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Structure of a transcribing RNA polymerase II-U1 snRNP complex

Electron Microscopy
3.6Å resolution
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:
Assembly composition:
hetero 25-mer (preferred)
Entry contents: 21 distinct polypeptide molecules
2 distinct DNA molecules
2 distinct RNA molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero 25-mer
Accessible surface area: 223814.96 Å2
Buried surface area: 106388.11 Å2
Dissociation area: 872.79 Å2
Dissociation energy (ΔGdiss): 0.75 kcal/mol
Dissociation entropy (TΔSdiss): 14.77 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-236611

Macromolecules

DNA-directed RNA polymerase II subunit RPB1
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
Pfam:
InterPro:
DNA-directed RNA polymerase II subunit RPB1 in PDB entry 7b0y, assembly 1, front view.
DNA-directed RNA polymerase II subunit RPB1 in PDB entry 7b0y, assembly 1, side view.
DNA-directed RNA polymerase II subunit RPB1 in PDB entry 7b0y, assembly 1, top view.
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DNA-directed RNA polymerase subunit beta
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
Pfam:
InterPro:
DNA-directed RNA polymerase subunit beta in PDB entry 7b0y, assembly 1, front view.
DNA-directed RNA polymerase subunit beta in PDB entry 7b0y, assembly 1, side view.
DNA-directed RNA polymerase subunit beta in PDB entry 7b0y, assembly 1, top view.
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DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein
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
Pfam:
InterPro:
DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein in PDB entry 7b0y, assembly 1, front view.
DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein in PDB entry 7b0y, assembly 1, side view.
DNA-directed RNA polymerase RpoA/D/Rpb3-type domain-containing protein in PDB entry 7b0y, assembly 1, top view.
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RNA polymerase Rpb4/RPC9 core domain-containing protein
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
Pfam: RNA polymerase Rpb4
InterPro:
RNA polymerase Rpb4/RPC9 core domain-containing protein in PDB entry 7b0y, assembly 1, front view.
RNA polymerase Rpb4/RPC9 core domain-containing protein in PDB entry 7b0y, assembly 1, side view.
RNA polymerase Rpb4/RPC9 core domain-containing protein in PDB entry 7b0y, assembly 1, top view.
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DNA-directed RNA polymerase II subunit E
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
Pfam:
InterPro:
DNA-directed RNA polymerase II subunit E in PDB entry 7b0y, assembly 1, front view.
DNA-directed RNA polymerase II subunit E in PDB entry 7b0y, assembly 1, side view.
DNA-directed RNA polymerase II subunit E in PDB entry 7b0y, assembly 1, top view.
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DNA-directed RNA polymerases I, II, and III subunit RPABC2
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
Pfam: RNA polymerase Rpb6
InterPro:
DNA-directed RNA polymerase II subunit F in PDB entry 7b0y, assembly 1, front view.
DNA-directed RNA polymerase II subunit F in PDB entry 7b0y, assembly 1, side view.
DNA-directed RNA polymerase II subunit F in PDB entry 7b0y, assembly 1, top view.
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DNA-directed RNA polymerase II subunit RPB7
Chain: G
Length: 172 amino acids
Theoretical weight: 19.31 KDa
Source organism: Sus scrofa domesticus
InterPro:
DNA-directed RNA polymerase II subunit RPB7 in PDB entry 7b0y, assembly 1, front view.
DNA-directed RNA polymerase II subunit RPB7 in PDB entry 7b0y, assembly 1, side view.
DNA-directed RNA polymerase II subunit RPB7 in PDB entry 7b0y, assembly 1, top view.
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DNA-directed RNA polymerases I, II, and III subunit RPABC3
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
Pfam: RNA polymerase Rpb8
InterPro:
DNA-directed RNA polymerases I, II, and III subunit RPABC3 in PDB entry 7b0y, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC3 in PDB entry 7b0y, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC3 in PDB entry 7b0y, assembly 1, top view.
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DNA-directed RNA polymerase II subunit RPB9
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
Pfam:
InterPro:
DNA-directed RNA polymerase II subunit RPB9 in PDB entry 7b0y, assembly 1, front view.
DNA-directed RNA polymerase II subunit RPB9 in PDB entry 7b0y, assembly 1, side view.
DNA-directed RNA polymerase II subunit RPB9 in PDB entry 7b0y, assembly 1, top view.
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DNA-directed RNA polymerases I, II, and III subunit RPABC5
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
Pfam: RNA polymerases N / 8 kDa subunit
InterPro:
DNA-directed RNA polymerases I, II, and III subunit RPABC5 in PDB entry 7b0y, assembly 1, front view.
DNA-directed RNA polymerases I, II, and III subunit RPABC5 in PDB entry 7b0y, assembly 1, side view.
DNA-directed RNA polymerases I, II, and III subunit RPABC5 in PDB entry 7b0y, assembly 1, top view.
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DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein
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
Pfam:
InterPro:
DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein in PDB entry 7b0y, assembly 1, front view.
DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein in PDB entry 7b0y, assembly 1, side view.
DNA-directed RNA polymerase RBP11-like dimerisation domain-containing protein in PDB entry 7b0y, assembly 1, top view.
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DNA-directed RNA polymerases I, II, and III subunit RPABC4
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
Pfam: DNA directed RNA polymerase, 7 kDa subunit
InterPro:
RPB12 in PDB entry 7b0y, assembly 1, front view.
RPB12 in PDB entry 7b0y, assembly 1, side view.
RPB12 in PDB entry 7b0y, assembly 1, top view.
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U1 small nuclear ribonucleoprotein 70 kDa
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
Pfam:
InterPro:
U1 small nuclear ribonucleoprotein 70 kDa in PDB entry 7b0y, assembly 1, front view.
U1 small nuclear ribonucleoprotein 70 kDa in PDB entry 7b0y, assembly 1, side view.
U1 small nuclear ribonucleoprotein 70 kDa in PDB entry 7b0y, assembly 1, top view.
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U1 small nuclear ribonucleoprotein A
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
Pfam: RNA recognition motif
InterPro:
U1 small nuclear ribonucleoprotein A in PDB entry 7b0y, assembly 1, front view.
U1 small nuclear ribonucleoprotein A in PDB entry 7b0y, assembly 1, side view.
U1 small nuclear ribonucleoprotein A in PDB entry 7b0y, assembly 1, top view.
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Small nuclear ribonucleoprotein Sm D2
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
Pfam: LSM domain
InterPro:
Small nuclear ribonucleoprotein Sm D2 in PDB entry 7b0y, assembly 1, front view.
Small nuclear ribonucleoprotein Sm D2 in PDB entry 7b0y, assembly 1, side view.
Small nuclear ribonucleoprotein Sm D2 in PDB entry 7b0y, assembly 1, top view.
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Small nuclear ribonucleoprotein F
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
Pfam: LSM domain
InterPro:
Small nuclear ribonucleoprotein F in PDB entry 7b0y, assembly 1, front view.
Small nuclear ribonucleoprotein F in PDB entry 7b0y, assembly 1, side view.
Small nuclear ribonucleoprotein F in PDB entry 7b0y, assembly 1, top view.
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Small nuclear ribonucleoprotein E
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
Pfam: LSM domain
InterPro:
Small nuclear ribonucleoprotein E in PDB entry 7b0y, assembly 1, front view.
Small nuclear ribonucleoprotein E in PDB entry 7b0y, assembly 1, side view.
Small nuclear ribonucleoprotein E in PDB entry 7b0y, assembly 1, top view.
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Small nuclear ribonucleoprotein G
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
Pfam: LSM domain
InterPro:
Small nuclear ribonucleoprotein G in PDB entry 7b0y, assembly 1, front view.
Small nuclear ribonucleoprotein G in PDB entry 7b0y, assembly 1, side view.
Small nuclear ribonucleoprotein G in PDB entry 7b0y, assembly 1, top view.
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Small nuclear ribonucleoprotein Sm D3
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
Pfam: LSM domain
InterPro:
Small nuclear ribonucleoprotein Sm D3 in PDB entry 7b0y, assembly 1, front view.
Small nuclear ribonucleoprotein Sm D3 in PDB entry 7b0y, assembly 1, side view.
Small nuclear ribonucleoprotein Sm D3 in PDB entry 7b0y, assembly 1, top view.
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Small nuclear ribonucleoprotein-associated protein
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
Pfam: LSM domain
InterPro:
Small nuclear ribonucleoprotein-associated protein in PDB entry 7b0y, assembly 1, front view.
Small nuclear ribonucleoprotein-associated protein in PDB entry 7b0y, assembly 1, side view.
Small nuclear ribonucleoprotein-associated protein in PDB entry 7b0y, assembly 1, top view.
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Small nuclear ribonucleoprotein Sm D1
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
Pfam: LSM domain
InterPro:
Small nuclear ribonucleoprotein Sm D1 in PDB entry 7b0y, assembly 1, front view.
Small nuclear ribonucleoprotein Sm D1 in PDB entry 7b0y, assembly 1, side view.
Small nuclear ribonucleoprotein Sm D1 in PDB entry 7b0y, assembly 1, top view.
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DNA chain N
Name: Non-template DNA
Representative chains: N
Length: 48 nucleotides
Theoretical weight: 14.93 KDa
Non-template DNA in PDB entry 7b0y, assembly 1, front view.
Non-template DNA in PDB entry 7b0y, assembly 1, side view.
Non-template DNA in PDB entry 7b0y, assembly 1, top view.
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DNA chain T
Name: Template DNA
Representative chains: T
Length: 48 nucleotides
Theoretical weight: 14.67 KDa
Template DNA in PDB entry 7b0y, assembly 1, front view.
Template DNA in PDB entry 7b0y, assembly 1, side view.
Template DNA in PDB entry 7b0y, assembly 1, top view.
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RNA chain P
Name: 145-nt RNA
Representative chains: P
Length: 145 nucleotides
Theoretical weight: 46.78 KDa
145-nt RNA in PDB entry 7b0y, assembly 1, front view.
145-nt RNA in PDB entry 7b0y, assembly 1, side view.
145-nt RNA in PDB entry 7b0y, assembly 1, top view.
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RNA chain a
Name: U1 snRNA
Representative chains: a
Length: 164 nucleotides
Theoretical weight: 52.7 KDa
Rfam: U1 spliceosomal RNA
U1 snRNA in PDB entry 7b0y, assembly 1, front view.
U1 snRNA in PDB entry 7b0y, assembly 1, side view.
U1 snRNA in PDB entry 7b0y, assembly 1, top view.
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