8P2I

Cryo-EM structure of Pyrococcus furiosus apo form RNA polymerase contracted clamp conformation with Spt4/5

PDB DOI: https://doi.org/10.2210/pdb8P2I/pdb
EM Map EMD-17366: EMDB EMDataResource

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

Deposited: 2023-05-16 Released: 2024-04-24
Deposition Author(s): Tarau, D.M., Reichelt, R., Heiss, F.B., Pilsl, M., Hausner, W., Engel, C., Grohmann, D.
Funding Organization(s): German Research Foundation (DFG)

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

Structural basis of archaeal RNA polymerase transcription elongation and Spt4/5 recruitment

Tarau, D.M., Grunberger, F., Pilsl, M., Reichelt, R., Heiss, F.B., Koenig, S., Urlaub, H., Hausner, W., Engel, C., Grohmann, D.

(2024) Nucleic Acids Res

Macromolecule Content

Total Structure Weight: 407.21 kDa
Atom Count: 27,479
Modelled Residue Count: 3,430
Deposited Residue Count: 3,569
Unique protein chains: 13

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase subunit Rpo1N	A	910	Pyrococcus furiosus DSM 3638	Mutation(s): 0 Gene Names: rpoA1, rpo1N, PFDSM3638_07875 EC: 2.7.7.6
UniProt
Find proteins for A0A5C0XPL7 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore A0A5C0XPL7 Go to UniProtKB: A0A5C0XPL7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A5C0XPL7
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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	1,117	Pyrococcus furiosus DSM 3638	Mutation(s): 0 Gene Names: PF1564
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8U0M3
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Reference Sequence

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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 Gene Names: rpo1C, rpoA2, PF1562 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 Gene Names: rpo3, rpoD, PF1647 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 Gene Names: rpo7
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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 Gene Names: rpo4, rpoF, PF1036 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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 Rpo5	G [auth H]	82	Pyrococcus furiosus DSM 3638	Mutation(s): 0 Gene Names: rpo5, rpoH, PF1565 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8U0M2
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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 Rpo6	H [auth K]	57	Pyrococcus furiosus DSM 3638	Mutation(s): 0 Gene Names: rpo6, rpoK, PF1642 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8U0E8
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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 Rpo11	I [auth L]	95	Pyrococcus furiosus DSM 3638	Mutation(s): 0 Gene Names: rpo11, rpoL, PF0050 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8U4N1
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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 Rpo10	J [auth N]	65	Pyrococcus furiosus DSM 3638	Mutation(s): 0 Gene Names: rpo10, rpoN, PF1643 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60292
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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 Gene Names: rpo12, rpoP, PF2009 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8TZI3
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription elongation factor Spt5	L [auth G]	152	Pyrococcus furiosus DSM 3638	Mutation(s): 0 Gene Names: spt5, PF1990
UniProt
Find proteins for Q8TZK1 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8TZK1 Go to UniProtKB: Q8TZK1
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UniProt Group	Q8TZK1
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription elongation factor Spt4	M [auth I]	61	Pyrococcus furiosus DSM 3638	Mutation(s): 0 Gene Names: spt4, PF0255
UniProt
Find proteins for Q8U440 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U440 Go to UniProtKB: Q8U440
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8U440
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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 N [auth A] SDF format, chain O [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth N] SDF format, chain S [auth P] SDF format, chain T [auth I] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth N] MOL2 format, chain S [auth P] MOL2 format, chain T [auth I]	N [auth A] O [auth A] Q [auth B] R [auth N] S [auth P] N [auth A], O [auth A], Q [auth B], R [auth N], S [auth P], T [auth I]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth B] Focus chain R [auth N] Focus chain S [auth P] Focus chain T [auth I] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain Q [auth B] Focus chain R [auth N] Focus chain S [auth P] Focus chain T [auth I]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A]	P [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]