9ZO5 | pdb_00009zo5

Cryo-EM structure of the complete Pyrococcus furiosus RNA polymerase in open clamp conformation

PDB DOI: https://doi.org/10.2210/pdb9ZO5/pdb
EM Map EMD-74466: EMDB EMDataResource

Classification: TRANSCRIPTION
Organism(s): Pyrococcus furiosus DSM 3638
Mutation(s): No

Deposited: 2025-12-15 Released: 2026-08-05
Deposition Author(s): Fordjour, G.N.R., Armache, J.-P., Murakami, K.S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.05 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

Clamp conformational flexibility and dynamics in archaeal and eukaryotic RNA polymerases revealed by cryo-EM

Fordjour, G.N.R., Murakami, K., Armache, J.-P., Murakami, K.S.

To be published.

Macromolecule Content

Total Structure Weight: 382.99 kDa
Atom Count: 26,194
Modeled Residue Count: 3,266
Deposited Residue Count: 3,353
Unique protein chains: 11

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit Rpo1N	A	907	Pyrococcus furiosus DSM 3638	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q8U0M4 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U0M4 Go to UniProtKB: Q8U0M4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8U0M4
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Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit beta	B	1,117	Pyrococcus furiosus DSM 3638	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q8U0M3 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U0M3 Go to UniProtKB: Q8U0M3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8U0M3
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Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit Rpo1C	C	397	Pyrococcus furiosus DSM 3638	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q8U0M5 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U0M5 Go to UniProtKB: Q8U0M5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8U0M5
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit Rpo3	D	275	Pyrococcus furiosus DSM 3638	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q8U0E4 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U0E4 Go to UniProtKB: Q8U0E4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8U0E4
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit Rpo7	E	189	Pyrococcus furiosus DSM 3638	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q8U439 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U439 Go to UniProtKB: Q8U439
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8U439
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit Rpo4	F	120	Pyrococcus furiosus DSM 3638	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q8U216 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U216 Go to UniProtKB: Q8U216
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8U216
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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 Rpo11	G [auth L]	95	Pyrococcus furiosus DSM 3638	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q8U4N1 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U4N1 Go to UniProtKB: Q8U4N1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8U4N1
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit Rpo5	H	82	Pyrococcus furiosus DSM 3638	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q8U0M2 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U0M2 Go to UniProtKB: Q8U0M2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8U0M2
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit Rpo10	I [auth N]	65	Pyrococcus furiosus DSM 3638	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for P60292 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore P60292 Go to UniProtKB: P60292
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P60292
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit Rpo6	J [auth K]	57	Pyrococcus furiosus DSM 3638	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q8U0E8 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U0E8 Go to UniProtKB: Q8U0E8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8U0E8
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit Rpo12	K [auth P]	49	Pyrococcus furiosus DSM 3638	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for Q8TZI3 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8TZI3 Go to UniProtKB: Q8TZI3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q8TZI3
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Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain P SDF format, chain O [auth N] SDF format, chain N [auth B] SDF format, chain M [auth A] SDF format, chain L [auth A] MOL2 format, chain P MOL2 format, chain O [auth N] MOL2 format, chain N [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] mmCIF format, chain P mmCIF format, chain O [auth N] mmCIF format, chain N [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A]	L [auth A], M [auth A], N [auth B], O [auth N], P	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth N] Focus chain P Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth N] Focus chain P