8QW8 | pdb_00008qw8

In condensate RNAPII elongation complex bound to RECQ5

PDB DOI: https://doi.org/10.2210/pdb8QW8/pdb
EM Map EMD-18682: EMDB EMDataResource
NAKB: 8QW8

Classification: TRANSCRIPTION
Organism(s): Bos taurus, synthetic construct, Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2023-10-19 Released: 2025-04-30
Deposition Author(s): Skubnik, K., Sebesta, M., Stefl, R.
Funding Organization(s): Czech Science Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 7.70 Å
Aggregation State: PARTICLE
Reconstruction Method: SUBTOMOGRAM AVERAGING

wwPDB Validation 3D Report Full Report

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

Literature

Spatial organization of RNA polymerase II-RECQ5 transcriptional condensate

Sebesta, M., Skubnik, K., Stefl, R.

To be published.

Macromolecule Content

Total Structure Weight: 628.21 kDa
Atom Count: 32,675
Modeled Residue Count: 4,010
Deposited Residue Count: 5,360
Unique protein chains: 13
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	Bos taurus	Mutation(s): 0 EC: 3.1.13 (UniProt), 2.7.7.48 (UniProt), 2.7.7.6 (UniProt)
UniProt
Find proteins for G3MZY8 (Bos taurus) Explore G3MZY8 Go to UniProtKB: G3MZY8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	G3MZY8
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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	1,174	Bos taurus	Mutation(s): 0 EC: 3.1.13 (UniProt), 2.7.7.48 (UniProt), 2.7.7.6 (UniProt)
UniProt
Find proteins for A5PJW8 (Bos taurus) Explore A5PJW8 Go to UniProtKB: A5PJW8
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A5PJW8
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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	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q3T0Q3 (Bos taurus) Explore Q3T0Q3 Go to UniProtKB: Q3T0Q3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q3T0Q3
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC1	D [auth E]	210	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q2T9T3 (Bos taurus) Explore Q2T9T3 Go to UniProtKB: Q2T9T3
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UniProt Group	Q2T9T3
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC2	E [auth F]	127	Bos taurus	Mutation(s): 1
UniProt
Find proteins for Q32PE0 (Bos taurus) Explore Q32PE0 Go to UniProtKB: Q32PE0
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UniProt Group	Q32PE0
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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 RPABC3	F [auth H]	150	Bos taurus	Mutation(s): 0
UniProt
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UniProt Group	F2Z4H3
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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 RPB9	G [auth I]	125	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q32P73 (Bos taurus) Explore Q32P73 Go to UniProtKB: Q32P73
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UniProt Group	Q32P73
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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 RPABC5	H [auth J]	67	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q32P78 (Bos taurus) Explore Q32P78 Go to UniProtKB: Q32P78
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UniProt Group	Q32P78
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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	I [auth K]	117	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q32P79 (Bos taurus) Explore Q32P79 Go to UniProtKB: Q32P79
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UniProt Group	Q32P79
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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 RPABC4	J [auth L]	58	Bos taurus	Mutation(s): 0
UniProt
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UniProt Group	Q3ZBC0
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Polymerase (RNA) II (DNA directed) polypeptide D	K [auth D]	142	Bos taurus	Mutation(s): 0
UniProt
Find proteins for Q1JQ91 (Bos taurus) Explore Q1JQ91 Go to UniProtKB: Q1JQ91
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UniProt Group	Q1JQ91
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB7	L [auth G]	172	Bos taurus	Mutation(s): 0
UniProt
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UniProt Group	Q5E9B8
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Reference Sequence

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Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
ATP-dependent DNA helicase Q5	P [auth R]	650	Homo sapiens	Mutation(s): 0 Gene Names: RECQL5, RECQ5 EC: 3.6.4.12 (PDB Primary Data), 5.6.2.4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O94762 (Homo sapiens) Explore O94762 Go to UniProtKB: O94762
PHAROS: O94762 GTEx: ENSG00000108469
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UniProt Group	O94762
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Length	Organism	Image
RNA, DNA-RNA ELONGATION SCAFFOLD	M [auth P]	17	synthetic construct
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Reference Sequence

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Entity ID: 14
Molecule	Chains	Length	Organism	Image
DNA, DNA-RNA ELONGATION SCAFFOLD	N [auth T]	51	synthetic construct
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Reference Sequence

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Entity ID: 15
Molecule	Chains	Length	Organism	Image
DNA, DNA-RNA ELONGATION SCAFFOLD	O [auth N]	55	synthetic construct
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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 Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth C] SDF format, chain T [auth I] SDF format, chain U [auth I] SDF format, chain V [auth J] SDF format, chain W [auth L] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth C] MOL2 format, chain T [auth I] MOL2 format, chain U [auth I] MOL2 format, chain V [auth J] MOL2 format, chain W [auth L] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth C] mmCIF format, chain T [auth I] mmCIF format, chain U [auth I] mmCIF format, chain V [auth J] mmCIF format, chain W [auth L]	Q [auth A] R [auth A] S [auth C] T [auth I] U [auth I] Q [auth A], R [auth A], S [auth C], T [auth I], U [auth I], V [auth J], W [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth C] Focus chain T [auth I] Focus chain U [auth I] Focus chain V [auth J] Focus chain W [auth L] Interactions & Density Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth C] Focus chain T [auth I] Focus chain U [auth I] Focus chain V [auth J] Focus chain W [auth L]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain X [auth P] MOL2 format, chain X [auth P] mmCIF format, chain X [auth P]	X [auth P]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain X [auth P] Interactions & Density Focus chain X [auth P]