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Crystal structure of human U1 snRNP

X-ray diffraction
4.4Å resolution
PDB entry 3pgw coloured by chain, front view.
PDB entry 3pgw coloured by chain, side view.
PDB entry 3pgw coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero undecamer (preferred)
Entry contents: 9 distinct polypeptide molecules
1 distinct DNA molecule
1 distinct RNA molecule

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero undecamer
PDBe Complex ID: PDB-CPX-116696
Assembly 2
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Multimeric state: hetero undecamer
PDBe Complex ID: PDB-CPX-116696

Macromolecules

U1 small nuclear ribonucleoprotein A
Chains: A, P
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 3pgw, assembly 1, front view.
U1 small nuclear ribonucleoprotein A in PDB entry 3pgw, assembly 1, side view.
U1 small nuclear ribonucleoprotein A in PDB entry 3pgw, assembly 1, top view.
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U1 small nuclear ribonucleoprotein 70 kDa
Chains: L, S
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 3pgw, assembly 1, front view.
U1 small nuclear ribonucleoprotein 70 kDa in PDB entry 3pgw, assembly 1, side view.
U1 small nuclear ribonucleoprotein 70 kDa in PDB entry 3pgw, assembly 1, top view.
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Small nuclear ribonucleoprotein Sm D3
Chains: W, Z
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 3pgw, assembly 1, front view.
Small nuclear ribonucleoprotein Sm D3 in PDB entry 3pgw, assembly 1, side view.
Small nuclear ribonucleoprotein Sm D3 in PDB entry 3pgw, assembly 1, top view.
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Small nuclear ribonucleoprotein-associated proteins B and B'
Chains: B, Q
Length: 231 amino acids
Theoretical weight: 23.69 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: P14678 (Residues: 1-229; Coverage: 95%)
Gene names: COD, SNRPB, SNRPB1
Pfam: LSM domain
InterPro:
Small nuclear ribonucleoprotein-associated proteins B and B' in PDB entry 3pgw, assembly 1, front view.
Small nuclear ribonucleoprotein-associated proteins B and B' in PDB entry 3pgw, assembly 1, side view.
Small nuclear ribonucleoprotein-associated proteins B and B' in PDB entry 3pgw, assembly 1, top view.
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Small nuclear ribonucleoprotein Sm D1
Chains: U, X
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 3pgw, assembly 1, front view.
Small nuclear ribonucleoprotein Sm D1 in PDB entry 3pgw, assembly 1, side view.
Small nuclear ribonucleoprotein Sm D1 in PDB entry 3pgw, assembly 1, top view.
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Small nuclear ribonucleoprotein Sm D2
Chains: V, Y
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 3pgw, assembly 1, front view.
Small nuclear ribonucleoprotein Sm D2 in PDB entry 3pgw, assembly 1, side view.
Small nuclear ribonucleoprotein Sm D2 in PDB entry 3pgw, assembly 1, top view.
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Small nuclear ribonucleoprotein F
Chains: F, I
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 3pgw, assembly 1, front view.
Small nuclear ribonucleoprotein F in PDB entry 3pgw, assembly 1, side view.
Small nuclear ribonucleoprotein F in PDB entry 3pgw, assembly 1, top view.
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Small nuclear ribonucleoprotein E
Chains: E, H
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 3pgw, assembly 1, front view.
Small nuclear ribonucleoprotein E in PDB entry 3pgw, assembly 1, side view.
Small nuclear ribonucleoprotein E in PDB entry 3pgw, assembly 1, top view.
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Small nuclear ribonucleoprotein G
Chains: G, J
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 3pgw, assembly 1, front view.
Small nuclear ribonucleoprotein G in PDB entry 3pgw, assembly 1, side view.
Small nuclear ribonucleoprotein G in PDB entry 3pgw, assembly 1, top view.
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DNA chains D, M
Name: DNA 5'-D(*AP*GP*GP*TP*AP*AP*GP*TP*A)-3'
Representative chains: D, M
Length: 9 nucleotides
Theoretical weight: 2.8 KDa
DNA 5'-D(*AP*GP*GP*TP*AP*AP*GP*TP*A)-3' in PDB entry 3pgw, assembly 1, front view.
DNA 5'-D(*AP*GP*GP*TP*AP*AP*GP*TP*A)-3' in PDB entry 3pgw, assembly 1, side view.
DNA 5'-D(*AP*GP*GP*TP*AP*AP*GP*TP*A)-3' in PDB entry 3pgw, assembly 1, top view.
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RNA chains N, R
Name: U1 snRNA
Representative chains: N, R
Length: 164 nucleotides
Theoretical weight: 52.7 KDa
Rfam: U1 spliceosomal RNA
U1 snRNA in PDB entry 3pgw, assembly 1, front view.
U1 snRNA in PDB entry 3pgw, assembly 1, side view.
U1 snRNA in PDB entry 3pgw, assembly 1, top view.
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