2Y0S image
Deposition Date 2010-12-07
Release Date 2011-02-16
Last Version Date 2024-11-06
Entry Detail
PDB ID:
2Y0S
Keywords:
TRANSFERASE
Title:
Crystal structure of Sulfolobus shibatae RNA polymerase in P21 space group
Biological Source:
Source Organism:
SULFOLOBUS SHIBATAE (Taxon ID: 2286)
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
3.80 Å
R-Value Free:
0.35
R-Value Work:
0.29
R-Value Observed:
0.30
Space Group:
P 1 21 1
2Y0S validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASE
Gene (Uniprot):rpo1N
Chain IDs:A, W
Chain Length:880
Number of Molecules:2
Biological Source:SULFOLOBUS SHIBATAE
UniProt ID:B8YB53 Pfam ID:PF04997, PF00623, PF04983, PF05000, PF04998 EC:2.7.7.6
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASE
Gene (Uniprot):rpo2
Chain IDs:B, R
Chain Length:1131
Number of Molecules:2
Biological Source:SULFOLOBUS SHIBATAE
UniProt ID:B8YB55 Pfam ID:PF04563, PF04561, PF04565, PF04566, PF04567, PF00562, PF04560 EC:2.7.7.6
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASE SUBUNIT A''
Gene (Uniprot):rpo1C
Chain IDs:C, Y
Chain Length:395
Number of Molecules:2
Biological Source:SULFOLOBUS SHIBATAE
UniProt ID:B8YB54 Pfam ID:PF04998 EC:2.7.7.6
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASE SUBUNIT D
Gene (Uniprot):rpo3
Chain IDs:D, S
Chain Length:265
Number of Molecules:2
Biological Source:SULFOLOBUS SHIBATAE
UniProt ID:B8YB56 Pfam ID:PF01193, PF01000 EC:2.7.7.6
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA POLYMERASE SUBUNIT 4
Gene (Uniprot):rpo7
Chain IDs:E, T
Chain Length:180
Number of Molecules:2
Biological Source:SULFOLOBUS SHIBATAE
UniProt ID:B8YB57 Pfam ID:PF03876, PF00575 EC:2.7.7.6
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA POLYMERASE SUBUNIT 7
Gene (Uniprot):rpo4
Chain IDs:F, U
Chain Length:113
Number of Molecules:2
Biological Source:SULFOLOBUS SHIBATAE
UniProt ID:B8YB58 Pfam ID:PF03874 EC:2.7.7.6
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA POLYMERASE SUBUNIT 8
Gene (Uniprot):rpo8
Chain IDs:G, V
Chain Length:132
Number of Molecules:2
Biological Source:SULFOLOBUS SHIBATAE
UniProt ID:B8YB59 Pfam ID:PF16992 EC:2.7.7.6
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASE SUBUNIT H
Gene (Uniprot):rpo5
Chain IDs:H, Z
Chain Length:84
Number of Molecules:2
Biological Source:SULFOLOBUS SHIBATAE
UniProt ID:B8YB60 Pfam ID:PF01191 EC:2.7.7.6
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASE SUBUNIT K
Gene (Uniprot):rpo6
Chain IDs:I, K
Chain Length:95
Number of Molecules:2
Biological Source:SULFOLOBUS SHIBATAE
UniProt ID:B8YB61 Pfam ID:PF01192 EC:2.7.7.6
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA POLYMERASE SUBUNIT 13
Gene (Uniprot):rpo13
Chain IDs:J, Q
Chain Length:104
Number of Molecules:2
Biological Source:SULFOLOBUS SHIBATAE
UniProt ID:B8YB65 Pfam ID:PF12136 EC:2.7.7.6
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASE SUBUNIT L
Gene (Uniprot):rpo11
Chain IDs:L, M
Chain Length:92
Number of Molecules:2
Biological Source:SULFOLOBUS SHIBATAE
UniProt ID:B8YB62 Pfam ID:PF13656 EC:2.7.7.6
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASE SUBUNIT N
Gene (Uniprot):rpo10
Chain IDs:N, O
Chain Length:66
Number of Molecules:2
Biological Source:SULFOLOBUS SHIBATAE
UniProt ID:B8YB63 Pfam ID:PF01194 EC:2.7.7.6
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA POLYMERASE SUBUNIT 12
Gene (Uniprot):rpo12
Chain IDs:P, X
Chain Length:48
Number of Molecules:2
Biological Source:SULFOLOBUS SHIBATAE
UniProt ID:B8YB64 EC:2.7.7.6
Ligand Molecules
F3S
MG
ZN
Primary Citation
Archaeal RNA polymerase: the influence of the protruding stalk in crystal packing and preliminary biophysical analysis of the Rpo13 subunit.
Biochem. Soc. Trans. 39 25 30 (2011)
PMID: 21265742 DOI: 10.1042/BST0390025

Abstact

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.

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Primary Citation of related structures
2Y0S