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

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

Currently 9W8S does not have a validation slider image.

This is version 1.0 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

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| 3D Structure

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
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Reference Sequence

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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
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB4	D	142	Sus scrofa	Mutation(s): 0

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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
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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

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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
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Reference Sequence

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

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

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Molecule	Chains	Length	Organism
Entity ID: 15
DNA (TS, template strand)	O [auth T]	25	synthetic construct
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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 P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth B] SDF format, chain S [auth C] SDF format, chain T [auth I] SDF format, chain V [auth J] SDF format, chain W [auth L] SDF format, chain U [auth I] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth C] MOL2 format, chain T [auth I] MOL2 format, chain V [auth J] MOL2 format, chain W [auth L] MOL2 format, chain U [auth I] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth C] mmCIF format, chain T [auth I] mmCIF format, chain V [auth J] mmCIF format, chain W [auth L] mmCIF format, chain U [auth I]	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]