› 7zwd

Electron Microscopy
3Å resolution

Structure of SNAPc containing Pol II pre-initiation complex bound to U5 snRNA promoter (CC)

Released:
DOI: 10.2210/pdb7zwd/pdb
PDB entry 7zwd coloured by chain, front view.
PDB entry 7zwd coloured by chain, side view.
PDB entry 7zwd coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of SNAPc-dependent snRNA transcription initiation by RNA polymerase II.
Rengachari S, Schilbach S, Kaliyappan T, Gouge J, Zumer K, Schwarz J, Urlaub H, Dienemann C, Vannini A, Cramer P
Nat Struct Mol Biol (2022)
PMID: 36424526
Related structures: EMD-14997

Function and Biology Details

Reactions catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Acetyl-CoA + [protein]-L-lysine = CoA + [protein]-N(6)-acetyl-L-lysine
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 24-mer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-236753 (preferred)
Entry contents:
22 distinct polypeptide molecules
2 distinct DNA molecules
Macromolecules (24 distinct):
DNA-directed RNA polymerase subunit Chain: A
Molecule details ›
Chain: A
Length: 1970 amino acids
Theoretical weight: 217.45 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A8D1DPV6 (Residues: 1-1970; Coverage: 100%)
Gene name: POLR2A
Sequence domains:
DNA-directed RNA polymerase subunit beta Chain: B
Molecule details ›
Chain: B
Length: 1174 amino acids
Theoretical weight: 134.04 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LGP4 (Residues: 127-1300; Coverage: 90%)
Gene name: POLR2B
Sequence domains:
DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein Chain: C
Molecule details ›
Chain: C
Length: 275 amino acids
Theoretical weight: 31.44 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LCH3 (Residues: 1-275; Coverage: 100%)
Gene name: POLR2C
Sequence domains:
RNA polymerase Rpb4/RPC9 core domain-containing protein Chain: D
Molecule details ›
Chain: D
Length: 142 amino acids
Theoretical weight: 16.33 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A287ADR4 (Residues: 43-184; Coverage: 77%)
Gene name: POLR2D
Sequence domains: RNA polymerase Rpb4
DNA-directed RNA polymerase II subunit E Chain: E
Molecule details ›
Chain: E
Length: 210 amino acids
Theoretical weight: 24.64 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LSI7 (Residues: 1-210; Coverage: 100%)
Gene name: POLR2E
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC2 Chain: F
Molecule details ›
Chain: F
Length: 127 amino acids
Theoretical weight: 14.48 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VEK9 (Residues: 1-127; Coverage: 100%)
Gene name: POLR2F
Sequence domains: RNA polymerase Rpb6
DNA-directed RNA polymerase II subunit RPB7 Chain: G
Molecule details ›
Chain: G
Length: 172 amino acids
Theoretical weight: 19.31 KDa
Source organism: Sus scrofa
DNA-directed RNA polymerases I, II, and III subunit RPABC3 Chain: H
Molecule details ›
Chain: H
Length: 150 amino acids
Theoretical weight: 17.16 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: I3LCB2 (Residues: 1-150; Coverage: 100%)
Gene name: POLR2H
Sequence domains: RNA polymerase Rpb8
DNA-directed RNA polymerase II subunit RPB9 Chain: I
Molecule details ›
Chain: I
Length: 125 amino acids
Theoretical weight: 14.54 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: P60899 (Residues: 1-125; Coverage: 100%)
Gene name: POLR2I
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC5 Chain: J
Molecule details ›
Chain: J
Length: 67 amino acids
Theoretical weight: 7.66 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1VYD0 (Residues: 1-67; Coverage: 100%)
Gene name: POLR2L
Sequence domains: RNA polymerases N / 8 kDa subunit
DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein Chain: K
Molecule details ›
Chain: K
Length: 117 amino acids
Theoretical weight: 13.31 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: F1RKE4 (Residues: 1-117; Coverage: 100%)
Gene name: POLR2J
Sequence domains:
DNA-directed RNA polymerases I, II, and III subunit RPABC4 Chain: L
Molecule details ›
Chain: L
Length: 58 amino acids
Theoretical weight: 7.02 KDa
Source organism: Sus scrofa
UniProt:
  • Canonical: A0A4X1TRS6 (Residues: 1-58; Coverage: 100%)
Gene name: POLR2K
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
Transcription initiation factor IIB Chain: M
Molecule details ›
Chain: M
Length: 316 amino acids
Theoretical weight: 34.88 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q00403 (Residues: 1-316; Coverage: 100%)
Gene names: GTF2B, TF2B, TFIIB
Sequence domains:
TATA-box-binding protein Chain: O
Molecule details ›
Chain: O
Length: 339 amino acids
Theoretical weight: 37.73 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P20226 (Residues: 1-339; Coverage: 100%)
Gene names: GTF2D1, TBP, TF2D, TFIID
Sequence domains: Transcription factor TFIID (or TATA-binding protein, TBP)
General transcription factor IIF subunit 1 Chain: Q
Molecule details ›
Chain: Q
Length: 517 amino acids
Theoretical weight: 58.34 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P35269 (Residues: 1-517; Coverage: 100%)
Gene names: GTF2F1, RAP74
Sequence domains: Transcription initiation factor IIF, alpha subunit (TFIIF-alpha)
General transcription factor IIF subunit 2 Chain: R
Molecule details ›
Chain: R
Length: 249 amino acids
Theoretical weight: 28.43 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P13984 (Residues: 1-249; Coverage: 100%)
Gene names: GTF2F2, RAP30
Sequence domains:
Transcription initiation factor IIA subunit 1 Chain: U
Molecule details ›
Chain: U
Length: 376 amino acids
Theoretical weight: 41.54 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P52655 (Residues: 1-376; Coverage: 100%)
Gene names: GTF2A1, TF2A1
Sequence domains: Transcription factor IIA, alpha/beta subunit
Transcription initiation factor IIA subunit 2 Chain: V
Molecule details ›
Chain: V
Length: 109 amino acids
Theoretical weight: 12.47 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P52657 (Residues: 1-109; Coverage: 100%)
Gene names: GTF2A2, TF2A2
Sequence domains:
snRNA-activating protein complex subunit 1 Chain: a
Molecule details ›
Chain: a
Length: 368 amino acids
Theoretical weight: 43.07 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q16533 (Residues: 1-368; Coverage: 100%)
Gene names: SNAP43, SNAPC1
Sequence domains: Small nuclear RNA activating complex (SNAPc), subunit 1
snRNA-activating protein complex subunit 3 Chain: b
Molecule details ›
Chain: b
Length: 411 amino acids
Theoretical weight: 46.81 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q92966 (Residues: 1-411; Coverage: 100%)
Gene names: SNAP50, SNAPC3
Sequence domains: snRNA-activating protein complex (SNAPc), subunit 3
snRNA-activating protein complex subunit 4 Chain: c
Molecule details ›
Chain: c
Length: 1469 amino acids
Theoretical weight: 159.65 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q5SXM2 (Residues: 1-1469; Coverage: 100%)
Gene names: SNAP190, SNAPC4
Sequence domains: Myb-like DNA-binding domain
snRNA-activating protein complex subunit 5 Chain: d
Molecule details ›
Chain: d
Length: 98 amino acids
Theoretical weight: 11.34 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: O75971 (Residues: 1-98; Coverage: 100%)
Gene names: SNAP19, SNAPC5
Sequence domains: snRNA-activating protein complex subunit 19, SNAPc subunit 19
Non-template strand Chain: N
Molecule details ›
Chain: N
Length: 96 nucleotides
Theoretical weight: 29.68 KDa
Template strand Chain: T
Molecule details ›
Chain: T
Length: 96 nucleotides
Theoretical weight: 29.54 KDa

Ligands and Environments

2 bound ligands:
Ligand ZN 11 x ZN
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3Å
Relevant EMDB volumes: EMD-14997
Expression systems:
  • Escherichia coli
  • Trichoplusia ni

Quick links

Citations

3 citation in other articles

Functionally distinct promoter classes initiate transcription via different mechanisms reflected in focused versus dispersed initiation patterns.
Serebreni et al. (2023)
2 more

1 mention without citation

Structural basis of SNAPc-dependent snRNA transcription initiation by RNA polymerase II.
Rengachari et al. (2022)