6CNC image
Deposition Date 2018-03-08
Release Date 2018-08-22
Last Version Date 2024-11-13
Entry Detail
PDB ID:
6CNC
Keywords:
transcription/dna
Title:
Yeast RNA polymerase III open complex
Biological Source:
Source Organism:
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Taxon ID: 559292)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
4.10 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
6CNC validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase III subunit RPC1
Gene (Uniprot):RPO31
Chain IDs:A
Chain Length:1460
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P04051 Pfam ID:PF04997, PF00623, PF04983, PF05000, PF04998
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase III subunit RPC2
Gene (Uniprot):RET1
Chain IDs:B
Chain Length:1149
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P22276 Pfam ID:PF04563, PF04561, PF04565, PF04566, PF04567, PF00562, PF04560
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase III subunit RPC9
Gene (Uniprot):RPC17
Chain IDs:D
Chain Length:161
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P47076 Pfam ID:PF03874
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
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase III subunit RPC8
Gene (Uniprot):RPC25
Chain IDs:G
Chain Length:212
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P35718 Pfam ID:PF03876, PF08292
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase III subunit RPC10
Gene (Uniprot):RPC11
Chain IDs:I
Chain Length:110
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:Q04307 Pfam ID:PF02150, PF01096
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
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
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
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase III subunit RPC5
Gene (Uniprot):RPC37
Chain IDs:M
Chain Length:282
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P36121 Pfam ID:PF04801
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase III subunit RPC4
Gene (Uniprot):RPC53
Chain IDs:N
Chain Length:422
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P25441 Pfam ID:PF05132
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase III subunit RPC3
Gene (Uniprot):RPC82
Chain IDs:O
Chain Length:654
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P32349 Pfam ID:PF08221, PF05645, PF22536, PF20912
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase III subunit RPC6
Gene (Uniprot):RPC34
Chain IDs:P
Chain Length:317
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P32910 Pfam ID:PF05158
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase III subunit RPC7,DNA-directed RNA polymerase III subunit RPC7,DNA-directed RNA polymerase III subunit RPC7,DNA-directed RNA polymerase III subunit RPC7,DNA-directed RNA polymerase III subunit RPC7
Gene (Uniprot):RPC31
Chain IDs:Q
Chain Length:251
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P17890 Pfam ID:PF11705
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription factor IIIB 70 kDa subunit,TATA-box-binding protein,Transcription factor IIIB 70 kDa subunit
Gene (Uniprot):SPT15, BRF1
Mutations:C438S
Chain IDs:R
Chain Length:736
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
UniProt ID:P29056,P13393 Pfam ID:PF08271, PF00382, PF00352, PF07741
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription factor TFIIIB component B'',Transcription factor TFIIIB component B'',Transcription factor TFIIIB component B'',Transcription factor TFIIIB component B'',Transcription factor TFIIIB component B''
Gene (Uniprot):BDP1
Chain IDs:S
Chain Length:594
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Saccharomyces cerevisiae S288c
UniProt ID:P46678 Pfam ID:PF00249
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (71-MER)
Chain IDs:T (auth: X)
Chain Length:71
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Polymer Type:polydeoxyribonucleotide
Molecule:DNA (71-MER)
Chain IDs:U (auth: Y)
Chain Length:71
Number of Molecules:1
Biological Source:Saccharomyces cerevisiae S288c
Ligand Molecules
ZN
Primary Citation
Structural visualization of RNA polymerase III transcription machineries.
Cell Discov 4 40 40 (2018)
PMID: 30083386 DOI: 10.1038/s41421-018-0044-z

Abstact

RNA polymerase III (Pol III) transcription initiation requires the action of the transcription factor IIIB (TFIIIB) and is highly regulated. Here, we determine the structures of Pol III pre-initiation complexes (PICs) using single particle cryo-electron microscopy (cryo-EM). We observe stable Pol III-TFIIIB complexes using nucleic acid scaffolds mimicking various functional states, in which TFIIIB tightly encircles the upstream promoter DNA. There is an intricate interaction between TFIIIB and Pol III, which stabilizes the winged-helix domains of the C34 subunit of Pol III over the active site cleft. The architecture of Pol III PIC more resembles that of the Pol II PIC than the Pol I PIC. In addition, we also obtain a 3D reconstruction of Pol III in complex with TFIIIB using the elongation complex (EC) scaffold, shedding light on the mechanism of facilitated recycling of Pol III prior to transcription re-initiation.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
6CNC