› 5xjt

X-ray diffraction
2.92Å resolution

Crystal Structure of the Gemin2-binding domain of SMN, Gemin2 in Complex with SmD1(1-82)/D2.R61A/F/E/G from Human

Released:
DOI: 10.2210/pdb5xjt/pdb
PDB entry 5xjt coloured by chain, front view.
PDB entry 5xjt coloured by chain, side view.
PDB entry 5xjt coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Yi H, Zhang R

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero heptamer (preferred)
PDBe Complex ID:
PDB-CPX-127184 (preferred)
Entry contents:
7 distinct polypeptide molecules
Macromolecules (7 distinct):
Gem-associated protein 2 Chain: 2
Molecule details ›
Chain: 2
Length: 280 amino acids
Theoretical weight: 31.62 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O14893 (Residues: 1-280; Coverage: 100%)
Gene names: GEMIN2, SIP1
Sequence domains: Survival motor neuron (SMN) interacting protein 1 (SIP1)
Small nuclear ribonucleoprotein Sm D1 Chain: A
Molecule details ›
Chain: A
Length: 82 amino acids
Theoretical weight: 9.3 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62314 (Residues: 1-82; Coverage: 69%)
Gene name: SNRPD1
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein Sm D2 Chain: B
Molecule details ›
Chain: B
Length: 118 amino acids
Theoretical weight: 13.47 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
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 Chain: E
Molecule details ›
Chain: E
Length: 92 amino acids
Theoretical weight: 10.82 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62304 (Residues: 1-92; Coverage: 100%)
Gene name: SNRPE
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein F Chain: F
Molecule details ›
Chain: F
Length: 86 amino acids
Theoretical weight: 9.73 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62306 (Residues: 1-86; Coverage: 100%)
Gene names: PBSCF, SNRPF
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Small nuclear ribonucleoprotein G Chain: G
Molecule details ›
Chain: G
Length: 76 amino acids
Theoretical weight: 8.51 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62308 (Residues: 1-76; Coverage: 100%)
Gene names: PBSCG, SNRPG
Sequence domains: LSM domain
Structure domains: SH3 type barrels.
Survival motor neuron protein Chain: M
Molecule details ›
Chain: M
Length: 37 amino acids
Theoretical weight: 4.05 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q16637 (Residues: 26-62; Coverage: 13%)
Gene names: SMN, SMN1, SMN2, SMNC, SMNT
Sequence domains: Survival Motor Neuron, Gemin2-binding domain

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P212121
Unit cell:
a: 82.64Å b: 84.76Å c: 114.33Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.203 0.199 0.281
Expression system: Escherichia coli

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