9QEB | pdb_00009qeb

CryoEM structure of transcribing RNA polymerase II elongation complex

PDB DOI: https://doi.org/10.2210/pdb9QEB/pdb
EM Map EMD-53053: EMDB EMDataResource

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

Deposited: 2025-03-08 Released: 2026-05-27
Deposition Author(s): Yi, G., Li, Q., Wang, D., Zhang, P.
Funding Organization(s): Wellcome Trust, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.26 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

CryoEM structure of transcribing RNA polymerase II

Li, Q., Yi, G., Zhang, P., Wang, D.

To be published.

Macromolecule Content

Total Structure Weight: 545.17 kDa
Atom Count: 33,807
Modeled Residue Count: 4,005
Deposited Residue Count: 4,662
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	1,733	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: RPO21, RPB1, RPB220, SUA8, YDL140C, D2150 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

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| 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 Gene Names: RPB2, RPB150, RPO22, YOR151C 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

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| 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 Gene Names: RPB3, YIL021W
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

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| 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 Gene Names: RPB4, YJL140W, J0654
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

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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	215	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: RPB5, RPA7, RPC9, YBR154C, YBR1204
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

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| 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 Gene Names: RPO26, RPB6, YPR187W, P9677.8
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
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB7	G	171	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: RPB7, YDR404C, D9509.22
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
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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	146	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: RPB8, YOR224C, YOR50-14
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

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB9	I	122	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: RPB9, YGL070C
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
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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	70	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: RPB10, YOR210W
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
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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	K	120	Saccharomyces cerevisiae	Mutation(s): 0 Gene Names: RPB11, YOL005C
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

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| 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 Gene Names: RPC10, RPB12, YHR143W-A, YHR143BW
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

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Molecule	Chains	Length	Organism
Entity ID: 13
DNA (44-MER)	M [auth N]	44	Saccharomyces cerevisiae
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 14
RNA (5'-R(PAPUPCPGPAPGPAPGP*G)-3')	N [auth R]	9	Saccharomyces cerevisiae
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Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 15
DNA (44-MER)	O [auth T]	44	Saccharomyces cerevisiae
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ATP (Subject of Investigation/LOI) Query on ATP Download:Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A] mmCIF format, chain P [auth A]	P [auth A]	ADENOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₃ P₃ ZKHQWZAMYRWXGA-KQYNXXCUSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain Z [auth J] SDF format, chain Y [auth I] SDF format, chain X [auth I] SDF format, chain W [auth C] SDF format, chain V [auth B] SDF format, chain U [auth A] SDF format, chain T [auth A] SDF format, chain AA [auth L] MOL2 format, chain Z [auth J] MOL2 format, chain Y [auth I] MOL2 format, chain X [auth I] MOL2 format, chain W [auth C] MOL2 format, chain V [auth B] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain AA [auth L] mmCIF format, chain Z [auth J] mmCIF format, chain Y [auth I] mmCIF format, chain X [auth I] mmCIF format, chain W [auth C] mmCIF format, chain V [auth B] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A] mmCIF format, chain AA [auth L]	AA [auth L] T [auth A] U [auth A] V [auth B] W [auth C] AA [auth L], T [auth A], U [auth A], V [auth B], W [auth C], X [auth I], Y [auth I], Z [auth J]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth L] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth I] Focus chain Y [auth I] Focus chain Z [auth J] Interactions & Density Focus chain AA [auth L] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth C] Focus chain X [auth I] Focus chain Y [auth I] Focus chain Z [auth J]
K (Subject of Investigation/LOI) Query on K Download:Ideal Coordinates CCD File SDF format, chain S [auth A] MOL2 format, chain S [auth A] mmCIF format, chain S [auth A]	S [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain S [auth A] Interactions & Density Focus chain S [auth A]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A]	Q [auth A], R [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain Q [auth A] Focus chain R [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.26 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21_5207
RECONSTRUCTION	PHENIX
RECONSTRUCTION	Coot

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-05-27

Deposition Author(s):

Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	206422/Z/17/Z
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM102362
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM148476
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM147652
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	AI170791-7522
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	CA280467

Revision History (Full details and data files)

Version 1.0: 2026-05-27
Type: Initial release

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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.

9QEB | pdb_00009qeb

CryoEM structure of transcribing RNA polymerase II elongation complex

Literature

CryoEM structure of transcribing RNA polymerase II

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

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Sequence Annotations

Entity ID: 4

UniProt

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Sequence Annotations

Entity ID: 5

UniProt

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Sequence Annotations

Entity ID: 6

UniProt

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Sequence Annotations

Entity ID: 7

UniProt

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Sequence Annotations

Entity ID: 8

UniProt

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Sequence Annotations

Entity ID: 9

UniProt

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Sequence Annotations

Entity ID: 10

UniProt

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Sequence Annotations

Entity ID: 11

UniProt

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Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

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)