› 7b0y

Electron Microscopy
3.6Å resolution

Structure of a transcribing RNA polymerase II-U1 snRNP complex

Released:
DOI: 10.2210/pdb7b0y/pdb
PDB 7b0y coloured by chain and viewed from the front.
PDB 7b0y coloured by chain and viewed from the side.
PDB 7b0y coloured by chain and viewed from the top.
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 domain:

Structure analysis Details

Assembly composition:
hetero 25-mer (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:
RPOLD 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 Rpb3/RpoA insert domain
RPOL4c 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
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
DNA-directed RNA polymerase II subunit F Chain: F
Molecule details ›
Chain: F
Length: 127 amino acids
Theoretical weight: 14.48 KDa
Source organism: Sus scrofa domesticus
UniProt:
  • Canonical: F1SKN8 (Residues: 1-127; Coverage: 100%)
Gene name: POLR2F
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
UniProt:
  • Canonical: I3LJZ9 (Residues: 1-172; Coverage: 100%)
Gene name: POLR2G
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
RNA_pol_L_2 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
RNA polymerase II subunit K Chain: L
Molecule details ›
Chain: L
Length: 58 amino acids
Theoretical weight: 7.02 KDa
Source organism: Sus scrofa domesticus
UniProt:
  • Canonical: I3LN51 (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 of 70kDa MW N terminal
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. (a.k.a. RRM, RBD, or RNP domain)
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
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
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
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
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
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
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
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

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