PDBsum entry 4v1o

Transcription

PDB id: 4v1o

Contents

Protein chains

1422 a.a.

1156 a.a.

266 a.a.

178 a.a.

214 a.a.

84 a.a.

171 a.a.

133 a.a.

119 a.a.

65 a.a.

115 a.a.

46 a.a.

300 a.a.

180 a.a.

122 a.a.

105 a.a.

139 a.a.

158 a.a.

99 a.a.

419 a.a.

232 a.a.

203 a.a.

88 a.a.

DNA/RNA

Metals

_MG

_ZN ×9

PDB id:

4v1o

Name:

Transcription

Title:

Architecture of the RNA polymerase ii-mediator core transcription initiation complex

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. DNA-directed RNA polymerase ii subunit rpb2. Chain: b. Synonym: RNA polymerase ii subunit 2, b150, DNA-directed RNA polymerase ii 140 kda polypeptide.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Strain: bj5464 rpb3 his-bio. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic construct. Organism_taxid: 32630.

Authors:

C.Plaschka,L.Lariviere,L.Wenzeck,M.Hemann,D.Tegunov,E.V.Petrotchenko, C.H.Borchers,W.Baumeister,F.Herzog,E.Villa,P.Cramer

Key ref:

C.Plaschka et al. (2015). Architecture of the RNA polymerase II-Mediator core initiation complex. Nature, 518, 376-380. PubMed id: 25652824 DOI: 10.1038/nature14229

Date:

29-Sep-14 Release date: 04-Feb-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: 1422 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: 1156 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: 266 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: 84 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: 133 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: 119 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: 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: 46 a.a.

Protein chain

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

Seq: 345 a.a.

Struc: 300 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

A0A0H2UKZ8  (A0A0H2UKZ8_SACMI) -  Transcription initiation factor IIF subunit alpha from Saccharomyces mikatae

Seq: 734 a.a.

Struc: 122 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: 105 a.a.*

Protein chain

P38782  (MED6_YEAST) -  Mediator of RNA polymerase II transcription subunit 6 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 295 a.a.

Struc: 139 a.a.

Protein chain

P38304  (MED8_YEAST) -  Mediator of RNA polymerase II transcription subunit 8 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 223 a.a.

Struc: 158 a.a.

Protein chain

Q99278  (MED11_YEAST) -  Mediator of RNA polymerase II transcription subunit 11 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 115 a.a.

Struc: 99 a.a.

Protein chain

P32569  (MED17_YEAST) -  Mediator of RNA polymerase II transcription subunit 17 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 687 a.a.

Struc: 419 a.a.

Protein chain

P32585  (MED18_YEAST) -  Mediator of RNA polymerase II transcription subunit 18 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 307 a.a.

Struc: 232 a.a.

Protein chain

P34162  (MED20_YEAST) -  Mediator of RNA polymerase II transcription subunit 20 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 210 a.a.

Struc: 203 a.a.

Protein chain

P32570  (MED22_YEAST) -  Mediator of RNA polymerase II transcription subunit 22 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 121 a.a.

Struc: 88 a.a.

* PDB and UniProt seqs differ at 63 residue positions (black crosses)

DNA/RNA chains

A-A-C-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- 50 bases

A-U-A-U-C-A 6 bases

G-C-G-C-A-G-T-T-G-T-G-C-T-A-T-G-A-T-A-T-T-T-T-A-C-A-A-C-A-C-A-C-T-A-T-T-A-T-A- 58 bases

Enzyme reactions

• Enzyme class 2: 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 3: 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/nature14229

Nature 518:376-380 (2015)

PubMed id: 25652824

Architecture of the RNA polymerase II-Mediator core initiation complex.

C.Plaschka, L.Larivière, L.Wenzeck, M.Seizl, M.Hemann, D.Tegunov, E.V.Petrotchenko, C.H.Borchers, W.Baumeister, F.Herzog, E.Villa, P.Cramer.

ABSTRACT

The conserved co-activator complex Mediator enables regulated transcription initiation by RNA polymerase (Pol) II. Here we reconstitute an active 15-subunit core Mediator (cMed) comprising all essential Mediator subunits from Saccharomyces cerevisiae. The cryo-electron microscopic structure of cMed bound to a core initiation complex was determined at 9.7 Å resolution. cMed binds Pol II around the Rpb4-Rpb7 stalk near the carboxy-terminal domain (CTD). The Mediator head module binds the Pol II dock and the TFIIB ribbon and stabilizes the initiation complex. The Mediator middle module extends to the Pol II foot with a 'plank' that may influence polymerase conformation. The Mediator subunit Med14 forms a 'beam' between the head and middle modules and connects to the tail module that is predicted to bind transcription activators located on upstream DNA. The Mediator 'arm' and 'hook' domains contribute to a 'cradle' that may position the CTD and TFIIH kinase to stimulate Pol II phosphorylation.