6RRD image
Deposition Date 2019-05-17
Release Date 2019-12-11
Last Version Date 2024-05-22
Entry Detail
PDB ID:
6RRD
Keywords:
TRANSCRIPTION
Title:
RNA Polymerase I Pre-initiation complex DNA opening intermediate 1
Biological Source:
Source Organism(s):
synthetic construct (Taxon ID: 32630)
Saccharomyces cerevisiae (Taxon ID: 4932)
Expression System(s):
Synthetic construct, Escherichia coli, Saccharomyces cerevisiae
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.10 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
6RRD 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:I (auth: A)
Chain Length:1664
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
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:J (auth: B)
Chain Length:1203
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
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:K (auth: C)
Chain Length:335
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
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:L (auth: D)
Chain Length:137
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
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:M (auth: E)
Chain Length:215
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
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:N (auth: F)
Chain Length:155
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
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:O (auth: G)
Chain Length:326
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
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:P (auth: H)
Chain Length:146
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
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:F (auth: I)
Chain Length:125
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
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:Q (auth: J)
Chain Length:70
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
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:R (auth: K)
Chain Length:142
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
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:S (auth: L)
Chain Length:70
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
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:H (auth: M)
Chain Length:415
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
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:G (auth: N)
Chain Length:233
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
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 RRN3
Gene (Uniprot):RRN3
Chain IDs:T (auth: O)
Chain Length:627
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P36070 Pfam ID:PF05327
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:C (auth: Q)
Chain Length:514
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P40992 Pfam ID:PF20644, PF11781, 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:E (auth: R)
Chain Length:507
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:Q04712 Pfam ID:PF04090
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:D (auth: S)
Chain Length:894
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae
UniProt ID:P32786 Pfam ID:PF20640, PF10214, PF20639
Polymer Type:polydeoxyribonucleotide
Molecule:Template strand
Chain IDs:A (auth: T)
Chain Length:70
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
Molecule:Nontemplate strand
Chain IDs:B (auth: U)
Chain Length:70
Number of Molecules:1
Biological Source:synthetic construct
Ligand Molecules
ZN
Primary Citation
Molecular insight into RNA polymerase I promoter recognition and promoter melting.
Nat Commun 10 5543 5543 (2019)
PMID: 31804486 DOI: 10.1038/s41467-019-13510-w

Abstact

RNA polymerase I (Pol I) assembles with core factor (CF) and Rrn3 on the rDNA core promoter for transcription initiation. Here, we report cryo-EM structures of closed, intermediate and open Pol I initiation complexes from 2.7 to 3.7 Å resolution to visualize Pol I promoter melting and to structurally and biochemically characterize the recognition mechanism of Pol I promoter DNA. In the closed complex, double-stranded DNA runs outside the DNA-binding cleft. Rotation of CF and upstream DNA with respect to Pol I and Rrn3 results in the spontaneous loading and opening of the promoter followed by cleft closure and positioning of the Pol I A49 tandem winged helix domain (tWH) onto DNA. Conformational rearrangement of A49 tWH leads to a clash with Rrn3 to initiate complex disassembly and promoter escape. Comprehensive insight into the Pol I transcription initiation cycle allows comparisons with promoter opening by Pol II and Pol III.

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Disease

Primary Citation of related structures
6RRD
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