8B3D

Structure of the Pol II-TCR-ELOF1 complex.

PDB DOI: https://doi.org/10.2210/pdb8B3D/pdb
EM Map EMD-15825: EMDB EMDataResource
NAKB: 8B3D

Classification: TRANSCRIPTION
Organism(s): Sus scrofa domesticus, Homo sapiens
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2022-09-16 Released: 2023-09-27
Deposition Author(s): Kokic, G., Cramer, P.
Funding Organization(s): German Research Foundation (DFG), European Research Council (ERC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.60 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 the Pol II-TCR-ELOF1 complex.

Kokic, G., Cramer, P.

To be published.

Macromolecule Content

Total Structure Weight: 991.71 kDa
Atom Count: 48,854
Modelled Residue Count: 5,978
Deposited Residue Count: 8,597
Unique protein chains: 17
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	1,167	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 polymerase II subunit F	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
RPB7	G	254	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 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_pol_L_2 domain-containing protein	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 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	83	Homo sapiens	Mutation(s): 0 Gene Names: ELOF1, hCG_29982
UniProt
Find proteins for A0A8D1B522 (Sus scrofa) Explore A0A8D1B522 Go to UniProtKB: A0A8D1B522
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A8D1B522
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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]	396	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 excision repair protein ERCC-6	R [auth b]	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: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
UV-stimulated scaffold protein A	S [auth c]	709	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: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA damage-binding protein 1	T [auth d]	1,140	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: 14
Molecule	Chains	Length	Organism	Image
NTS	N	52	Homo sapiens
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Length	Organism	Image
RNA	O [auth P]	10	Homo sapiens
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Length	Organism	Image
TS	P [auth T]	52	Homo sapiens
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Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain EA [auth b] MOL2 format, chain EA [auth b]	EA [auth b]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain EA [auth b] Interactions & Density Focus chain EA [auth b]
BEF Query on BEF Download Ideal Coordinates CCD File SDF format, chain FA [auth b] MOL2 format, chain FA [auth b]	FA [auth b]	BERYLLIUM TRIFLUORIDE ION Be F₃ OGIAHMCCNXDTIE-UHFFFAOYSA-K		Interactions Focus chain FA [auth b] Interactions & Density Focus chain FA [auth b]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth I] SDF format, chain BA [auth J] SDF format, chain CA [auth L] SDF format, chain DA [auth M] SDF format, chain HA [auth c] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain X [auth B] SDF format, chain Y [auth C] SDF format, chain Z [auth I] MOL2 format, chain AA [auth I] MOL2 format, chain BA [auth J] MOL2 format, chain CA [auth L] MOL2 format, chain DA [auth M] MOL2 format, chain HA [auth c] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth C] MOL2 format, chain Z [auth I]	AA [auth I] BA [auth J] CA [auth L] DA [auth M] HA [auth c] AA [auth I], BA [auth J], CA [auth L], DA [auth M], HA [auth c], U [auth A], V [auth A], X [auth B], Y [auth C], Z [auth I]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth I] Focus chain BA [auth J] Focus chain CA [auth L] Focus chain DA [auth M] Focus chain HA [auth c] Focus chain U [auth A] Focus chain V [auth A] Focus chain X [auth B] Focus chain Y [auth C] Focus chain Z [auth I] Interactions & Density Focus chain AA [auth I] Focus chain BA [auth J] Focus chain CA [auth L] Focus chain DA [auth M] Focus chain HA [auth c] Focus chain U [auth A] Focus chain V [auth A] Focus chain X [auth B] Focus chain Y [auth C] Focus chain Z [auth I]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain GA [auth b] SDF format, chain W [auth A] MOL2 format, chain GA [auth b] MOL2 format, chain W [auth A]	GA [auth b], W [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain GA [auth b] Focus chain W [auth A] Interactions & Density Focus chain GA [auth b] Focus chain W [auth A]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2023-09-27

Deposition Author(s):

Kokic, G.

Cramer, P.

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	EXC 2067/1-390729940
European Research Council (ERC)	European Union	Advanced Investigator Grant CHROMATRANS (grant agreement No. 882357)

Revision History (Full details and data files)

Version 1.0: 2023-09-27
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.

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8B3D

Structure of the Pol II-TCR-ELOF1 complex.

Structure of the Pol II-TCR-ELOF1 complex.

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UniProt

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UniProt & NIH Common Fund Data Resources

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Entity ID: 18

UniProt & NIH Common Fund Data Resources

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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

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Sequence Annotations

Entity ID: 16