5W66 image
Deposition Date 2017-06-16
Release Date 2017-07-26
Last Version Date 2024-10-23
Entry Detail
PDB ID:
5W66
Keywords:
TRANSCRIPTION
Title:
RNA polymerase I Initial Transcribing Complex State 3
Biological Source:
Source Organism(s):
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Taxon ID: 559292)
Expression System(s):
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.90 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
5W66 validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I subunit RPA190
Gene (Uniprot):RPA190
Chain IDs:A
Chain Length:1664
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P10964 Pfam ID:PF04997, PF00623, PF04983, PF05000, PF04998
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I subunit RPA135
Gene (Uniprot):RPA135
Chain IDs:B
Chain Length:1203
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P22138 Pfam ID:PF04563, PF04561, PF04565, PF06883, PF00562, PF04560
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I and III subunit RPAC1
Gene (Uniprot):RPC40
Chain IDs:C
Chain Length:335
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P07703 Pfam ID:PF01193, PF01000
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I subunit RPA14
Gene (Uniprot):RPA14
Chain IDs:D
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P50106 Pfam ID:PF08203
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC1
Gene (Uniprot):RPB5
Chain IDs:E
Chain Length:215
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P20434 Pfam ID:PF03871, PF01191
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC2
Gene (Uniprot):RPO26
Chain IDs:F
Chain Length:155
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P20435 Pfam ID:PF01192
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I subunit RPA43
Gene (Uniprot):RPA43
Chain IDs:G
Chain Length:326
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P46669 Pfam ID:PF03876, PF17875
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC3
Gene (Uniprot):RPB8
Chain IDs:H
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P20436 Pfam ID:PF03870
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I subunit RPA12
Gene (Uniprot):RPA12
Chain IDs:I
Chain Length:125
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P32529 Pfam ID:PF02150, PF01096
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC5
Gene (Uniprot):RPB10
Chain IDs:J
Chain Length:70
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P22139 Pfam ID:PF01194
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I and III subunit RPAC2
Gene (Uniprot):RPC19
Chain IDs:K
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P28000 Pfam ID:PF13656
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC4
Gene (Uniprot):RPC10
Chain IDs:L
Chain Length:70
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P40422 Pfam ID:PF03604
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I subunit RPA49
Gene (Uniprot):RPA49
Chain IDs:M
Chain Length:415
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q01080 Pfam ID:PF06870
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase I subunit RPA34
Gene (Uniprot):RPA34
Chain IDs:N
Chain Length:233
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P47006 Pfam ID:PF08208
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase I-specific transcription initiation factor RRN6
Gene (Uniprot):RRN6
Chain IDs:O
Chain Length:894
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P32786 Pfam ID:PF10214, PF20640, PF20639
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase I-specific transcription initiation factor RRN7
Gene (Uniprot):RRN7
Chain IDs:P
Chain Length:514
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P40992 Pfam ID:PF11781, PF20644, PF20645
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase I-specific transcription initiation factor RRN11
Gene (Uniprot):RRN11
Chain IDs:Q
Chain Length:507
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q04712 Pfam ID:PF04090
Polymer Type:polyribonucleotide
Molecule:RNA
Chain IDs:R
Chain Length:6
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polydeoxyribonucleotide
Molecule:non-template strand DNA
Chain IDs:S
Chain Length:54
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polydeoxyribonucleotide
Molecule:template strand DNA
Chain IDs:T
Chain Length:54
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Ligand Molecules
ZN
Primary Citation
Structural mechanism of ATP-independent transcription initiation by RNA polymerase I.
Elife 6 ? ? (2017)
PMID: 28623663 DOI: 10.7554/eLife.27414

Abstact

Transcription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a structure of Saccharomyces cerevisiae Pol I-CF-DNA to 3.8 Å resolution using single-particle cryo-electron microscopy. The structure reveals a bipartite architecture of Core Factor and its recognition of the promoter from -27 to -16. Core Factor's intrinsic mobility correlates well with different conformational states of the Pol I cleft, in addition to the stabilization of either Rrn7 N-terminal domain near Pol I wall or the tandem winged helix domain of A49 at a partially overlapping location. Comparison of the three states in this study with the Pol II system suggests that a ratchet motion of the Core Factor-DNA sub-complex at upstream facilitates promoter melting in an ATP-independent manner, distinct from a DNA translocase actively threading the downstream DNA in the Pol II PIC.

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Primary Citation of related structures
5W66
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