9YD5 | pdb_00009yd5

RNA polymerase II on Super pause sequence in the pre-translocated state

PDB DOI: https://doi.org/10.2210/pdb9YD5/pdb
EM Map EMD-72795: EMDB EMDataResource

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

Deposited: 2025-09-21 Released: 2026-09-23
Deposition Author(s): Vazquez Nunez, R., Vos, S.M.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: 2D ARRAY
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

RNA polymerase II on Super pause sequence in the pre-translocated state

Vazquez Nunez, R., Vos, S.M.

To be published.

Macromolecule Content

Total Structure Weight: 480.98 kDa
Atom Count: 31,405
Modeled Residue Count: 3,810
Deposited Residue Count: 4,062
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 subunit	A	1,474	Sus scrofa	Mutation(s): 0 Gene Names: POLR2A EC: 2.7.7.6
UniProt
Find proteins for A0A8D1DPV6 (Sus scrofa) Explore A0A8D1DPV6 Go to UniProtKB: A0A8D1DPV6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8D1DPV6
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 subunit beta	B	1,158	Sus scrofa	Mutation(s): 0 Gene Names: POLR2B 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	265	Sus scrofa	Mutation(s): 0 Gene Names: POLR2C
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	128	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8D1GCS3 (Sus scrofa) Explore A0A8D1GCS3 Go to UniProtKB: A0A8D1GCS3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8D1GCS3
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	209	Sus scrofa	Mutation(s): 0 Gene Names: POLR2E
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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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC2	F	75	Sus scrofa	Mutation(s): 0 Gene Names: POLR2F
UniProt
Find proteins for A0A8D1KNW4 (Sus scrofa) Explore A0A8D1KNW4 Go to UniProtKB: A0A8D1KNW4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8D1KNW4
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit	G	171	Sus scrofa	Mutation(s): 0 Gene Names: POLR2G
UniProt
Find proteins for A0A4X1VKG7 (Sus scrofa) Explore A0A4X1VKG7 Go to UniProtKB: A0A4X1VKG7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A4X1VKG7
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Reference Sequence

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| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC3	H	147	Sus scrofa	Mutation(s): 0 Gene Names: POLR2H
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
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB9	I	125	Sus scrofa	Mutation(s): 0 Gene Names: POLR2I
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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| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC5	J	64	Sus scrofa	Mutation(s): 0 Gene Names: POLR2L
UniProt
Find proteins for Q32P78 (Bos taurus) Explore Q32P78 Go to UniProtKB: Q32P78
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q32P78
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Reference Sequence

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| 3D Structure

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 Gene Names: POLR2J
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
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	44	Sus scrofa	Mutation(s): 0 Gene Names: POLR2K
UniProt
Find proteins for A0A8D0JYF1 (Sus scrofa) Explore A0A8D0JYF1 Go to UniProtKB: A0A8D0JYF1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A8D0JYF1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 13
DNA non-template strand	M [auth N]	36	synthetic construct
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 14
RNA transcript	N [auth P]	15	synthetic construct
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 15
DNA template strand	O [auth T]	36	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.80 Å
Aggregation State: 2D ARRAY
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.2_5419
RECONSTRUCTION	cryoSPARC	4.7

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-09-23

Deposition Author(s):

Vazquez Nunez, R.

Vos, S.M.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	DP2-GM146254

Revision History (Full details and data files)

Version 1.0: 2026-09-23
Type: Initial release

9YD5 | pdb_00009yd5

RNA polymerase II on Super pause sequence in the pre-translocated state

Literature

RNA polymerase II on Super pause sequence in the pre-translocated state

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

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)