9EGY

RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-nucleosome, bp +27

PDB DOI: https://doi.org/10.2210/pdb9EGY/pdb
EM Map EMD-48040: EMDB EMDataResource

Classification: TRANSCRIPTION, TRANSFERASE/RNA/DNA
Organism(s): Sus scrofa, Homo sapiens, synthetic construct, Xenopus laevis
Expression System: Trichoplusia ni, Escherichia coli
Mutation(s): Yes

Deposited: 2024-11-21 Released: 2024-12-18
Deposition Author(s): Markert, J., Farnung, L.
Funding Organization(s): Richard and Susan Smith Family Foundation, Damon Runyon Cancer Research Foundation, Rita Allen Foundation, National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 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

Structural basis of H3K36 trimethylation by SETD2 during chromatin transcription

Markert, J.W., Soffers, J.H., Farnung, L.

(2024) Science

DOI: https://doi.org/10.1126/science.adn6319

Macromolecule Content

Total Structure Weight: 1,679.71 kDa
Atom Count: 66,649
Modelled Residue Count: 8,719
Deposited Residue Count: 14,091
Unique protein chains: 27
Unique nucleic acid chains: 3

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit	A	1,984	Sus scrofa	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for A0A7M4DUC2 (Sus scrofa) Explore A0A7M4DUC2 Go to UniProtKB: A0A7M4DUC2
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A7M4DUC2
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	B	1,251	Sus scrofa	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for A0A4X1TVZ5 (Sus scrofa) Explore A0A4X1TVZ5 Go to UniProtKB: A0A4X1TVZ5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4X1TVZ5
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB3	C	275	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A481DF93 (Sus scrofa) Explore A0A481DF93 Go to UniProtKB: A0A481DF93
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A481DF93
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase Rpb4/RPC9 core domain-containing protein	D	142	Sus scrofa	Mutation(s): 0
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit E	E	210	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A4X1VTX4 (Sus scrofa) Explore A0A4X1VTX4 Go to UniProtKB: A0A4X1VTX4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4X1VTX4
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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 RPABC2	F	127	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A4X1VEK9 (Sus scrofa) Explore A0A4X1VEK9 Go to UniProtKB: A0A4X1VEK9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4X1VEK9
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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	172	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A4X1VKG7 (Sus scrofa) Explore A0A4X1VKG7 Go to UniProtKB: A0A4X1VKG7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4X1VKG7
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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	150	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8D1AQR7 (Sus scrofa) Explore A0A8D1AQR7 Go to UniProtKB: A0A8D1AQR7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8D1AQR7
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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 RPB9	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60899
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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	67	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8W4F9W9 (Sus scrofa) Explore A0A8W4F9W9 Go to UniProtKB: A0A8W4F9W9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8W4F9W9
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase II subunit J	K	117	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A8D0TE17 (Sus scrofa) Explore A0A8D0TE17 Go to UniProtKB: A0A8D0TE17
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8D0TE17
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase II subunit K	L	58	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A4X1TRS6 (Sus scrofa) Explore A0A4X1TRS6 Go to UniProtKB: A0A4X1TRS6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4X1TRS6
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription elongation factor SPT6	M	1,729	Homo sapiens	Mutation(s): 0 Gene Names: SUPT6H, KIAA0162, SPT6H
UniProt & NIH Common Fund Data Resources
Find proteins for Q7KZ85 (Homo sapiens) Explore Q7KZ85 Go to UniProtKB: Q7KZ85
PHAROS: Q7KZ85 GTEx: ENSG00000109111
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7KZ85
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein IWS1 homolog	O	821	Homo sapiens	Mutation(s): 0 Gene Names: IWS1, IWS1L
UniProt & NIH Common Fund Data Resources
Find proteins for Q96ST2 (Homo sapiens) Explore Q96ST2 Go to UniProtKB: Q96ST2
PHAROS: Q96ST2 GTEx: ENSG00000163166
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q96ST2
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase-associated protein CTR9 homolog	Q	1,179	Homo sapiens	Mutation(s): 0 Gene Names: CTR9, KIAA0155, SH2BP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q6PD62 (Homo sapiens) Explore Q6PD62 Go to UniProtKB: Q6PD62
PHAROS: Q6PD62 GTEx: ENSG00000198730
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6PD62
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase-associated protein RTF1 homolog	R	713	Homo sapiens	Mutation(s): 0 Gene Names: RTF1, KIAA0252
UniProt & NIH Common Fund Data Resources
Find proteins for Q92541 (Homo sapiens) Explore Q92541 Go to UniProtKB: Q92541
PHAROS: Q92541 GTEx: ENSG00000137815
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q92541
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Reference Sequence

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription elongation factor A protein 1	S	304	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P23193 (Homo sapiens) Explore P23193 Go to UniProtKB: P23193
PHAROS: P23193 GTEx: ENSG00000187735
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23193
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Reference Sequence

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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase-associated protein LEO1	U	666	Homo sapiens	Mutation(s): 0 Gene Names: LEO1, RDL
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WVC0 (Homo sapiens) Explore Q8WVC0 Go to UniProtKB: Q8WVC0
PHAROS: Q8WVC0 GTEx: ENSG00000166477
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8WVC0
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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase II-associated factor 1 homolog	V	531	Homo sapiens	Mutation(s): 0 Gene Names: PAF1, PD2
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N7H5 (Homo sapiens) Explore Q8N7H5 Go to UniProtKB: Q8N7H5
PHAROS: Q8N7H5 GTEx: ENSG00000006712
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8N7H5
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Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
WDR61	W	305	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9GZS3 (Homo sapiens) Explore Q9GZS3 Go to UniProtKB: Q9GZS3
PHAROS: Q9GZS3 GTEx: ENSG00000140395
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9GZS3
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Reference Sequence

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Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
Parafibromin	X	531	Homo sapiens	Mutation(s): 0 Gene Names: CDC73, C1orf28, HRPT2
UniProt & NIH Common Fund Data Resources
Find proteins for Q6P1J9 (Homo sapiens) Explore Q6P1J9 Go to UniProtKB: Q6P1J9
PHAROS: Q6P1J9 GTEx: ENSG00000134371
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6P1J9
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Reference Sequence

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Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription elongation factor SPT4	Y	121	Homo sapiens	Mutation(s): 0 Gene Names: SUPT4H1, SPT4H, SUPT4H
UniProt & NIH Common Fund Data Resources
Find proteins for P63272 (Homo sapiens) Explore P63272 Go to UniProtKB: P63272
PHAROS: P63272 GTEx: ENSG00000213246
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63272
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Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription elongation factor SPT5	Z	1,087	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for O00267 (Homo sapiens) Explore O00267 Go to UniProtKB: O00267
PHAROS: O00267 GTEx: ENSG00000196235
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UniProt Group	O00267
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Reference Sequence

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Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3	AA [auth a], EA [auth e]	136	Xenopus laevis	Mutation(s): 1 Gene Names: XELAEV_18002543mg
UniProt
Find proteins for A0A310TTQ1 (Xenopus laevis) Explore A0A310TTQ1 Go to UniProtKB: A0A310TTQ1
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UniProt Group	A0A310TTQ1
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Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	BA [auth b], FA [auth f]	103	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P62799 (Xenopus laevis) Explore P62799 Go to UniProtKB: P62799
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62799
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Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2A type 1	CA [auth c], GA [auth g]	130	Xenopus laevis	Mutation(s): 0
UniProt
Find proteins for P06897 (Xenopus laevis) Explore P06897 Go to UniProtKB: P06897
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06897
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Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H2B 1.1	DA [auth d], HA [auth h]	123	Xenopus laevis	Mutation(s): 1
UniProt
Find proteins for P02281 (Xenopus laevis) Explore P02281 Go to UniProtKB: P02281
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02281
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Length	Organism	Image
Non-template DNA	N	206	synthetic construct
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Entity ID: 16
Molecule	Chains	Length	Organism	Image
RNA	P	21	synthetic construct
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Entity ID: 20
Molecule	Chains	Length	Organism	Image
Template DNA	T	215	synthetic construct
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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 IA [auth A] SDF format, chain JA [auth A] SDF format, chain LA [auth B] SDF format, chain MA [auth C] SDF format, chain NA [auth I] SDF format, chain OA [auth I] SDF format, chain PA [auth J] SDF format, chain QA [auth L] SDF format, chain RA [auth Y] MOL2 format, chain IA [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth I] MOL2 format, chain OA [auth I] MOL2 format, chain PA [auth J] MOL2 format, chain QA [auth L] MOL2 format, chain RA [auth Y] mmCIF format, chain IA [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain MA [auth C] mmCIF format, chain NA [auth I] mmCIF format, chain OA [auth I] mmCIF format, chain PA [auth J] mmCIF format, chain QA [auth L] mmCIF format, chain RA [auth Y]	IA [auth A] JA [auth A] LA [auth B] MA [auth C] NA [auth I] IA [auth A], JA [auth A], LA [auth B], MA [auth C], NA [auth I], OA [auth I], PA [auth J], QA [auth L], RA [auth Y]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain IA [auth A] Focus chain JA [auth A] Focus chain LA [auth B] Focus chain MA [auth C] Focus chain NA [auth I] Focus chain OA [auth I] Focus chain PA [auth J] Focus chain QA [auth L] Focus chain RA [auth Y] Interactions & Density Focus chain IA [auth A] Focus chain JA [auth A] Focus chain LA [auth B] Focus chain MA [auth C] Focus chain NA [auth I] Focus chain OA [auth I] Focus chain PA [auth J] Focus chain QA [auth L] Focus chain RA [auth Y]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain KA [auth A] MOL2 format, chain KA [auth A] mmCIF format, chain KA [auth A]	KA [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain KA [auth A] Interactions & Density Focus chain KA [auth A]

Modified Residues 2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP Query on SEP	A	L-PEPTIDE LINKING	C₃ H₈ N O₆ P		SER
TPO Query on TPO	A	L-PEPTIDE LINKING	C₄ H₁₀ N O₆ P		THR

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-12-18

Deposition Author(s):

Markert, J.

Farnung, L.

Funding Organization	Location	Grant Number
Richard and Susan Smith Family Foundation	United States	--
Damon Runyon Cancer Research Foundation	United States	--
Rita Allen Foundation	United States	--
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2024-12-18
Type: Initial release

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.

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9EGY

RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-nucleosome, bp +27

Structural basis of H3K36 trimethylation by SETD2 during chromatin transcription

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Entity ID: 17

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Entity ID: 22

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