PDBsum entry 5fyw

Transcription

PDB id: 5fyw

Contents

Protein chains

1398 a.a.

1157 a.a.

262 a.a.

157 a.a.

213 a.a.

83 a.a.

171 a.a.

136 a.a.

116 a.a.

65 a.a.

112 a.a.

45 a.a.

231 a.a.

180 a.a.

148 a.a.

199 a.a.

92 a.a.

100 a.a.

168 a.a.

143 a.a.

DNA/RNA

Metals

_MG

_ZN ×10

PDB id:

5fyw

Name:

Transcription

Title:

Transcription initiation complex structures elucidate DNA opening (oc)

Structure:

DNA-directed RNA polymerase ii subunit rpb1. Chain: a. Synonym: RNA polymerase ii subunit 1, RNA polymerase ii subunit b1, DNA-directed RNA polymerase iii largest subunit, RNA polymerase ii subunit b220, rpb1. DNA-directed RNA polymerase ii subunit rpb2. Chain: b. Synonym: RNA polymerase ii subunit 2, b150, DNA-directed RNA polymerase ii 140 kda polypeptide, rpb2.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: bj5464 rpb3 his-bio. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: ril. Synthetic: yes. Synthetic construct.

Authors:

C.Plaschka,M.Hantsche,C.Dienemann,C.Burzinski,J.Plitzko,P.Cramer

Key ref:

C.Plaschka et al. (2016). Transcription initiation complex structures elucidate DNA opening. Nature, 533, 353-358. PubMed id: 27193681 DOI: 10.1038/nature17990

Date:

10-Mar-16 Release date: 18-May-16

Protein chain

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

Seq: 1733 a.a.

Struc: 1398 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: 1157 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: 262 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: 157 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: 213 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: 83 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: 136 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: 116 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: 65 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: 112 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: 45 a.a.

Protein chain

P29055  (TF2B_YEAST) -  Transcription initiation factor IIB from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 345 a.a.

Struc: 231 a.a.

Protein chain

P13393  (TBP_YEAST) -  TATA-box-binding protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 240 a.a.

Struc: 180 a.a.

Protein chain

P41895  (T2FA_YEAST) -  Transcription initiation factor IIF subunit alpha from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 735 a.a.

Struc: 148 a.a.*

Protein chain

P41896  (T2FB_YEAST) -  Transcription initiation factor IIF subunit beta from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 400 a.a.

Struc: 199 a.a.

Protein chain

P32773  (TOA1_YEAST) -  Transcription initiation factor IIA large subunit from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 286 a.a.

Struc: 92 a.a.*

Protein chain

P32774  (T2AG_YEAST) -  Transcription initiation factor IIA subunit 2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 122 a.a.

Struc: 100 a.a.

Protein chain

P36100  (T2EA_YEAST) -  Transcription initiation factor IIE subunit alpha from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 482 a.a.

Struc: 168 a.a.

Protein chain

P36145  (T2EB_YEAST) -  Transcription initiation factor IIE subunit beta from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 328 a.a.

Struc: 143 a.a.

* PDB and UniProt seqs differ at 103 residue positions (black crosses)

DNA/RNA chains

A-G-T-A-G-C-A-C-G-C-T-G-T-G-T-A-T-A-T-A-A-T-A-G-T-G-T-G-T-T-G-T-A-C-A-G-C-A-C- 47 bases

G-C-G-C-A-G-T-T-G-T-G-C-T-A-T-A-C-A-A-C-A-C-A-C-T-A-T-T-A-T-A-T-A-C-A-C-A-G-C- 47 bases

Enzyme reactions

• Enzyme class 1: Chains A, B: E.C.2.7.7.6 - DNA-directed Rna polymerase.
• Reaction: RNA(n) + a ribonucleoside 5'-triphosphate = RNA(n+1) + diphosphate
• Enzyme class 2: Chain R: E.C.3.6.4.12 - Dna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

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

reference

DOI no: 10.1038/nature17990

Nature 533:353-358 (2016)

PubMed id: 27193681

Transcription initiation complex structures elucidate DNA opening.

C.Plaschka, M.Hantsche, C.Dienemann, C.Burzinski, J.Plitzko, P.Cramer.

ABSTRACT

Transcription of eukaryotic protein-coding genes begins with assembly of the RNA polymerase (Pol) II initiation complex and promoter DNA opening. Here we report cryo-electron microscopy (cryo-EM) structures of yeast initiation complexes containing closed and open DNA at resolutions of 8.8 Å and 3.6 Å, respectively. DNA is positioned and retained over the Pol II cleft by a network of interactions between the TATA-box-binding protein TBP and transcription factors TFIIA, TFIIB, TFIIE, and TFIIF. DNA opening occurs around the tip of the Pol II clamp and the TFIIE 'extended winged helix' domain, and can occur in the absence of TFIIH. Loading of the DNA template strand into the active centre may be facilitated by movements of obstructing protein elements triggered by allosteric binding of the TFIIE 'E-ribbon' domain. The results suggest a unified model for transcription initiation with a key event, the trapping of open promoter DNA by extended protein-protein and protein-DNA contacts.