7ZX7 image
Deposition Date 2022-05-20
Release Date 2022-11-30
Last Version Date 2024-07-24
Entry Detail
PDB ID:
7ZX7
Keywords:
TRANSCRIPTION
Title:
Structure of SNAPc containing Pol II pre-initiation complex bound to U1 snRNA promoter (CC)
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Sus scrofa (Taxon ID: 9823)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
ELECTRON MICROSCOPY
Resolution:
3.40 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
7ZX7 validation report
Macromolecular Entities
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit
Gene (Uniprot):POLR2A
Chain IDs:A
Chain Length:368
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A8D1DPV6 Pfam ID:PF04997, PF00623, PF04983, PF05000, PF04998, PF04992, PF04990, PF05001
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase subunit beta
Gene (Uniprot):POLR2B
Chain IDs:B
Chain Length:1174
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:I3LGP4 Pfam ID:PF04563, PF04561, PF04565, PF04566, PF04567, PF00562, PF04560
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB3
Gene (Uniprot):POLR2C
Chain IDs:C
Chain Length:1469
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:I3LCH3 Pfam ID:PF01193, PF01000
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase II subunit D
Gene (Uniprot):POLR2D
Chain IDs:D
Chain Length:142
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A287ADR4 Pfam ID:PF03874
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit E
Gene (Uniprot):POLR2E
Chain IDs:E
Chain Length:210
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:I3LSI7 Pfam ID:PF03871, PF01191
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit F
Chain IDs:F
Chain Length:127
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A4X1VEK9 Pfam ID:PF01192
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB7
Chain IDs:G
Chain Length:172
Number of Molecules:1
Biological Source:Sus scrofa
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC3
Chain IDs:H
Chain Length:150
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:I3LCB2 Pfam ID:PF03870
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerase II subunit RPB9
Gene (Uniprot):POLR2I
Chain IDs:I
Chain Length:125
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:P60899 Pfam ID:PF02150, PF01096
Protein Blast
Polymer Type:polypeptide(L)
Molecule:DNA-directed RNA polymerases I, II, and III subunit RPABC5
Gene (Uniprot):POLR2L
Chain IDs:J
Chain Length:67
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A4X1VYD0 Pfam ID:PF01194
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase II subunit J
Chain IDs:K
Chain Length:117
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:F1RKE4 Pfam ID:PF13656
Protein Blast
Polymer Type:polypeptide(L)
Molecule:RNA polymerase II subunit K
Chain IDs:L
Chain Length:58
Number of Molecules:1
Biological Source:Sus scrofa
UniProt ID:A0A4X1TRS6 Pfam ID:PF03604
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIB
Gene (Uniprot):GTF2B
Chain IDs:M
Chain Length:316
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q00403 Pfam ID:PF08271, PF00382
Polymer Type:polydeoxyribonucleotide
Molecule:Non-template strand
Chain IDs:N
Chain Length:96
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:TATA-box-binding protein
Gene (Uniprot):TBP
Chain IDs:O
Chain Length:339
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P20226 Pfam ID:PF00352
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription factor IIF subunit 1
Gene (Uniprot):GTF2F1
Chain IDs:P (auth: Q)
Chain Length:517
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P35269 Pfam ID:PF05793
Protein Blast
Polymer Type:polypeptide(L)
Molecule:General transcription factor IIF subunit 2
Gene (Uniprot):GTF2F2
Chain IDs:Q (auth: R)
Chain Length:249
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P13984 Pfam ID:PF17683, PF02270
Polymer Type:polydeoxyribonucleotide
Molecule:Template strand
Chain IDs:R (auth: T)
Chain Length:96
Number of Molecules:1
Biological Source:Homo sapiens
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIA subunit 1
Gene (Uniprot):GTF2A1
Chain IDs:S (auth: U)
Chain Length:376
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P52655 Pfam ID:PF03153
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Transcription initiation factor IIA subunit 2
Gene (Uniprot):GTF2A2
Chain IDs:T (auth: V)
Chain Length:109
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P52657 Pfam ID:PF02268, PF02751
Protein Blast
Polymer Type:polypeptide(L)
Molecule:snRNA-activating protein complex subunit 1
Gene (Uniprot):SNAPC1
Chain IDs:U (auth: a)
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 3
Gene (Uniprot):SNAPC3
Chain IDs:V (auth: b)
Chain Length:1174
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q92966 Pfam ID:PF12251
Protein Blast
Polymer Type:polypeptide(L)
Molecule:snRNA-activating protein complex subunit 4
Gene (Uniprot):SNAPC4
Chain IDs:W (auth: c)
Chain Length:1469
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:Q5SXM2 Pfam ID:PF13921
Protein Blast
Polymer Type:polypeptide(L)
Molecule:snRNA-activating protein complex subunit 5
Gene (Uniprot):SNAPC5
Chain IDs:X (auth: d)
Chain Length:142
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:O75971 Pfam ID:PF15497
Ligand Molecules
MG
ZN
Primary Citation
Structural basis of SNAPc-dependent snRNA transcription initiation by RNA polymerase II.
Nat.Struct.Mol.Biol. 29 1159 1169 (2022)
PMID: 36424526 DOI: 10.1038/s41594-022-00857-w

Abstact

RNA polymerase II (Pol II) carries out transcription of both protein-coding and non-coding genes. Whereas Pol II initiation at protein-coding genes has been studied in detail, Pol II initiation at non-coding genes, such as small nuclear RNA (snRNA) genes, is less well understood at the structural level. Here, we study Pol II initiation at snRNA gene promoters and show that the snRNA-activating protein complex (SNAPc) enables DNA opening and transcription initiation independent of TFIIE and TFIIH in vitro. We then resolve cryo-EM structures of the SNAPc-containing Pol IIpre-initiation complex (PIC) assembled on U1 and U5 snRNA promoters. The core of SNAPc binds two turns of DNA and recognizes the snRNA promoter-specific proximal sequence element (PSE), located upstream of the TATA box-binding protein TBP. Two extensions of SNAPc, called wing-1 and wing-2, bind TFIIA and TFIIB, respectively, explaining how SNAPc directs Pol II to snRNA promoters. Comparison of structures of closed and open promoter complexes elucidates TFIIH-independent DNA opening. These results provide the structural basis of Pol II initiation at non-coding RNA gene promoters.

Legend

Protein

Chemical

Disease

Primary Citation of related structures
7ZX7