PDBe 3pgw

X-ray diffraction
4.4Å resolution

Crystal structure of human U1 snRNP

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 11-mer (preferred)
Entry contents:
9 distinct polypeptide molecules
1 distinct DNA molecule
1 distinct RNA molecule
Macromolecules (11 distinct):
U1 small nuclear ribonucleoprotein A Chains: A, P
Molecule details ›
Chains: A, P
Length: 282 amino acids
Theoretical weight: 31.32 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: NEW P09012 (Residues: 1-282; Coverage: 100%)
Gene name: SNRPA
Sequence domains: RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain)
U1 small nuclear ribonucleoprotein 70 kDa Chains: L, S
Molecule details ›
Chains: L, S
Length: 437 amino acids
Theoretical weight: 51.68 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: NEW P08621 (Residues: 1-437; Coverage: 100%)
Gene names: RNPU1Z, RPU1, SNRNP70, SNRP70, U1AP1
Sequence domains:
Small nuclear ribonucleoprotein Sm D3 Chains: W, Z
Molecule details ›
Chains: W, Z
Length: 126 amino acids
Theoretical weight: 13.94 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: NEW P62318 (Residues: 1-126; Coverage: 100%)
Gene name: SNRPD3
Sequence domains: LSM domain
Small nuclear ribonucleoprotein-associated proteins B and B' Chains: B, Q
Molecule details ›
Chains: B, Q
Length: 231 amino acids
Theoretical weight: 23.69 KDa
Source organism: Homo sapiens
UniProt: Gene names: COD, SNRPB, SNRPB1
Sequence domains: LSM domain
Small nuclear ribonucleoprotein Sm D1 Chains: U, X
Molecule details ›
Chains: U, X
Length: 119 amino acids
Theoretical weight: 13.31 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: NEW P62314 (Residues: 1-119; Coverage: 100%)
Gene name: SNRPD1
Sequence domains: LSM domain
Small nuclear ribonucleoprotein Sm D2 Chains: V, Y
Molecule details ›
Chains: V, Y
Length: 118 amino acids
Theoretical weight: 13.55 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: NEW P62316 (Residues: 1-118; Coverage: 100%)
Gene names: SNRPD1, SNRPD2
Sequence domains: LSM domain
Small nuclear ribonucleoprotein F Chains: F, I
Molecule details ›
Chains: F, I
Length: 86 amino acids
Theoretical weight: 9.73 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: NEW P62306 (Residues: 1-86; Coverage: 100%)
Gene names: PBSCF, SNRPF
Sequence domains: LSM domain
Small nuclear ribonucleoprotein E Chains: E, H
Molecule details ›
Chains: E, H
Length: 92 amino acids
Theoretical weight: 10.82 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: NEW P62304 (Residues: 1-92; Coverage: 100%)
Gene name: SNRPE
Sequence domains: LSM domain
Small nuclear ribonucleoprotein G Chains: G, J
Molecule details ›
Chains: G, J
Length: 76 amino acids
Theoretical weight: 8.51 KDa
Source organism: Homo sapiens
UniProt:
  • Canonical: NEW P62308 (Residues: 1-76; Coverage: 100%)
Gene names: PBSCG, SNRPG
Sequence domains: LSM domain
DNA 5'-D(*AP*GP*GP*TP*AP*AP*GP*TP*A)-3' Chains: D, M
Molecule details ›
Chains: D, M
Length: 9 nucleotides
Theoretical weight: 2.8 KDa
U1 snRNA Chains: N, R
Molecule details ›
Chains: N, R
Length: 164 nucleotides
Theoretical weight: 52.7 KDa
Sequence domains: U1 spliceosomal RNA

Ligands and Environments

No bound ligands

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06SA
Spacegroup: C2
Unit cell:
a: 358.42Å b: 88.22Å c: 150.9Å
α: 90° β: 111.88° γ: 90°
R-values:
R R work R free
0.299 0.299 0.348