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

X-ray diffraction
3.28Å resolution
PDB entry 5xjq coloured by chain, front view.
PDB entry 5xjq coloured by chain, side view.
PDB entry 5xjq coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
hetero heptamer (preferred)
Entry contents: 7 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero heptamer
Accessible surface area: 27984.93 Å2
Buried surface area: 12995.11 Å2
Dissociation area: 794.05 Å2
Dissociation energy (ΔGdiss): 3.29 kcal/mol
Dissociation entropy (TΔSdiss): 10.85 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-127184

Macromolecules

Gem-associated protein 2
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
Pfam: Survival motor neuron (SMN) interacting protein 1 (SIP1)
InterPro:
Gem-associated protein 2 in PDB entry 5xjq, assembly 1, front view.
Gem-associated protein 2 in PDB entry 5xjq, assembly 1, side view.
Gem-associated protein 2 in PDB entry 5xjq, assembly 1, top view.
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Small nuclear ribonucleoprotein Sm D1
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
Pfam: LSM domain
InterPro:
CATH: SH3 type barrels.
Small nuclear ribonucleoprotein Sm D1 in PDB entry 5xjq, assembly 1, front view.
Small nuclear ribonucleoprotein Sm D1 in PDB entry 5xjq, assembly 1, side view.
Small nuclear ribonucleoprotein Sm D1 in PDB entry 5xjq, assembly 1, top view.
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Small nuclear ribonucleoprotein Sm D2
Chain: B
Length: 118 amino acids
Theoretical weight: 13.55 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62316 (Residues: 1-118; Coverage: 100%)
Gene names: SNRPD1, SNRPD2
Pfam: LSM domain
InterPro:
CATH: SH3 type barrels.
Small nuclear ribonucleoprotein Sm D2 in PDB entry 5xjq, assembly 1, front view.
Small nuclear ribonucleoprotein Sm D2 in PDB entry 5xjq, assembly 1, side view.
Small nuclear ribonucleoprotein Sm D2 in PDB entry 5xjq, assembly 1, top view.
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Small nuclear ribonucleoprotein E
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
Pfam: LSM domain
InterPro:
CATH: SH3 type barrels.
Small nuclear ribonucleoprotein E in PDB entry 5xjq, assembly 1, front view.
Small nuclear ribonucleoprotein E in PDB entry 5xjq, assembly 1, side view.
Small nuclear ribonucleoprotein E in PDB entry 5xjq, assembly 1, top view.
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Small nuclear ribonucleoprotein F
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
Pfam: LSM domain
InterPro:
CATH: SH3 type barrels.
Small nuclear ribonucleoprotein F in PDB entry 5xjq, assembly 1, front view.
Small nuclear ribonucleoprotein F in PDB entry 5xjq, assembly 1, side view.
Small nuclear ribonucleoprotein F in PDB entry 5xjq, assembly 1, top view.
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Small nuclear ribonucleoprotein G
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
Pfam: LSM domain
InterPro:
CATH: SH3 type barrels.
Small nuclear ribonucleoprotein G in PDB entry 5xjq, assembly 1, front view.
Small nuclear ribonucleoprotein G in PDB entry 5xjq, assembly 1, side view.
Small nuclear ribonucleoprotein G in PDB entry 5xjq, assembly 1, top view.
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Survival motor neuron protein
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
Pfam: Survival Motor Neuron, Gemin2-binding domain
InterPro: Survival motor neuron, Tudor domain
Survival motor neuron protein in PDB entry 5xjq, assembly 1, front view.
Survival motor neuron protein in PDB entry 5xjq, assembly 1, side view.
Survival motor neuron protein in PDB entry 5xjq, assembly 1, top view.
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