9FSQ image
Deposition Date 2024-06-21
Release Date 2025-01-15
Last Version Date 2025-01-15
Entry Detail
PDB ID:
9FSQ
Keywords:
TRANSCRIPTION
Title:
RNA Polymerase III Class III Melting Pre-Initiation Complex (MC)
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.51 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
9FSQ validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase III subunit RPC1
Gene (Uniprot):POLR3A
Chain IDs:A
Chain Length:1390
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O14802 Pfam ID:PF04997, PF00623, PF04983, PF05000, PF04998
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase III subunit RPC2
Gene (Uniprot):POLR3B
Chain IDs:B
Chain Length:1133
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NW08 Pfam ID:PF04563, PF04561, PF04565, PF04566, PF04567, PF00562, PF04560
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase III subunit RPC3
Gene (Uniprot):POLR3C
Chain IDs:C
Chain Length:534
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9BUI4 Pfam ID:PF08221, PF05645, PF22536, PF20912
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase III subunit RPC4
Gene (Uniprot):POLR3D
Chain IDs:D
Chain Length:398
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P05423 Pfam ID:PF05132
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase III subunit RPC5
Gene (Uniprot):POLR3E
Chain IDs:E
Chain Length:708
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9NVU0 Pfam ID:PF04801, PF19725
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase III subunit RPC6
Gene (Uniprot):POLR3F
Chain IDs:F
Chain Length:316
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9H1D9 Pfam ID:PF05158
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase III subunit RPC7
Gene (Uniprot):POLR3G
Chain IDs:G
Chain Length:223
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O15318 Pfam ID:PF11705
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase III subunit RPC8
Gene (Uniprot):POLR3H
Chain IDs:H
Chain Length:204
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y535 Pfam ID:PF03876, PF08292
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase III subunit RPC9
Gene (Uniprot):CRCP
Chain IDs:I
Chain Length:148
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O75575 Pfam ID:PF03874
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase III subunit RPC10
Gene (Uniprot):POLR3K
Chain IDs:J
Chain Length:108
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9Y2Y1 Pfam ID:PF02150, PF01096
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I and III subunit RPAC1
Gene (Uniprot):POLR1C
Chain IDs:K
Chain Length:346
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O15160 Pfam ID:PF01193, PF01000
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I and III subunit RPAC2
Gene (Uniprot):POLR1D
Chain IDs:L
Chain Length:133
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P0DPB6 Pfam ID:PF13656
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC1
Gene (Uniprot):POLR2E
Chain IDs:M
Chain Length:210
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P19388 Pfam ID:PF03871, PF01191
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC2
Gene (Uniprot):POLR2F
Chain IDs:N
Chain Length:127
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P61218 Pfam ID:PF01192
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC3
Gene (Uniprot):POLR2H
Chain IDs:O
Chain Length:150
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P52434 Pfam ID:PF03870
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC4
Gene (Uniprot):POLR2K
Chain IDs:P
Chain Length:58
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P53803 Pfam ID:PF03604
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC5
Gene (Uniprot):POLR2L
Chain IDs:Q
Chain Length:67
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P62875 Pfam ID:PF01194
Protein Blast
Polymer Type:polypeptide(L)
Molecule:TATA-box-binding protein
Gene (Uniprot):TBP
Chain IDs:R
Chain Length:200
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P20226 Pfam ID:PF00352
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription factor IIIB 50 kDa subunit
Gene (Uniprot):BRF2
Chain IDs:S
Chain Length:419
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q9HAW0 Pfam ID:PF08271, PF21886
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription factor TFIIIB component B'' homolog
Gene (Uniprot):BDP1
Chain IDs:T
Chain Length:484
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:A6H8Y1 Pfam ID:PF15963
Protein Blast
Polymer Type:polypeptide(L)
Molecule:snRNA-activating protein complex subunit 1
Gene (Uniprot):SNAPC1
Chain IDs:U
Chain Length:368
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q16533 Pfam ID:PF09808
Protein Blast
Polymer Type:polypeptide(L)
Molecule:snRNA-activating protein complex subunit 4
Gene (Uniprot):SNAPC4
Chain IDs:V (auth: W)
Chain Length:1519
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q5SXM2 Pfam ID:PF13921
Polymer Type:polydeoxyribonucleotide
Molecule:U6_2_Template
Chain IDs:W (auth: X)
Chain Length:98
Number of Molecules:1
Biological Source:Homo sapiens
Polymer Type:polydeoxyribonucleotide
Molecule:U6_2_Non template
Chain IDs:X (auth: Y)
Chain Length:98
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:snRNA-activating protein complex subunit 3
Gene (Uniprot):SNAPC3
Chain IDs:Y (auth: Z)
Chain Length:411
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q92966 Pfam ID:PF12251
Ligand Molecules
MG
SF4
ZN
Primary Citation
Structural insights into distinct mechanisms of RNA polymerase II and III recruitment to snRNA promoters.
Nat Commun 16 141 141 (2025)
PMID: 39747245 DOI: 10.1038/s41467-024-55553-8

Abstact

RNA polymerase III (Pol III) transcribes short, essential RNAs, including the U6 small nuclear RNA (snRNA). At U6 snRNA genes, Pol III is recruited by the snRNA Activating Protein Complex (SNAPc) and a Brf2-containing TFIIIB complex, forming a pre-initiation complex (PIC). Uniquely, SNAPc also recruits Pol II at the remaining splicesosomal snRNA genes (U1, 2, 4 and 5). The mechanism of SNAPc cross-polymerase engagement and the role of the SNAPC2 and SNAPC5 subunits remain poorly defined. Here, we present cryo-EM structures of the full-length SNAPc-containing Pol III PIC assembled on the U6 snRNA promoter in the open and melting states at 3.2-4.2 Å resolution. The structural comparison revealed differences with the Saccharomyces cerevisiae Pol III PIC and the basis of selective SNAPc engagement within Pol III and Pol II PICs. Additionally, crosslinking mass spectrometry localizes SNAPC2 and SNAPC5 near the promoter DNA, expanding upon existing descriptions of snRNA Pol III PIC structure.

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Disease

Primary Citation of related structures
9FSQ