› 4v98

X-ray diffraction
3.1Å resolution

The 8S snRNP Assembly Intermediate

Released:
DOI: 10.2210/pdb4v98/pdb
PDB entry 4v98 coloured by chain, front view.
PDB entry 4v98 coloured by chain, side view.
PDB entry 4v98 coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of assembly chaperone- mediated snRNP formation.
Grimm C, Chari A, Pelz JP, Kuper J, Kisker C, Diederichs K, Stark H, Schindelin H, Fischer U
Mol Cell 49 692-703 (2013)
PMID: 23333303

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-106793 (preferred)
Entry contents:
8 distinct polypeptide molecules
Macromolecules (8 distinct):
Small nuclear ribonucleoprotein Sm D1 Chains: AA, AI, AQ, AY, Ag, Ao, Aw, BA, BI, BQ, BY, Bg, Bo, Bw, CA, CI, CQ, CY, Cg, Co
Molecule details ›
Chains: AA, AI, AQ, AY, Ag, Ao, Aw, BA, BI, BQ, BY, Bg, Bo, Bw, CA, CI, CQ, CY, Cg, Co
Length: 119 amino acids
Theoretical weight: 13.31 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P62314 (Residues: 1-119; Coverage: 100%)
Gene name: SNRPD1
Sequence domains: LSM domain
Small nuclear ribonucleoprotein Sm D2 Chains: AB, AJ, AR, AZ, Ah, Ap, Ax, BB, BJ, BR, BZ, Bh, Bp, Bx, CB, CJ, CR, CZ, Ch, Cp
Molecule details ›
Chains: AB, AJ, AR, AZ, Ah, Ap, Ax, BB, BJ, BR, BZ, Bh, Bp, Bx, CB, CJ, CR, CZ, Ch, Cp
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 E Chains: AC, AK, AS, Aa, Ai, Aq, Ay, BC, BK, BS, Ba, Bi, Bq, By, CC, CK, CS, Ca, Ci, Cq
Molecule details ›
Chains: AC, AK, AS, Aa, Ai, Aq, Ay, BC, BK, BS, Ba, Bi, Bq, By, CC, CK, CS, Ca, Ci, Cq
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 F Chains: AD, AL, AT, Ab, Aj, Ar, Az, BD, BL, BT, Bb, Bj, Br, Bz, CD, CL, CT, Cb, Cj, Cr
Molecule details ›
Chains: AD, AL, AT, Ab, Aj, Ar, Az, BD, BL, BT, Bb, Bj, Br, Bz, CD, CL, CT, Cb, Cj, Cr
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
Survival motor neuron protein Chains: A1, AE, AM, AU, Ac, Ak, As, B1, BE, BM, BU, Bc, Bk, Bs, CE, CM, CU, Cc, Ck, Cs
Molecule details ›
Chains: A1, AE, AM, AU, Ac, Ak, As, B1, BE, BM, BU, Bc, Bk, Bs, CE, CM, CU, Cc, Ck, Cs
Length: 124 amino acids
Theoretical weight: 13.36 KDa
Source organism: Drosophila melanogaster
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9VV74 (Residues: 1-122; Coverage: 54%)
Gene names: CG16725, Smn
Sequence domains: Survival motor neuron protein (SMN), Tudor domain
Protein Gemin2 Chains: A2, AF, AN, AV, Ad, Al, At, B2, BF, BN, BV, Bd, Bl, Bt, CF, CN, CV, Cd, Cl, Ct
Molecule details ›
Chains: A2, AF, AN, AV, Ad, Al, At, B2, BF, BN, BV, Bd, Bl, Bt, CF, CN, CV, Cd, Cl, Ct
Length: 247 amino acids
Theoretical weight: 28.91 KDa
Source organism: Drosophila melanogaster
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q9VVX0 (Residues: 1-245; Coverage: 100%)
Gene names: CG10419, Gem2
Sequence domains: Survival motor neuron (SMN) interacting protein 1 (SIP1)
Methylosome subunit pICln Chains: A3, AG, AO, AW, Ae, Am, Au, B3, BG, BO, BW, Be, Bm, Bu, CG, CO, CW, Ce, Cm, Cu
Molecule details ›
Chains: A3, AG, AO, AW, Ae, Am, Au, B3, BG, BO, BW, Be, Bm, Bu, CG, CO, CW, Ce, Cm, Cu
Length: 186 amino acids
Theoretical weight: 20.6 KDa
Source organism: Drosophila melanogaster
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: A1ZAW5 (Residues: 1-180; Coverage: 84%)
Gene names: CG4924, icln
Sequence domains: Regulator of volume decrease after cellular swelling
Small nuclear ribonucleoprotein G Chains: A4, AH, AP, AX, Af, An, Av, B4, BH, BP, BX, Bf, Bn, Bv, CH, CP, CX, Cf, Cn, Cv
Molecule details ›
Chains: A4, AH, AP, AX, Af, An, Av, B4, BH, BP, BX, Bf, Bn, Bv, CH, CP, CX, Cf, Cn, Cv
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

Ligands and Environments

1 bound ligand:
Ligand SO4 10 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: P21
Unit cell:
a: 150.93Å b: 356.81Å c: 230.75Å
α: 90° β: 97.31° γ: 90°
R-values:
R R work R free
0.234 0.232 0.256
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

15 review citations

A day in the life of the spliceosome.
Matera et al. (2014)
14 more

3 mentions without citation

A missense mutation in SNRPE linked to non-syndromal microcephaly interferes with U snRNP assembly and pre-mRNA splicing.
Chen et al. (2019)
2 more