9ZPK | pdb_00009zpk

Cryo-EM structure of the complete Saccharomyces cerevisiae RNA polymerase II in closed clamp conformation

PDB DOI: https://doi.org/10.2210/pdb9ZPK/pdb
EM Map EMD-74528: EMDB EMDataResource

Classification: TRANSCRIPTION
Organism(s): Saccharomyces cerevisiae
Mutation(s): No

Deposited: 2025-12-16 Released: 2026-08-05
Deposition Author(s): Fordjour, G.N.R., Murakami, K., Armache, J.-P., Murakami, K.S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.31 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Clamp conformational flexibility and dynamics in archaeal and eukaryotic RNA polymerases revealed by cryo-EM

Fordjour, G.N.R., Murakami, K., Armache, J.-P., Murakami, K.S.

To be published.

Macromolecule Content

Total Structure Weight: 514.68 kDa
Atom Count: 31,439
Modeled Residue Count: 3,965
Deposited Residue Count: 4,565
Unique protein chains: 12

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB1	A	1,733	Saccharomyces cerevisiae	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB2	B	1,224	Saccharomyces cerevisiae	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB3	C	318	Saccharomyces cerevisiae	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB4	D	221	Saccharomyces cerevisiae	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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC1	E	215	Saccharomyces cerevisiae	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	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	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 polymerases I, II, and III subunit RPABC3	H	146	Saccharomyces cerevisiae	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 proteins by:

| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB9	I	122	Saccharomyces cerevisiae	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: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC5	J	70	Saccharomyces cerevisiae	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: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB11	K	120	Saccharomyces cerevisiae	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: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC4	L	70	Saccharomyces cerevisiae	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain S [auth J] SDF format, chain T [auth L] SDF format, chain R [auth I] SDF format, chain Q [auth I] SDF format, chain P [auth C] SDF format, chain O [auth B] SDF format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain S [auth J] MOL2 format, chain T [auth L] MOL2 format, chain R [auth I] MOL2 format, chain Q [auth I] MOL2 format, chain P [auth C] MOL2 format, chain O [auth B] MOL2 format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain S [auth J] mmCIF format, chain T [auth L] mmCIF format, chain R [auth I] mmCIF format, chain Q [auth I] mmCIF format, chain P [auth C] mmCIF format, chain O [auth B] mmCIF format, chain M [auth A]	M [auth A] N [auth A] O [auth B] P [auth C] Q [auth I] M [auth A], N [auth A], O [auth B], P [auth C], Q [auth I], R [auth I], S [auth J], T [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth I] Focus chain R [auth I] Focus chain S [auth J] Focus chain T [auth L] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth I] Focus chain R [auth I] Focus chain S [auth J] Focus chain T [auth L]