› 4wzj

X-ray diffraction
3.6Å resolution

Spliceosomal U4 snRNP core domain

Released:
DOI: 10.2210/pdb4wzj/pdb
PDB entry 4wzj coloured by chain, front view.
PDB entry 4wzj coloured by chain, side view.
PDB entry 4wzj coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of the spliceosomal U4 snRNP core domain and its implication for snRNP biogenesis.
Leung AK, Nagai K, Li J
Nature 473 536-9 (2011)
PMID: 21516107

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
PDBe Complex ID:
PDB-CPX-147023 (preferred)
Entry contents:
7 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (8 distinct):
Small nuclear ribonucleoprotein Sm D3 Chains: A, AA, AAA, AAAA, H, HH, HHH, HHHH, O, OO, OOO, OOOO
Molecule details ›
Chains: A, AA, AAA, AAAA, H, HH, HHH, HHHH, O, OO, OOO, OOOO
Length: 125 amino acids
Theoretical weight: 13.78 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P62318 (Residues: 1-125; Coverage: 99%)
Gene name: SNRPD3
Sequence domains: LSM domain
Small nuclear ribonucleoprotein-associated proteins B and B' Chains: B, BB, BBB, BBBB, I, II, III, IIII, P, PP, PPP, PPPP
Molecule details ›
Chains: B, BB, BBB, BBBB, I, II, III, IIII, P, PP, PPP, PPPP
Length: 95 amino acids
Theoretical weight: 10.91 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P14678 (Residues: 1-95; Coverage: 40%)
Gene names: COD, SNRPB, SNRPB1
Sequence domains: LSM domain
Small nuclear ribonucleoprotein Sm D1 Chains: C, CC, CCC, CCCC, J, JJ, JJJ, JJJJ, Q, QQ, QQQ, QQQQ
Molecule details ›
Chains: C, CC, CCC, CCCC, J, JJ, JJJ, JJJJ, Q, QQ, QQQ, QQQQ
Length: 118 amino acids
Theoretical weight: 13.15 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62314 (Residues: 1-118; Coverage: 99%)
Gene name: SNRPD1
Sequence domains: LSM domain
Small nuclear ribonucleoprotein Sm D2 Chains: D, DD, DDD, DDDD, K, KK, KKK, KKKK, R, RR, RRR, RRRR
Molecule details ›
Chains: D, DD, DDD, DDDD, K, KK, KKK, KKKK, R, RR, RRR, RRRR
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
Small nuclear ribonucleoprotein F Chains: F, FF, FFF, FFFF, M, MM, MMM, MMMM, T, TT, TTT, TTTT
Molecule details ›
Chains: F, FF, FFF, FFFF, M, MM, MMM, MMMM, T, TT, TTT, TTTT
Length: 86 amino acids
Theoretical weight: 9.73 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62306 (Residues: 1-86; Coverage: 100%)
Gene names: PBSCF, SNRPF
Sequence domains: LSM domain
Small nuclear ribonucleoprotein E Chains: E, EE, EEE, EEEE, L, LL, LLL, LLLL, S, SS, SSS, SSSS
Molecule details ›
Chains: E, EE, EEE, EEEE, L, LL, LLL, LLLL, S, SS, SSS, SSSS
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
Small nuclear ribonucleoprotein G Chains: G, GG, GGG, GGGG, N, NN, NNN, NNNN, U, UU, UUU, UUUU
Molecule details ›
Chains: G, GG, GGG, GGGG, N, NN, NNN, NNNN, U, UU, UUU, UUUU
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
U4 small nuclear RNA variant: Native sequence 85-145, of which nucleotides 97-104 are replaced with GAAA tetraloop and nucleotides 134-137 are replaced with GAAA tetraloop receptor. Chains: V, VV, VVV, VVVV, X, XX, XXX, XXXX, Y, YY, YYY, YYYY
Molecule details ›
Chains: V, VV, VVV, VVVV, X, XX, XXX, XXXX, Y, YY, YYY, YYYY
Length: 68 nucleotides
Theoretical weight: 21.96 KDa

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SRS BEAMLINE PX9.6
Spacegroup: P31
Unit cell:
a: 248.01Å b: 248.01Å c: 251.94Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.179 0.177 0.224
Expression systems:
  • Escherichia coli K-12
  • Escherichia coli BL21(DE3)

Quick links

Citations

22 review citations

The noncoding RNA revolution-trashing old rules to forge new ones.
Cech et al. (2014)
21 more

10 mentions without citation

An RNA-centric historical narrative around the Protein Data Bank.
Westhof et al. (2021)
9 more