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RNA Recognition and Cleavage by an Splicing Endonuclease

X-ray diffraction
2.85Å resolution
PDB entry 2gjw coloured by chain, front view.
PDB entry 2gjw coloured by chain, side view.
PDB entry 2gjw coloured by chain, top view.
Source organism: Archaeoglobus fulgidus
Assembly composition:
hetero pentamer (preferred)
Entry contents: 1 distinct polypeptide molecule
3 distinct RNA molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: tRNA-splicing endonuclease and RNA
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Multimeric state: hetero pentamer
Accessible surface area: 30093.77 Å2
Buried surface area: 11588.03 Å2
Dissociation area: 1,806.67 Å2
Dissociation energy (ΔGdiss): 23.69 kcal/mol
Dissociation entropy (TΔSdiss): 11.51 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-128118
Assembly 2
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Assembly Name: tRNA-splicing endonuclease and RNA
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Multimeric state: hetero pentamer
Accessible surface area: 30459.22 Å2
Buried surface area: 11567.49 Å2
Dissociation area: 1,880.21 Å2
Dissociation energy (ΔGdiss): 21.67 kcal/mol
Dissociation entropy (TΔSdiss): 11.67 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-128118

Macromolecules

tRNA-splicing endonuclease
Chains: A, B, C, D
Length: 313 amino acids
Theoretical weight: 37.11 KDa
Source organism: Archaeoglobus fulgidus
Expression system: Escherichia coli
UniProt:
  • Canonical: O29362 (Residues: 2-305; Coverage: 100%)
Gene names: AF_0900, endA
Pfam:
InterPro:
CATH:
SCOP:
tRNA-splicing endonuclease in PDB entry 2gjw, assembly 1, front view.
tRNA-splicing endonuclease in PDB entry 2gjw, assembly 1, side view.
tRNA-splicing endonuclease in PDB entry 2gjw, assembly 1, top view.
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RNA chains E, I
Name: 5'-R(*GP*CP*GP*AP*CP*CP*GP*AP*CP*CP*AP*(DU)P*AP*GP*CP*UP*GP*CP*A)-3'
Representative chains: E, I
Source organism: Archaeoglobus fulgidus [2234]
Expression system: Not provided
Length: 19 nucleotides
Theoretical weight: 6.06 KDa
5'-R(*GP*CP*GP*AP*CP*CP*GP*AP*CP*CP*AP*(DU)P*AP*GP*CP*UP*GP*CP*A)-3' in PDB entry 2gjw, assembly 1, front view.
5'-R(*GP*CP*GP*AP*CP*CP*GP*AP*CP*CP*AP*(DU)P*AP*GP*CP*UP*GP*CP*A)-3' in PDB entry 2gjw, assembly 1, side view.
5'-R(*GP*CP*GP*AP*CP*CP*GP*AP*CP*CP*AP*(DU)P*AP*GP*CP*UP*GP*CP*A)-3' in PDB entry 2gjw, assembly 1, top view.
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RNA chains F, J
Name: 5'-R(*UP*GP*CP*AP*GP*CP*GP*GP*UP*CP*AP*(A23))-3'
Representative chains: F, J
Source organism: Archaeoglobus fulgidus [2234]
Expression system: Not provided
Length: 12 nucleotides
Theoretical weight: 3.91 KDa
5'-R(*UP*GP*CP*AP*GP*CP*GP*GP*UP*CP*AP*(A23))-3' in PDB entry 2gjw, assembly 1, front view.
5'-R(*UP*GP*CP*AP*GP*CP*GP*GP*UP*CP*AP*(A23))-3' in PDB entry 2gjw, assembly 1, side view.
5'-R(*UP*GP*CP*AP*GP*CP*GP*GP*UP*CP*AP*(A23))-3' in PDB entry 2gjw, assembly 1, top view.
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RNA chains H, L
Name: 5'-R(*AP*GP*GP*UP*CP*GP*C)-3'
Representative chains: H, L
Source organism: Archaeoglobus fulgidus [2234]
Expression system: Not provided
Length: 7 nucleotides
Theoretical weight: 2.24 KDa
5'-R(*AP*GP*GP*UP*CP*GP*C)-3' in PDB entry 2gjw, assembly 1, front view.
5'-R(*AP*GP*GP*UP*CP*GP*C)-3' in PDB entry 2gjw, assembly 1, side view.
5'-R(*AP*GP*GP*UP*CP*GP*C)-3' in PDB entry 2gjw, assembly 1, top view.
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