PDBsum entry 5c4x

Transferase/RNA/DNA

PDB id: 5c4x

Contents

Protein chains

1436 a.a.

1172 a.a.

265 a.a.

178 a.a.

214 a.a.

87 a.a.

171 a.a.

135 a.a.

114 a.a.

66 a.a.

115 a.a.

44 a.a.

DNA/RNA

Metals

_MG ×2

_ZN ×9

PDB id:

5c4x

Name:

Transferase/RNA/DNA

Title:

Crystal structure of a transcribing RNA polymerase ii complex reveals a complete transcription bubble

Structure:

DNA-directed RNA polymerase ii subunit rpb1. Chain: a. Synonym: RNA polymerase ii subunit b1,DNA-directed RNA polymerase iii largest subunit,RNA polymerase ii subunit b220. DNA-directed RNA polymerase ii subunit rpb2. Chain: b. Synonym: RNA polymerase ii subunit 2,b150,DNA-directed RNA polymerase ii 140 kda polypeptide. DNA-directed RNA polymerase ii subunit rpb3.

Source:

Saccharomyces cerevisiae (strain atcc 204508 / s288c). Baker's yeast. Organism_taxid: 559292. Strain: atcc 204508 / s288c. Atcc: 204508. Gene: rpb4, yjl140w, j0654. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

4.00Å R-factor: 0.210 R-free: 0.227

Authors:

C.O.Barnes,M.Calero,I.Malik,H.Spahr,Q.Zhang,F.Pullara,C.D.Kaplan, G.Calero

Key ref:

C.O.Barnes et al. (2015). Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble. Mol Cell, 59, 258-269. PubMed id: 26186291 DOI: 10.1016/j.molcel.2015.06.034

Date:

18-Jun-15 Release date: 26-Aug-15

Protein chain

P04050  (RPB1_YEAST) -  DNA-directed RNA polymerase II subunit RPB1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1733 a.a.

Struc: 1436 a.a.

Protein chain

P08518  (RPB2_YEAST) -  DNA-directed RNA polymerase II subunit RPB2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1224 a.a.

Struc: 1172 a.a.

Protein chain

P16370  (RPB3_YEAST) -  DNA-directed RNA polymerase II subunit RPB3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 318 a.a.

Struc: 265 a.a.

Protein chain

P20433  (RPB4_YEAST) -  DNA-directed RNA polymerase II subunit RPB4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 221 a.a.

Struc: 178 a.a.

Protein chain

P20434  (RPAB1_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 215 a.a.

Struc: 214 a.a.

Protein chain

P20435  (RPAB2_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 155 a.a.

Struc: 87 a.a.

Protein chain

P34087  (RPB7_YEAST) -  DNA-directed RNA polymerase II subunit RPB7 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 171 a.a.

Struc: 171 a.a.

Protein chain

P20436  (RPAB3_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 146 a.a.

Struc: 135 a.a.

Protein chain

P27999  (RPB9_YEAST) -  DNA-directed RNA polymerase II subunit RPB9 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 122 a.a.

Struc: 114 a.a.

Protein chain

P22139  (RPAB5_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 70 a.a.

Struc: 66 a.a.

Protein chain

P38902  (RPB11_YEAST) -  DNA-directed RNA polymerase II subunit RPB11 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 120 a.a.

Struc: 115 a.a.

Protein chain

P40422  (RPAB4_YEAST) -  DNA-directed RNA polymerases I, II, and III subunit RPABC4 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 70 a.a.

Struc: 44 a.a.

DNA/RNA chains

U-C-G-A-G-A-G-G-A 9 bases

G-G-A-G-T-C-C-G-T-G-G-A-A-G-C-T-A-T-C-A-G-C-A-G-T-G-C-T-T-A-T-C-G-G-T-A-G-G 38 bases

C-C-T-A-C-C-G-A-T-A-A-G-C-A-G-A-C-G-A-T-C-C-T-C-T-C-G-A-A-C-C-A-C-G-G-A-C-T-C- 40 bases

Enzyme reactions

• Enzyme class: Chains A, B: E.C.2.7.7.6 - DNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1016/j.molcel.2015.06.034

Mol Cell 59:258-269 (2015)

PubMed id: 26186291

Crystal Structure of a Transcribing RNA Polymerase II Complex Reveals a Complete Transcription Bubble.

C.O.Barnes, M.Calero, I.Malik, B.W.Graham, H.Spahr, G.Lin, A.E.Cohen, I.S.Brown, Q.Zhang, F.Pullara, M.A.Trakselis, C.D.Kaplan, G.Calero.

ABSTRACT

Notwithstanding numerous published structures of RNA Polymerase II (Pol II), structural details of Pol II engaging a complete nucleic acid scaffold have been lacking. Here, we report the structures of TFIIF-stabilized transcribing Pol II complexes, revealing the upstream duplex and full transcription bubble. The upstream duplex lies over a wedge-shaped loop from Rpb2 that engages its minor groove, providing part of the structural framework for DNA tracking during elongation. At the upstream transcription bubble fork, rudder and fork loop 1 residues spatially coordinate strand annealing and the nascent RNA transcript. At the downstream fork, a network of Pol II interactions with the non-template strand forms a rigid domain with the trigger loop (TL), allowing visualization of its open state. Overall, our observations suggest that "open/closed" conformational transitions of the TL may be linked to interactions with the non-template strand, possibly in a synchronized ratcheting manner conducive to polymerase translocation.