29TK | pdb_000029tk

RNA polymerase II elongation complex with the +1 nucleosome

PDB DOI: https://doi.org/10.2210/pdb29TK/pdb
EM Map EMD-57364: EMDB EMDataResource

Classification: TRANSCRIPTION
Organism(s): Sus scrofa, unidentified adenovirus, Homo sapiens, Xenopus laevis
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2026-04-07 Released: 2026-07-22
Deposition Author(s): Zhan, Y., Abril-Garrido, J., Dienemann, C., Cramer, P.
Funding Organization(s): Max Planck Society

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.90 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

RNA polymerase II elongation complex with the +1 nucleosome

Zhan, Y., Abril-Garrido, J.

To be published.

Macromolecule Content

Total Structure Weight: 941.24 kDa
Atom Count: 49,023
Modeled Residue Count: 5,506
Deposited Residue Count: 7,463
Unique protein chains: 19
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 RPB3	A [auth C]	275	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
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase II subunit D	B [auth D]	184	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A287ADR4 (Sus scrofa) Explore A0A287ADR4 Go to UniProtKB: A0A287ADR4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A287ADR4
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit E	C [auth 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
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC2	D [auth F]	127	Sus scrofa	Mutation(s): 0
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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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit	E [auth G]	171	Sus scrofa	Mutation(s): 0
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
Sequence Annotations Expand
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 RPABC3	F [auth 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
Sequence Annotations Expand
Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB9	G [auth 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
Sequence Annotations Expand
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 RPABC5	H [auth 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: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB11-a	I [auth K]	117	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: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase II subunit K	J [auth L]	58	Sus scrofa	Mutation(s): 0
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
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription factor IIF subunit 1	L [auth Q]	517	Homo sapiens	Mutation(s): 0 Gene Names: GTF2F1, RAP74
UniProt & NIH Common Fund Data Resources
Find proteins for P35269 (Homo sapiens) Explore P35269 Go to UniProtKB: P35269
GTEx: ENSG00000125651
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P35269
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription factor IIF subunit 2	M [auth R]	249	Homo sapiens	Mutation(s): 0 Gene Names: GTF2F2, RAP30 EC: 3.6.4.12
UniProt & NIH Common Fund Data Resources
Find proteins for P13984 (Homo sapiens) Explore P13984 Go to UniProtKB: P13984
PHAROS: P13984 GTEx: ENSG00000188342
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P13984
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
General transcription factor IIE subunit 1	O [auth W]	439	Homo sapiens	Mutation(s): 0 Gene Names: GTF2E1, TF2E1
UniProt & NIH Common Fund Data Resources
Find proteins for P29083 (Homo sapiens) Explore P29083 Go to UniProtKB: P29083
PHAROS: P29083 GTEx: ENSG00000153767
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P29083
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.2	P [auth a], T [auth e]	136	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P84233 (Xenopus laevis) Explore P84233 Go to UniProtKB: P84233
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P84233
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	Q [auth b], U [auth f]	103	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799 Go to UniProtKB: P62799
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62799
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1	R [auth c], V [auth g]	130	Xenopus laevis	Mutation(s): 1
UniProt
Find proteins for P06897 (Xenopus laevis) Explore P06897 Go to UniProtKB: P06897
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P06897
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Reference Sequence

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B 1.1	S [auth d], W [auth h]	126	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281 Go to UniProtKB: P02281
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02281
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Reference Sequence

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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit	X [auth A]	1,970	Sus scrofa	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for A0A7M4DUC2 (Sus scrofa) Explore A0A7M4DUC2 Go to UniProtKB: A0A7M4DUC2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A7M4DUC2
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Reference Sequence

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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	Y [auth B]	1,300	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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Molecule	Chains	Length	Organism
Entity ID: 11
RNA (5'-R(PAPCPAPCPCPCPAPGPCPC)-3')	K [auth P]	10	unidentified adenovirus
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Reference Sequence

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 14
DNA (199-MER)	N [auth T]	252	unidentified adenovirus
Sequence Annotations Expand
Reference Sequence

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Molecule	Chains	Length	Organism
Entity ID: 22
DNA (188-MER)	Z [auth N]	252	unidentified adenovirus
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN (Subject of Investigation/LOI) Query on ZN Download:Ideal Coordinates CCD File SDF format, chain JA [auth B] SDF format, chain IA [auth A] SDF format, chain HA [auth A] SDF format, chain FA [auth W] SDF format, chain EA [auth L] SDF format, chain DA [auth J] SDF format, chain CA [auth I] SDF format, chain BA [auth I] SDF format, chain AA [auth C] MOL2 format, chain JA [auth B] MOL2 format, chain IA [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain FA [auth W] MOL2 format, chain EA [auth L] MOL2 format, chain DA [auth J] MOL2 format, chain CA [auth I] MOL2 format, chain BA [auth I] MOL2 format, chain AA [auth C] mmCIF format, chain JA [auth B] mmCIF format, chain IA [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain FA [auth W] mmCIF format, chain EA [auth L] mmCIF format, chain DA [auth J] mmCIF format, chain CA [auth I] mmCIF format, chain BA [auth I] mmCIF format, chain AA [auth C]	AA [auth C] BA [auth I] CA [auth I] DA [auth J] EA [auth L] AA [auth C], BA [auth I], CA [auth I], DA [auth J], EA [auth L], FA [auth W], HA [auth A], IA [auth A], JA [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth I] Focus chain CA [auth I] Focus chain DA [auth J] Focus chain EA [auth L] Focus chain FA [auth W] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth B] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth I] Focus chain CA [auth I] Focus chain DA [auth J] Focus chain EA [auth L] Focus chain FA [auth W] Focus chain HA [auth A] Focus chain IA [auth A] Focus chain JA [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain GA [auth A] MOL2 format, chain GA [auth A] mmCIF format, chain GA [auth A]	GA [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain GA [auth A] Interactions & Density Focus chain GA [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	RELION	5.0

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-07-22

Deposition Author(s):

Funding Organization	Location	Grant Number
Max Planck Society	Germany	--

Revision History (Full details and data files)

Version 1.0: 2026-07-22
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.

29TK | pdb_000029tk

RNA polymerase II elongation complex with the +1 nucleosome

Literature

RNA polymerase II elongation complex with the +1 nucleosome

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: 12

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 15

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 16

UniProt

Entity Groups

Sequence Annotations

Entity ID: 17

UniProt

Entity Groups

Sequence Annotations

Entity ID: 18

UniProt

Entity Groups

Sequence Annotations

Entity ID: 19

UniProt

Entity Groups

Sequence Annotations

Entity ID: 20

UniProt

Entity Groups

Sequence Annotations

Entity ID: 21

UniProt