PDBsum entry 6tps

Transcription

PDB id: 6tps

Contents

Protein chains

1475 a.a.

1177 a.a.

305 a.a.

58 a.a.

212 a.a.

100 a.a.

193 a.a.

131 a.a.

73 a.a.

69 a.a.

101 a.a.

43 a.a.

105 a.a.

145 a.a.

463 a.a.

595 a.a.

461 a.a.

325 a.a.

DNA/RNA

Metals

_MG

_ZN ×7

PDB id:

6tps

Name:

Transcription

Title:

Early intermediate RNA polymerase i pre-initiation complex - eipic

Structure:

DNA-directed RNA polymerase i subunit rpa190. Chain: a. Synonym: DNA-directed RNA polymerase i 190 kda polypeptide,a190,DNA- directed RNA polymerase i largest subunit. Other_details: (.Zn)(.Zn)(.Mg). DNA-directed RNA polymerase i subunit rpa135. Chain: b. Synonym: DNA-directed RNA polymerase i 135 kda polypeptide,a135,DNA- directed RNA polymerase i polypeptide 2,RNA polymerase i subunit 2.

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Saccharomyces cerevisiae (strain atcc 204508 / s288c). Organism_taxid: 559292. Gene: rrn3, ykl125w. Expressed in: escherichia coli. Expression_system_taxid: 562.

Authors:

M.Pilsl,C.Engel

Key ref:

M.Pilsl and C.Engel (2020). Structural basis of RNA polymerase I pre-initiation complex formation and promoter melting. Nat Commun, 11, 1206. PubMed id: 32139698 DOI: 10.1038/s41467-020-15052-y

Date:

14-Dec-19 Release date: 18-Mar-20

Protein chain

P10964  (RPA1_YEAST) -  DNA-directed RNA polymerase I subunit RPA190 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1664 a.a.

Struc: 1475 a.a.

Protein chain

P22138  (RPA2_YEAST) -  DNA-directed RNA polymerase I subunit RPA135 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 1203 a.a.

Struc: 1177 a.a.

Protein chain

P07703  (RPAC1_YEAST) -  DNA-directed RNA polymerases I and III subunit RPAC1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 335 a.a.

Struc: 305 a.a.

Protein chain

P50106  (RPA14_YEAST) -  DNA-directed RNA polymerase I subunit RPA14 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 137 a.a.

Struc: 58 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: 212 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: 100 a.a.

Protein chain

P46669  (RPA43_YEAST) -  DNA-directed RNA polymerase I subunit RPA43 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 326 a.a.

Struc: 193 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: 131 a.a.

Protein chain

P32529  (RPA12_YEAST) -  DNA-directed RNA polymerase I subunit RPA12 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 125 a.a.

Struc: 73 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: 69 a.a.

Protein chain

P28000  (RPAC2_YEAST) -  DNA-directed RNA polymerases I and III subunit RPAC2 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 142 a.a.

Struc: 101 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: 43 a.a.

Protein chain

Q01080  (RPA49_YEAST) -  DNA-directed RNA polymerase I subunit RPA49 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 415 a.a.

Struc: 105 a.a.

Protein chain

P47006  (RPA34_YEAST) -  DNA-directed RNA polymerase I subunit RPA34 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 233 a.a.

Struc: 145 a.a.

Protein chain

P36070  (RRN3_YEAST) -  RNA polymerase I-specific transcription initiation factor RRN3 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 627 a.a.

Struc: 463 a.a.

Protein chain

P32786  (RRN6_YEAST) -  RNA polymerase I-specific transcription initiation factor RRN6 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 894 a.a.

Struc: 595 a.a.*

Protein chain

P40992  (RRN7_YEAST) -  RNA polymerase I-specific transcription initiation factor RRN7 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 514 a.a.

Struc: 461 a.a.

Protein chain

Q04712  (RRN11_YEAST) -  RNA polymerase I-specific transcription initiation factor RRN11 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

Seq: 507 a.a.

Struc: 325 a.a.

* PDB and UniProt seqs differ at 19 residue positions (black crosses)

DNA/RNA chains

A-A-A-A-A-A-A-A-A-A-A-A-A-A-A-A-A-A-A-A-A-A-A-A-A-A-A 27 bases

T-T-T-T-T-T-T-T-T-T-T-C-T-T-T-T-T-T-T-T-T-T-T-T-T-T-T 27 bases

G-G-G-G-G-G-G-G-G-G-G-G 12 bases

C-C-C-C-C-C-C-C-C-C-C-C 12 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: Chains C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R: E.C.?

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

Added reference

DOI no: 10.1038/s41467-020-15052-y

Nat Commun 11:1206 (2020)

PubMed id: 32139698

Structural basis of RNA polymerase I pre-initiation complex formation and promoter melting.

M.Pilsl, C.Engel.

ABSTRACT

Transcription of the ribosomal RNA precursor by RNA polymerase (Pol) I is a prerequisite for the biosynthesis of ribosomes in eukaryotes. Compared to Pols II and III, the mechanisms underlying promoter recognition, initiation complex formation and DNA melting by Pol I substantially diverge. Here, we report the high-resolution cryo-EM reconstruction of a Pol I early initiation intermediate assembled on a double-stranded promoter scaffold that prevents the establishment of downstream DNA contacts. Our analyses demonstrate how efficient promoter-backbone interaction is achieved by combined re-arrangements of flexible regions in the 'core factor' subunits Rrn7 and Rrn11. Furthermore, structure-function analysis illustrates how destabilization of the melted DNA region correlates with contraction of the polymerase cleft upon transcription activation, thereby combining promoter recruitment with DNA-melting. This suggests that molecular mechanisms and structural features of Pol I initiation have co-evolved to support the efficient melting, initial transcription and promoter clearance required for high-level rRNA synthesis.