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Cocrystal structure of a tyrosyl-tRNA synthetase splicing factor with a group I intron RNA

X-ray diffraction
4.5Å resolution
PDB entry 2rkj coloured by chain, front view.
PDB entry 2rkj coloured by chain, side view.
PDB entry 2rkj coloured by chain, top view.
Source organisms:
Assembly composition:
hetero tetramer (preferred)
Entry contents: 1 distinct polypeptide molecule
2 distinct RNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: Tyrosine--tRNA ligase, mitochondrial and RNA
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Multimeric state: hetero tetramer
Accessible surface area: 65633.71 Å2
Buried surface area: 6730.25 Å2
Dissociation area: 536.53 Å2
Dissociation energy (ΔGdiss): 17.65 kcal/mol
Dissociation entropy (TΔSdiss): 7.47 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-250172
Assembly 2
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Assembly Name: Tyrosine--tRNA ligase, mitochondrial and RNA
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Multimeric state: hetero tetramer
Accessible surface area: 65629.15 Å2
Buried surface area: 6763.59 Å2
Dissociation area: 539.22 Å2
Dissociation energy (ΔGdiss): 17.62 kcal/mol
Dissociation entropy (TΔSdiss): 7.47 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-250172
Assembly 3
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Assembly Name: Tyrosine--tRNA ligase, mitochondrial and RNA
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Multimeric state: hetero tetramer
Accessible surface area: 65663.4 Å2
Buried surface area: 6745.06 Å2
Dissociation area: 536.57 Å2
Dissociation energy (ΔGdiss): 17.24 kcal/mol
Dissociation entropy (TΔSdiss): 7.47 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-250172
Assembly 4
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Assembly Name: Tyrosine--tRNA ligase, mitochondrial and RNA
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Multimeric state: hetero tetramer
Accessible surface area: 65644.28 Å2
Buried surface area: 6736.71 Å2
Dissociation area: 538.34 Å2
Dissociation energy (ΔGdiss): 17.14 kcal/mol
Dissociation entropy (TΔSdiss): 7.47 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-250172

Macromolecules

Tyrosine--tRNA ligase, mitochondrial
Chains: A, B, E, F, I, J, M, N
Length: 392 amino acids
Theoretical weight: 44.92 KDa
Source organism: Neurospora crassa
Expression system: Escherichia coli
UniProt:
  • Canonical: P12063 (Residues: 33-423; Coverage: 58%)
Gene names: B18P24.070, NCU03030, cyt-18
Pfam: tRNA synthetases class I (W and Y)
InterPro:
Tyrosine--tRNA ligase, mitochondrial in PDB entry 2rkj, assembly 1, front view.
Tyrosine--tRNA ligase, mitochondrial in PDB entry 2rkj, assembly 1, side view.
Tyrosine--tRNA ligase, mitochondrial in PDB entry 2rkj, assembly 1, top view.
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RNA chains C, G, K, O
Name: RNA (238-MER)
Representative chains: C, G, K, O
Source organism: Staphylococcus virus Twort [55510]
Expression system: Staphylococcus virus Twort [55510]
Length: 246 nucleotides
Theoretical weight: 79.49 KDa
Rfam: Group I catalytic intron
RNA (238-MER) in PDB entry 2rkj, assembly 1, front view.
RNA (238-MER) in PDB entry 2rkj, assembly 1, side view.
RNA (238-MER) in PDB entry 2rkj, assembly 1, top view.
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RNA chains D, H, L, P
Name: RNA (5'-R(P*GP*CP*UP*U)-3')
Representative chains: D, H, L, P
Source organism: Neurospora crassa [5141]
Expression system: Not provided
Length: 4 nucleotides
Theoretical weight: 1.22 KDa
RNA (5'-R(P*GP*CP*UP*U)-3') in PDB entry 2rkj, assembly 1, front view.
RNA (5'-R(P*GP*CP*UP*U)-3') in PDB entry 2rkj, assembly 1, side view.
RNA (5'-R(P*GP*CP*UP*U)-3') in PDB entry 2rkj, assembly 1, top view.
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