9W8W | pdb_00009w8w

Structure of backtracked yeast Pol II in complex with a cisplatin-induced inter-strand crosslink lesion at the +2 position.

PDB DOI: https://doi.org/10.2210/pdb9W8W/pdb
EM Map EMD-65754: EMDB EMDataResource

Classification: TRANSCRIPTION
Organism(s): synthetic construct, Saccharomyces cerevisiae S288C
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: 2.91 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation

Currently 9W8W does not have a validation slider image.

This is version 1.0 of the entry. See complete history.

Literature

Structure of backtracked yeast Pol II in complex with a cisplatin-induced inter-strand crosslink lesion at the +2 position.

Xu, J., Zhu, L.

To be published.

Macromolecule Content

Total Structure Weight: 530.91 kDa
Atom Count: 32,389
Modeled Residue Count: 4,017
Deposited Residue Count: 4,616
Unique protein chains: 12
Unique nucleic acid chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB3	D [auth C]	318	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P16370 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P16370 Go to UniProtKB: P16370
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P16370
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC1	E	215	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20434 Go to UniProtKB: P20434
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20434
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC2	F	155	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20435 Go to UniProtKB: P20435
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20435
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB7	G	171	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P34087 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P34087 Go to UniProtKB: P34087
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P34087
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB9	H [auth I]	122	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P27999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P27999 Go to UniProtKB: P27999
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P27999
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC5	I [auth J]	70	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P22139 Go to UniProtKB: P22139
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22139
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB11	J [auth K]	120	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P38902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38902 Go to UniProtKB: P38902
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P38902
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC4	K [auth L]	70	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P40422 Go to UniProtKB: P40422
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P40422
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB1	L [auth A]	1,733	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04050 Go to UniProtKB: P04050
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04050
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB2	M [auth B]	1,224	Saccharomyces cerevisiae S288C	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P08518 Go to UniProtKB: P08518
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P08518
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB4	N [auth D]	221	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P20433 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20433 Go to UniProtKB: P20433
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20433
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC3	O [auth H]	146	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20436 Go to UniProtKB: P20436
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20436
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 1
DNA (NTS, non-template strand)	A [auth N]	10	synthetic construct
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 2
RNA (5'-R(UPAPCPAPAPUPGPUPUPGPGPAPAPAPGPGPAPGPAPGP*A)-3')	B [auth P]	21	synthetic construct
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism
Entity ID: 3
DNA (TS, template strand)	C [auth T]	20	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 P [auth T] MOL2 format, chain P [auth T] mmCIF format, chain P [auth T]	P [auth T]	Cisplatin Cl₂ H₆ N₂ Pt LXZZYRPGZAFOLE-UHFFFAOYSA-L		Interactions Focus chain P [auth T] Interactions & Density Focus chain P [auth T]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Y [auth B] SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain U [auth L] SDF format, chain T [auth J] SDF format, chain S [auth I] SDF format, chain R [auth I] SDF format, chain Q [auth C] MOL2 format, chain Y [auth B] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth L] MOL2 format, chain T [auth J] MOL2 format, chain S [auth I] MOL2 format, chain R [auth I] MOL2 format, chain Q [auth C] mmCIF format, chain Y [auth B] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth L] mmCIF format, chain T [auth J] mmCIF format, chain S [auth I] mmCIF format, chain R [auth I] mmCIF format, chain Q [auth C]	Q [auth C] R [auth I] S [auth I] T [auth J] U [auth L] Q [auth C], R [auth I], S [auth I], T [auth J], U [auth L], V [auth A], W [auth A], Y [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain Q [auth C] Focus chain R [auth I] Focus chain S [auth I] Focus chain T [auth J] Focus chain U [auth L] Focus chain V [auth A] Focus chain W [auth A] Focus chain Y [auth B] Interactions & Density Focus chain Q [auth C] Focus chain R [auth I] Focus chain S [auth I] Focus chain T [auth J] Focus chain U [auth L] Focus chain V [auth A] Focus chain W [auth A] Focus chain Y [auth B]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain X [auth A] MOL2 format, chain X [auth A] mmCIF format, chain X [auth A]	X [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain X [auth A] Interactions & Density Focus chain X [auth A]