9FD2

Structure of Pol II-TC-NER-STK19 complex

PDB DOI: https://doi.org/10.2210/pdb9FD2/pdb
EM Map EMD-50325: EMDB EMDataResource
NAKB: 9FD2

Classification: TRANSCRIPTION
Organism(s): Sus scrofa domesticus, Homo sapiens
Expression System: Escherichia coli, Spodoptera frugiperda
Mutation(s): No

Deposited: 2024-05-16 Released: 2024-11-13
Deposition Author(s): Lee, S.-H., Sixma, T.K.
Funding Organization(s): Netherlands Organisation for Scientific Research (NWO), Oncode Institute

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.40 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

Structure of Pol II-TC-NER-STK19 complex

Lee, S.-H., Sixma, T.K.

(2024) Mol Cell

DOI: https://doi.org/10.1016/j.molcel.2024.10.030

Macromolecule Content

Total Structure Weight: 1,058.54 kDa
Atom Count: 51,949
Modelled Residue Count: 6,336
Deposited Residue Count: 9,142
Unique protein chains: 19
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	1,970	Sus scrofa domesticus	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for A0A8D1DPV6 (Sus scrofa) Explore A0A8D1DPV6 Go to UniProtKB: A0A8D1DPV6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8D1DPV6
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	B	1,300	Sus scrofa domesticus	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I3LGP4
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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 domesticus	Mutation(s): 0
UniProt
Find proteins for I3LCH3 (Sus scrofa) Explore I3LCH3 Go to UniProtKB: I3LCH3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I3LCH3
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase II subunit D	D	142	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for A0A4X1VM56 (Sus scrofa) Explore A0A4X1VM56 Go to UniProtKB: A0A4X1VM56
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4X1VM56
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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 domesticus	Mutation(s): 0
UniProt
Find proteins for I3LSI7 (Sus scrofa) Explore I3LSI7 Go to UniProtKB: I3LSI7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I3LSI7
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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 domesticus	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 subunit	G	172	Sus scrofa domesticus	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 domesticus	Mutation(s): 0
UniProt
Find proteins for I3LCB2 (Sus scrofa) Explore I3LCB2 Go to UniProtKB: I3LCB2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I3LCB2
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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 domesticus	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 domesticus	Mutation(s): 0
UniProt
Find proteins for A0A4X1VYD0 (Sus scrofa) Explore A0A4X1VYD0 Go to UniProtKB: A0A4X1VYD0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4X1VYD0
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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-a	K	117	Sus scrofa domesticus	Mutation(s): 0
UniProt
Find proteins for F1RKE4 (Sus scrofa) Explore F1RKE4 Go to UniProtKB: F1RKE4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F1RKE4
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA polymerase II, I and III subunit K	L	58	Sus scrofa domesticus	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 1 homolog	M [auth f]	85	Homo sapiens	Mutation(s): 0 Gene Names: ELOF1
UniProt & NIH Common Fund Data Resources
Find proteins for P60002 (Homo sapiens) Explore P60002 Go to UniProtKB: P60002
PHAROS: P60002 GTEx: ENSG00000130165
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60002
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Reference Sequence

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Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA excision repair protein ERCC-8	Q [auth a]	408	Homo sapiens	Mutation(s): 0 Gene Names: ERCC8, CKN1, CSA
UniProt & NIH Common Fund Data Resources
Find proteins for Q13216 (Homo sapiens) Explore Q13216 Go to UniProtKB: Q13216
PHAROS: Q13216 GTEx: ENSG00000049167
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13216
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Reference Sequence

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Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA damage-binding protein 1	R [auth b]	1,160	Homo sapiens	Mutation(s): 0 Gene Names: DDB1, XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens) Explore Q16531 Go to UniProtKB: Q16531
PHAROS: Q16531 GTEx: ENSG00000167986
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q16531
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Reference Sequence

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Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
DET1- and DDB1-associated protein 1	S [auth c]	152	Homo sapiens	Mutation(s): 0 Gene Names: DDA1, C19orf58, PCIA1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BW61 (Homo sapiens) Explore Q9BW61 Go to UniProtKB: Q9BW61
PHAROS: Q9BW61 GTEx: ENSG00000130311
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9BW61
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Reference Sequence

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Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
Inactive serine/threonine-protein kinase 19	T [auth g]	257	Homo sapiens	Mutation(s): 0 Gene Names: STK19, G11, RP1
UniProt & NIH Common Fund Data Resources
Find proteins for P49842 (Homo sapiens) Explore P49842 Go to UniProtKB: P49842
PHAROS: P49842 GTEx: ENSG00000204344
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49842
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Reference Sequence

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Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA excision repair protein ERCC-6	U [auth e]	1,493	Homo sapiens	Mutation(s): 0 Gene Names: ERCC6, CSB EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q03468 (Homo sapiens) Explore Q03468 Go to UniProtKB: Q03468
PHAROS: Q03468 GTEx: ENSG00000225830
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q03468
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Reference Sequence

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Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
UV-stimulated scaffold protein A	V [auth d]	729	Homo sapiens	Mutation(s): 0 Gene Names: UVSSA, KIAA1530
UniProt & NIH Common Fund Data Resources
Find proteins for Q2YD98 (Homo sapiens) Explore Q2YD98 Go to UniProtKB: Q2YD98
PHAROS: Q2YD98 GTEx: ENSG00000163945
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q2YD98
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Length	Organism	Image
Non-template DNA	N	60	Homo sapiens
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Length	Organism	Image
RNA	O [auth M]	25	Homo sapiens
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Length	Organism	Image
Template DNA	P [auth T]	60	Homo sapiens
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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 AA [auth C] SDF format, chain BA [auth I] SDF format, chain CA [auth I] SDF format, chain DA [auth J] SDF format, chain EA [auth L] SDF format, chain FA [auth f] SDF format, chain GA [auth d] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Z [auth B] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth I] MOL2 format, chain CA [auth I] MOL2 format, chain DA [auth J] MOL2 format, chain EA [auth L] MOL2 format, chain FA [auth f] MOL2 format, chain GA [auth d] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Z [auth B] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth I] mmCIF format, chain CA [auth I] mmCIF format, chain DA [auth J] mmCIF format, chain EA [auth L] mmCIF format, chain FA [auth f] mmCIF format, chain GA [auth d] mmCIF format, chain W [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Z [auth B]	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 f], GA [auth d], W [auth A], X [auth A], Z [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 f] Focus chain GA [auth d] Focus chain W [auth A] Focus chain X [auth A] Focus chain Z [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 f] Focus chain GA [auth d] Focus chain W [auth A] Focus chain X [auth A] Focus chain Z [auth B]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain Y [auth A] MOL2 format, chain Y [auth A] mmCIF format, chain Y [auth A]	Y [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain Y [auth A] Interactions & Density Focus chain Y [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.40 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2024-11-13

Deposition Author(s):

Lee, S.-H.

Sixma, T.K.

Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research (NWO)	Netherlands	TOP 714.017.003
Oncode Institute	Netherlands	--

Revision History (Full details and data files)

Version 1.0: 2024-11-13
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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9FD2

Structure of Pol II-TC-NER-STK19 complex

Structure of Pol II-TC-NER-STK19 complex

Entity ID: 1

UniProt

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Sequence Annotations

Entity ID: 2

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Entity ID: 12

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Entity ID: 13

UniProt & NIH Common Fund Data Resources

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Entity ID: 17

UniProt & NIH Common Fund Data Resources

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Sequence Annotations

Entity ID: 18

UniProt & NIH Common Fund Data Resources

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Sequence Annotations

Entity ID: 19

UniProt & NIH Common Fund Data Resources

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Sequence Annotations

Entity ID: 20

UniProt & NIH Common Fund Data Resources

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Sequence Annotations

Entity ID: 21

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Entity ID: 22