› 7b0y

Electron Microscopy
3.6Å resolution

Structure of a transcribing RNA polymerase II-U1 snRNP complex

Released:
DOI: 10.2210/pdb7b0y/pdb
PDB entry 7b0y coloured by chain, front view.
PDB entry 7b0y coloured by chain, side view.
PDB entry 7b0y coloured by chain, top view.
Source organisms:
Primary publication:
Structure of a transcribing RNA polymerase II-U1 snRNP complex.
Zhang S, Aibara S, Vos SM, Agafonov DE, Lührmann R, Cramer P
Science 371 305-309 (2021)
PMID: 33446560
Related structures: EMD-11972

Function and Biology Details

Reaction catalysed: 
Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 25-mer (preferred)
PDBe Complex ID:
PDB-CPX-236611 (preferred)
Entry contents:
21 distinct polypeptide molecules
2 distinct DNA molecules
2 distinct RNA molecules
Macromolecules (25 distinct):
DNA-directed RNA polymerase II subunit RPB1 Chain: A
Molecule details ›
Chain: A
Length: 1970 amino acids
Theoretical weight: 217.45 KDa
Source organism: Sus scrofa domesticus
UniProt:
  • Canonical: P11414 (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 domesticus
UniProt:
  • Canonical: A0A0B8RVL1 (Residues: 1-1174; Coverage: 100%)
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 domesticus
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 domesticus
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 domesticus
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 domesticus
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 domesticus
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 domesticus
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 domesticus
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 domesticus
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 domesticus
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 domesticus
UniProt:
  • Canonical: A0A4X1TRS6 (Residues: 1-58; Coverage: 100%)
Gene name: POLR2K
Sequence domains: DNA directed RNA polymerase, 7 kDa subunit
U1 small nuclear ribonucleoprotein 70 kDa Chain: b
Molecule details ›
Chain: b
Length: 437 amino acids
Theoretical weight: 51.68 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P08621 (Residues: 1-437; Coverage: 100%)
Gene names: RNPU1Z, RPU1, SNRNP70, SNRP70, U1AP1
Sequence domains:
U1 small nuclear ribonucleoprotein A Chain: c
Molecule details ›
Chain: c
Length: 282 amino acids
Theoretical weight: 31.32 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P09012 (Residues: 1-282; Coverage: 100%)
Gene name: SNRPA
Sequence domains: RNA recognition motif
Small nuclear ribonucleoprotein Sm D2 Chain: e
Molecule details ›
Chain: e
Length: 118 amino acids
Theoretical weight: 13.55 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62316 (Residues: 1-118; Coverage: 100%)
Gene names: SNRPD1, SNRPD2
Sequence domains: LSM domain
Small nuclear ribonucleoprotein F Chain: f
Molecule details ›
Chain: f
Length: 86 amino acids
Theoretical weight: 9.73 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62306 (Residues: 1-86; Coverage: 100%)
Gene names: PBSCF, SNRPF
Sequence domains: LSM domain
Small nuclear ribonucleoprotein E Chain: g
Molecule details ›
Chain: g
Length: 92 amino acids
Theoretical weight: 10.82 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62304 (Residues: 1-92; Coverage: 100%)
Gene name: SNRPE
Sequence domains: LSM domain
Small nuclear ribonucleoprotein G Chain: h
Molecule details ›
Chain: h
Length: 76 amino acids
Theoretical weight: 8.51 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62308 (Residues: 1-76; Coverage: 100%)
Gene names: PBSCG, SNRPG
Sequence domains: LSM domain
Small nuclear ribonucleoprotein Sm D3 Chain: i
Molecule details ›
Chain: i
Length: 126 amino acids
Theoretical weight: 13.94 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62318 (Residues: 1-126; Coverage: 100%)
Gene name: SNRPD3
Sequence domains: LSM domain
Small nuclear ribonucleoprotein-associated protein Chain: j
Molecule details ›
Chain: j
Length: 231 amino acids
Theoretical weight: 23.69 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: Q66K91 (Residues: 1-231; Coverage: 100%)
Gene names: SNRPB, hCG_2039421
Sequence domains: LSM domain
Small nuclear ribonucleoprotein Sm D1 Chain: k
Molecule details ›
Chain: k
Length: 119 amino acids
Theoretical weight: 13.31 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P62314 (Residues: 1-119; Coverage: 100%)
Gene name: SNRPD1
Sequence domains: LSM domain
Non-template DNA Chain: N
Molecule details ›
Chain: N
Length: 48 nucleotides
Theoretical weight: 14.93 KDa
Template DNA Chain: T
Molecule details ›
Chain: T
Length: 48 nucleotides
Theoretical weight: 14.67 KDa
145-nt RNA Chain: P
Molecule details ›
Chain: P
Length: 145 nucleotides
Theoretical weight: 46.78 KDa
U1 snRNA Chain: a
Molecule details ›
Chain: a
Length: 164 nucleotides
Theoretical weight: 52.7 KDa
Sequence domains: U1 spliceosomal RNA

Ligands and Environments

2 bound ligands:
Ligand ZN 8 x ZN
Ligand MG 1 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.6Å
Relevant EMDB volumes: EMD-11972

Quick links

Citations

15 review citations

Nuclear compartmentalization as a mechanism of quantitative control of gene expression.
Bhat et al. (2021)
14 more

2 mentions without citation

Structural advances in transcription elongation.
Mohamed et al. (2022)
1 more