2Y0S

Crystal structure of Sulfolobus shibatae RNA polymerase in P21 space group

PDB DOI: https://doi.org/10.2210/pdb2Y0S/pdb

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

Deposited: 2010-12-07 Released: 2011-02-16
Deposition Author(s): Wojtas, M., Peralta, B., Ondiviela, M., Mogni, M., Bell, S.D., Abrescia, N.G.A.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.80 Å
R-Value Free: 0.354
R-Value Work: 0.300
R-Value Observed: 0.302

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.5 of the entry. See complete history.

Literature

Archaeal RNA polymerase: the influence of the protruding stalk in crystal packing and preliminary biophysical analysis of the Rpo13 subunit.

Wojtas, M., Peralta, B., Ondiviela, M., Mogni, M., Bell, S.D., Abrescia, N.G.

(2011) Biochem Soc Trans 39: 25-30

PubMed: 21265742 Search on PubMed
DOI: https://doi.org/10.1042/BST0390025
Primary Citation of Related Structures:
2Y0S

PubMed Abstract:
We review recent results on the complete structure of the archaeal RNAP (RNA polymerase) enzyme of Sulfolobus shibatae. We compare the three crystal forms in which this RNAP packs (space groups P2₁2₁2₁, P2₁2₁2 and P2₁) and provide a preliminary biophysical characterization of the newly identified 13-subunit Rpo13. The availability of different crystal forms for this RNAP allows the analysis of the packing degeneracy and the intermolecular interactions that determine this degeneracy. We observe the pivotal role played by the protruding stalk composed of subunits Rpo4 and Rpo7 in the lattice contacts. Aided by MALLS (multi-angle laser light scattering), we have initiated the biophysical characterization of the recombinantly expressed and purified subunit Rpo13, a necessary step towards the understanding of Rpo13's role in archaeal transcription.

Organizational Affiliation

Structural Biology Unit, CIC bioGUNE, CIBERehd, 48160 Derio, Spain.

Macromolecule Content

Total Structure Weight: 812.82 kDa
Atom Count: 52,472
Modelled Residue Count: 6,610
Deposited Residue Count: 7,170
Unique protein chains: 13

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE	A, W	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B8YB53
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE	B, R	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B8YB55
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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 A''	C, Y	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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 SUBUNIT D	D, S	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B8YB56
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA POLYMERASE SUBUNIT 4	E, T	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B8YB57
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA POLYMERASE SUBUNIT 7	F, U	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B8YB58
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA POLYMERASE SUBUNIT 8	G, V	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
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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 SUBUNIT H	H, Z	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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 SUBUNIT K	I, 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B8YB61
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Reference Sequence

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Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA POLYMERASE SUBUNIT 13	J, 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B8YB65
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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 L	L, M	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B8YB62
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Reference Sequence

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Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE SUBUNIT N	N, O	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B8YB63
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Reference Sequence

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Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA POLYMERASE SUBUNIT 12	P, X	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B8YB64
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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 GA [auth D] SDF format, chain NA [auth S] MOL2 format, chain GA [auth D] MOL2 format, chain NA [auth S] mmCIF format, chain GA [auth D] mmCIF format, chain NA [auth S]	GA [auth D], NA [auth S]	FE3-S4 CLUSTER Fe₃ S₄ FCXHZBQOKRZXKS-UHFFFAOYSA-N		Interactions Focus chain GA [auth D] Focus chain NA [auth S] Interactions & Density Focus chain GA [auth D] Focus chain NA [auth S]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain BA [auth A] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain HA [auth N] SDF format, chain IA [auth O] SDF format, chain JA [auth P] SDF format, chain KA [auth R] SDF format, chain LA [auth R] SDF format, chain MA [auth R] SDF format, chain OA [auth W] SDF format, chain PA [auth W] SDF format, chain RA [auth X] MOL2 format, chain AA [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain HA [auth N] MOL2 format, chain IA [auth O] MOL2 format, chain JA [auth P] MOL2 format, chain KA [auth R] MOL2 format, chain LA [auth R] MOL2 format, chain MA [auth R] MOL2 format, chain OA [auth W] MOL2 format, chain PA [auth W] MOL2 format, chain RA [auth X] mmCIF format, chain AA [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain HA [auth N] mmCIF format, chain IA [auth O] mmCIF format, chain JA [auth P] mmCIF format, chain KA [auth R] mmCIF format, chain LA [auth R] mmCIF format, chain MA [auth R] mmCIF format, chain OA [auth W] mmCIF format, chain PA [auth W] mmCIF format, chain RA [auth X]	AA [auth A] BA [auth A] DA [auth B] EA [auth B] FA [auth B] AA [auth A], BA [auth A], DA [auth B], EA [auth B], FA [auth B], HA [auth N], IA [auth O], JA [auth P], KA [auth R], LA [auth R], MA [auth R], OA [auth W], PA [auth W], RA [auth X]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain BA [auth A] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain HA [auth N] Focus chain IA [auth O] Focus chain JA [auth P] Focus chain KA [auth R] Focus chain LA [auth R] Focus chain MA [auth R] Focus chain OA [auth W] Focus chain PA [auth W] Focus chain RA [auth X] Interactions & Density Focus chain AA [auth A] Focus chain BA [auth A] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain HA [auth N] Focus chain IA [auth O] Focus chain JA [auth P] Focus chain KA [auth R] Focus chain LA [auth R] Focus chain MA [auth R] Focus chain OA [auth W] Focus chain PA [auth W] Focus chain RA [auth X]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain CA [auth A] SDF format, chain QA [auth W] MOL2 format, chain CA [auth A] MOL2 format, chain QA [auth W] mmCIF format, chain CA [auth A] mmCIF format, chain QA [auth W]	CA [auth A], QA [auth W]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth A] Focus chain QA [auth W] Interactions & Density Focus chain CA [auth A] Focus chain QA [auth W]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.80 Å
R-Value Free: 0.354
R-Value Work: 0.300
R-Value Observed: 0.302
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.33	α = 90
b = 195.909	β = 105.73
c = 212.451	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2011-02-16

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-02-16
Type: Initial release
Version 1.1: 2012-10-03
Changes: Derived calculations, Version format compliance
Version 1.2: 2019-01-30
Changes: Data collection, Database references
Version 1.3: 2019-10-30
Changes: Data collection, Derived calculations, Other
Version 1.4: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Refinement description
Version 1.5: 2024-11-06
Changes: Structure summary

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.

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Help and Resources

2Y0S

Crystal structure of Sulfolobus shibatae RNA polymerase in P21 space group

Archaeal RNA polymerase: the influence of the protruding stalk in crystal packing and preliminary biophysical analysis of the Rpo13 subunit.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

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Entity ID: 3

UniProt

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Entity ID: 8

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Entity ID: 9

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Entity ID: 10

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Entity ID: 11

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Entity ID: 12

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Entity ID: 13

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Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)