PDBe 4pjo

X-ray diffraction
3.3Å resolution

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero 11-mer (preferred)
Entry contents:
9 distinct polypeptide molecules
2 distinct RNA molecules
Macromolecules (11 distinct):
Small nuclear ribonucleoprotein Sm D3 Chains: A, O, a, o
Molecule details ›
Chains: A, O, a, o
Length: 126 amino acids
Theoretical weight: 13.94 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62318 (Residues: 1-126; Coverage: 100%)
Gene name: SNRPD3
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein-associated proteins B and B' Chains: B, P, b, p
Molecule details ›
Chains: B, P, b, p
Length: 95 amino acids
Theoretical weight: 10.91 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P14678 (Residues: 1-95; Coverage: 40%)
Gene names: COD, SNRPB, SNRPB1
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein Sm D1 Chains: C, Q, c, q
Molecule details ›
Chains: C, Q, c, q
Length: 91 amino acids
Theoretical weight: 10.03 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62314 (Residues: 2-85; Coverage: 71%)
Gene name: SNRPD1
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein Sm D2 Chains: D, R, d, r
Molecule details ›
Chains: D, R, d, r
Length: 118 amino acids
Theoretical weight: 13.55 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62316 (Residues: 1-118; Coverage: 100%)
Gene names: SNRPD1, SNRPD2
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein E Chains: E, S, e, s
Molecule details ›
Chains: E, S, e, s
Length: 92 amino acids
Theoretical weight: 10.82 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62304 (Residues: 1-92; Coverage: 100%)
Gene name: SNRPE
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein F Chains: F, T, f, t
Molecule details ›
Chains: F, T, f, t
Length: 75 amino acids
Theoretical weight: 8.37 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62306 (Residues: 1-75; Coverage: 87%)
Gene names: PBSCF, SNRPF
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein G Chains: G, U, g, u
Molecule details ›
Chains: G, U, g, u
Length: 76 amino acids
Theoretical weight: 8.51 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62308 (Residues: 1-76; Coverage: 100%)
Gene names: PBSCG, SNRPG
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
U1 small nuclear ribonucleoprotein 70 kDa Chains: K, N, k, n
Molecule details ›
Chains: K, N, k, n
Length: 60 amino acids
Theoretical weight: 6.86 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P08621 (Residues: 2-60; Coverage: 14%)
Gene names: RNPU1Z, RPU1, SNRNP70, SNRP70, U1AP1
U1 small nuclear ribonucleoprotein C Chains: L, M, l, m
Molecule details ›
Chains: L, M, l, m
Length: 61 amino acids
Theoretical weight: 7.28 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli B
UniProt:
  • Canonical: P09234 (Residues: 1-61; Coverage: 38%)
Gene name: SNRPC
Sequence domains: U1 zinc finger
U1 RNA variant (48-MER) with 4-helix junction replaced by kissing loop (HIV-1 (Mal) DIS) and shorter stem-loop 4. Chains: 1, 2, 3, 4
Molecule details ›
Chains: 1, 2, 3, 4
Length: 60 nucleotides
Theoretical weight: 19.58 KDa
RNA (5'-R(*AP*GP*GP*UP*AP*AP*GP*UP*CP*C)-3') Chains: X, Y, x, y
Molecule details ›
Chains: X, Y, x, y
Length: 10 nucleotides
Theoretical weight: 3.2 KDa

Ligands and Environments

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I02
Spacegroup: P212121
Unit cell:
a: 120.359Å b: 172.627Å c: 256.322Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.209 0.207 0.255
Expression systems:
  • Escherichia coli
  • Escherichia coli BL21(DE3)
  • Escherichia coli B