	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
DNA-directed RNA polymerase II subunit RPB4	D	142	Sus scrofa	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
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Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC1	E	210	Sus scrofa	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 polymerases I, II, and III subunit RPABC2	F	127	Sus scrofa	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
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit RPB7	G	171	Sus scrofa	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
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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	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	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	Mutation(s): 0
UniProt
Find proteins for A0A4X1VYD0 (Sus scrofa) Explore A0A4X1VYD0 Go to UniProtKB: A0A4X1VYD0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A4X1VYD0
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB11-a	K	115	Sus scrofa	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
DNA-directed RNA polymerases I, II, and III subunit RPABC4	L	58	Sus scrofa	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
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 13
DNA (NTS, non-template strand)	M [auth N]	18	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 14
RNA (5'-R(UPAPCPAPAPUPGPUPUPGPGPAPAPAPGPGPAPGPAPG)-3')	N [auth P]	20	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 15
DNA (TS, template strand)	O [auth T]	25	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CPT (Subject of Investigation/LOI) Query on CPT Download:Ideal Coordinates CCD File SDF format, chain X [auth N] MOL2 format, chain X [auth N] mmCIF format, chain X [auth N]	X [auth N]	Cisplatin Cl₂ H₆ N₂ Pt LXZZYRPGZAFOLE-UHFFFAOYSA-L		Interactions Focus chain X [auth N] Interactions & Density Focus chain X [auth N]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain W [auth L] SDF format, chain V [auth J] SDF format, chain U [auth I] SDF format, chain T [auth I] SDF format, chain S [auth C] SDF format, chain R [auth B] SDF format, chain Q [auth A] SDF format, chain P [auth A] MOL2 format, chain W [auth L] MOL2 format, chain V [auth J] MOL2 format, chain U [auth I] MOL2 format, chain T [auth I] MOL2 format, chain S [auth C] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] mmCIF format, chain W [auth L] mmCIF format, chain V [auth J] mmCIF format, chain U [auth I] mmCIF format, chain T [auth I] mmCIF format, chain S [auth C] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A]	P [auth A] Q [auth A] R [auth B] S [auth C] T [auth I] P [auth A], Q [auth A], R [auth B], S [auth C], T [auth I], U [auth I], V [auth J], W [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth I] Focus chain U [auth I] Focus chain V [auth J] Focus chain W [auth L] Interactions & Density Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth B] Focus chain S [auth C] Focus chain T [auth I] Focus chain U [auth I] Focus chain V [auth J] Focus chain W [auth L]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Y [auth P] MOL2 format, chain Y [auth P] mmCIF format, chain Y [auth P]	Y [auth P]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain Y [auth P] Interactions & Density Focus chain Y [auth P]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.04 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-06-24

Deposition Author(s):

Xu, J.

Zhu, L.

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32370590

Revision History (Full details and data files)

Version 1.0: 2026-06-24
Type: Initial release
Version 1.1: 2026-08-12
Type: Remediation
Reason: Metalloprotein remediation
Changes: Data collection, Derived calculations

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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.

9W8S | pdb_00009w8s

Structure of mammalian RNA polymerase II stalled by a cisplatin-induced inter-strand crosslink lesion at the +2 position.

Literature

Structure of mammalian RNA polymerase II stalled by a cisplatin-induced inter-strand crosslink lesion at the +2 position.

Biological Assembly 1

Macromolecules

Entity ID: 1

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

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UniProt

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UniProt

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Entity ID: 7

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UniProt

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Entity ID: 9

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Entity ID: 10

UniProt

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Entity ID: 11

UniProt

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Entity ID: 12

UniProt

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Entity ID: 13

Sequence Annotations

Entity ID: 14

Sequence Annotations

Entity ID: 15

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)