PDBsum entry 5fmf

Transcription

PDB id: 5fmf

Contents

Protein chains

473 a.a.

174 a.a.

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.

116 a.a.

101 a.a.

293 a.a.

180 a.a.

118 a.a.

121 a.a.

150 a.a.

174 a.a.

62 a.a.

63 a.a.

578 a.a.

DNA/RNA

Metals

_ZN ×9

_MG ×2

PDB id:

5fmf

Name:

Transcription

Title:

The p-lobe of RNA polymerase ii pre-initiation complex

Structure:

DNA repair helicase rad25, ssl2. Chain: 1. Synonym: general transcription and DNA repair factor iih subunit rad25, tfiih subunit rad25, suppressor of stem-loop mutation 2. Transcription elongation factor s-ii, dst1. Chain: 2. Synonym: DNA strand transfer protein alpha, stp-alpha, DNA strand transferase 1, pyrimidine pathway regulatory protein 2. DNA-directed RNA polymerase ii subunit rpb1.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Organism_taxid: 4932

Authors:

K.Murakami,K.Tsai,N.Kalisman,D.A.Bushnell,F.J.Asturias,R.D.Kornberg

Key ref:

K.Murakami et al. (2015). Structure of an RNA polymerase II preinitiation complex. Proc Natl Acad Sci U S A, 112, 13543-13548. PubMed id: 26483468 DOI: 10.1073/pnas.1518255112

Date:

03-Nov-15 Release date: 25-Nov-15

Protein chain

Q00578  (RAD25_YEAST) -  General transcription and DNA repair factor IIH helicase/translocase subunit XPB/SSL2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 843 a.a.

Struc: 473 a.a.

Protein chain

P07273  (TFS2_YEAST) -  Transcription elongation factor S-II from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 309 a.a.

Struc: 174 a.a.

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

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

Seq: 286 a.a.

Struc: 116 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: 101 a.a.

Protein chain

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

Seq: 345 a.a.

Struc: 293 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

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

Seq: 482 a.a.

Struc: 118 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: 121 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: 150 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: 174 a.a.

Protein chain

Q02939  (TFB2_YEAST) -  General transcription and DNA repair factor IIH subunit TFB2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 513 a.a.

Struc: 62 a.a.

Protein chain

Q3E7C1  (TFB5_YEAST) -  General transcription and DNA repair factor IIH subunit TFB5 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 72 a.a.

Struc: 63 a.a.

Protein chain

P06839  (RAD3_YEAST) -  General transcription and DNA repair factor IIH helicase subunit XPD/RAD3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 778 a.a.

Struc: 578 a.a.

* PDB and UniProt seqs differ at 43 residue positions (black crosses)

DNA/RNA chains

A-A-A-A-A-A-A-A-A-A-G-G-C-G-C-C-T-A-T-A-A-A-A-G-G-G-G-T-T-T-C-A-A-T-G-T-A-T-C- 72 bases

C-C-C-C-A-C-C-C-C-C-T-T-T-A-G-T-A-C-T-T-A-T-G-C-C-T-G-G-T-T-A-T-A-G-A-T-A-C-A- 72 bases

Enzyme reactions

• Enzyme class 1: Chain 1: E.C.5.6.2.4 - Dna 3'-5' helicase.
• 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 V: E.C.3.6.4.12 - Dna helicase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺
• Enzyme class 4: Chain Y: E.C.5.6.2.3 - Dna 5'-3' helicase.

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: 10.1073/pnas.1518255112

Proc Natl Acad Sci U S A 112:13543-13548 (2015)

PubMed id: 26483468

Structure of an RNA polymerase II preinitiation complex.

K.Murakami, K.L.Tsai, N.Kalisman, D.A.Bushnell, F.J.Asturias, R.D.Kornberg.

ABSTRACT

The structure of a 33-protein, 1.5-MDa RNA polymerase II preinitiation complex (PIC) was determined by cryo-EM and image processing at a resolution of 6-11 Å. Atomic structures of over 50% of the mass were fitted into the electron density map in a manner consistent with protein-protein cross-links previously identified by mass spectrometry. The resulting model of the PIC confirmed the main conclusions from previous cryo-EM at lower resolution, including the association of promoter DNA only with general transcription factors and not with the polymerase. Electron density due to DNA was identifiable by the grooves of the double helix and exhibited sharp bends at points downstream of the TATA box, with an important consequence: The DNA at the downstream end coincides with the DNA in a transcribing polymerase. The structure of the PIC is therefore conducive to promoter melting, start-site scanning, and the initiation of transcription.