2WAQ | pdb_00002waq

The complete structure of the archaeal 13-subunit DNA-directed RNA Polymerase

PDB DOI: https://doi.org/10.2210/pdb2WAQ/pdb

Classification: TRANSCRIPTION
Organism(s): Saccharolobus shibatae
Mutation(s): No

Deposited: 2009-02-11 Released: 2009-05-19
Deposition Author(s): Korkhin, Y., Unligil, U.M., Littlefield, O., Nelson, P.J., Stuart, D.I., Sigler, P.B., Bell, S.D., Abrescia, N.G.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.35 Å
R-Value Free:
0.341 (Depositor), 0.338 (DCC)
R-Value Work:
0.271 (Depositor), 0.270 (DCC)
R-Value Observed:
0.274 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.7 of the entry. See complete history.

Literature

Evolution of complex RNA polymerases: the complete archaeal RNA polymerase structure.

Korkhin, Y., Unligil, U.M., Littlefield, O., Nelson, P.J., Stuart, D.I., Sigler, P.B., Bell, S.D., Abrescia, N.G.

(2009) PLoS Biol 7: e1000102-e1000102

PubMed: 19419240 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1371/journal.pbio.1000102
Primary Citation Related Structures:
2WAQ, 2WB1

PubMed Abstract:
The archaeal RNA polymerase (RNAP) shares structural similarities with eukaryotic RNAP II but requires a reduced subset of general transcription factors for promoter-dependent initiation. To deepen our knowledge of cellular transcription, we have determined the structure of the 13-subunit DNA-directed RNAP from Sulfolobus shibatae at 3.35 Å resolution. The structure contains the full complement of subunits, including RpoG/Rpb8 and the equivalent of the clamp-head and jaw domains of the eukaryotic Rpb1. Furthermore, we have identified subunit Rpo13, an RNAP component in the order Sulfolobales, which contains a helix-turn-helix motif that interacts with the RpoH/Rpb5 and RpoA'/Rpb1 subunits. Its location and topology suggest a role in the formation of the transcription bubble.

Organizational Affiliation

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.

Macromolecule Content

Total Structure Weight: 406.6 kDa
Atom Count: 26,471
Modeled Residue Count: 3,334
Deposited Residue Count: 3,585
Unique protein chains: 13

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE RPO1N SUBUNIT	A	880	Saccharolobus shibatae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for B8YB53 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)) Explore B8YB53 Go to UniProtKB: B8YB53
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8YB53
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE RPO2 SUBUNIT	B	1,131	Saccharolobus shibatae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for B8YB55 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)) Explore B8YB55 Go to UniProtKB: B8YB55
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8YB55
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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 RPO1C SUBUNIT	C	395	Saccharolobus shibatae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for B8YB54 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)) Explore B8YB54 Go to UniProtKB: B8YB54
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8YB54
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE RPO3 SUBUNIT	D	265	Saccharolobus shibatae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for B8YB56 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)) Explore B8YB56 Go to UniProtKB: B8YB56
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8YB56
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE RPO7 SUBUNIT	E	180	Saccharolobus shibatae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for B8YB57 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)) Explore B8YB57 Go to UniProtKB: B8YB57
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8YB57
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE RPO4 SUBUNIT	F	113	Saccharolobus shibatae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for B8YB58 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)) Explore B8YB58 Go to UniProtKB: B8YB58
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8YB58
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE RPO8 SUBUNIT	G	132	Saccharolobus shibatae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for B8YB59 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)) Explore B8YB59 Go to UniProtKB: B8YB59
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8YB59
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Reference Sequence

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Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE RPO5 SUBUNIT	H	84	Saccharolobus shibatae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for B8YB60 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)) Explore B8YB60 Go to UniProtKB: B8YB60
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8YB60
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Reference Sequence

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Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE RPO6 SUBUNIT	I [auth K]	95	Saccharolobus shibatae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for B8YB61 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)) Explore B8YB61 Go to UniProtKB: B8YB61
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8YB61
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE RPO11 SUBUNIT	J [auth L]	92	Saccharolobus shibatae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for B8YB62 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)) Explore B8YB62 Go to UniProtKB: B8YB62
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8YB62
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Reference Sequence

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Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE RPO10 SUBUNIT	K [auth N]	66	Saccharolobus shibatae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for B8YB63 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)) Explore B8YB63 Go to UniProtKB: B8YB63
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8YB63
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE RPO12 SUBUNIT	L [auth P]	48	Saccharolobus shibatae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for B8YB64 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)) Explore B8YB64 Go to UniProtKB: B8YB64
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Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8YB64
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE RPO13 SUBUNIT	M [auth Q]	104	Saccharolobus shibatae	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for B8YB65 (Saccharolobus shibatae (strain ATCC 51178 / DSM 5389 / JCM 8931 / NBRC 15437 / B12)) Explore B8YB65 Go to UniProtKB: B8YB65
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B8YB65
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Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
F3S Query on F3S Download:Ideal Coordinates CCD File SDF format, chain V [auth D] MOL2 format, chain V [auth D] mmCIF format, chain V [auth D]	V [auth D]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain V [auth D] Interactions & Density Focus chain V [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth C] SDF format, chain W [auth N] SDF format, chain X [auth P] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth C] MOL2 format, chain W [auth N] MOL2 format, chain X [auth P] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth C] mmCIF format, chain W [auth N] mmCIF format, chain X [auth P]	N [auth A] O [auth A] P [auth A] R [auth B] S [auth B] N [auth A], O [auth A], P [auth A], R [auth B], S [auth B], T [auth B], U [auth C], W [auth N], X [auth P]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth C] Focus chain W [auth N] Focus chain X [auth P] Interactions & Density Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth C] Focus chain W [auth N] Focus chain X [auth P]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Q [auth A] MOL2 format, chain Q [auth A] mmCIF format, chain Q [auth A]	Q [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Interactions & Density Focus chain Q [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.35 Å
R-Value Free: 0.341 (Depositor), 0.338 (DCC)
R-Value Work: 0.271 (Depositor), 0.270 (DCC)
R-Value Observed: 0.274 (Depositor)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 193.501	α = 90
b = 212.62	β = 90
c = 128.998	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
GLRF	phasing
MOLREP	phasing
SOLVE	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2009-05-19

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2009-05-19
Type: Initial release
Version 1.1: 2011-05-08
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Version format compliance
Version 1.3: 2019-01-30
Changes: Data collection, Database references, Experimental preparation
Version 1.4: 2019-08-28
Changes: Data collection, Database references
Version 1.5: 2021-04-28
Changes: Data collection, Derived calculations, Other
Version 1.6: 2023-12-13
Changes: Data collection, Database references, Refinement description
Version 1.7: 2024-11-13
Changes: Structure summary

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

2WAQ | pdb_00002waq

The complete structure of the archaeal 13-subunit DNA-directed RNA Polymerase

Literature

Evolution of complex RNA polymerases: the complete archaeal RNA polymerase structure.

Biological Assembly 1

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

UniProt

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

UniProt

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt

Entity Groups

Sequence Annotations

Small Molecules

Experimental Data & Validation

Experimental Data

Structure Validation

Entry History

Deposition Data

Revision History (Full details and data files)