› 6oe7

X-ray diffraction
2.2Å resolution

Crystal structure of HMCES cross-linked to DNA abasic site

Released:
DOI: 10.2210/pdb6oe7/pdb
PDB entry 6oe7 coloured by chain, front view.
PDB entry 6oe7 coloured by chain, side view.
PDB entry 6oe7 coloured by chain, top view.
Source organisms:
Primary publication:
Structural basis of HMCES interactions with abasic DNA and multivalent substrate recognition.
Halabelian L, Ravichandran M, Li Y, Zeng H, Rao A, Aravind L, Arrowsmith CH
Nat Struct Mol Biol 26 607-612 (2019)
PMID: 31235913

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-120381 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
Abasic site processing protein HMCES Chain: A
Molecule details ›
Chain: A
Length: 276 amino acids
Theoretical weight: 31.67 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96FZ2 (Residues: 2-270; Coverage: 76%)
Gene names: C3orf37, DC12, HMCES, SRAPD1
Sequence domains: SOS response associated peptidase (SRAP)
Structure domains: SOS response associated peptidase-like
DNA (5'-D(*GP*TP*CP*TP*GP*G)-3') Chain: C
Molecule details ›
Chain: C
Length: 6 nucleotides
Theoretical weight: 1.84 KDa
Source organism: synthetic construct
Expression system: Not provided
DNA (5'-D(*CP*CP*AP*GP*AP*CP*GP*TP*(DRZ)P*GP*TP*T)-3') Chain: B
Molecule details ›
Chain: B
Length: 12 nucleotides
Theoretical weight: 3.55 KDa
Source organism: synthetic construct
Expression system: Not provided

Ligands and Environments

2 bound ligands:
Ligand UNX 4 x UNX
Ligand EDO 5 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 24-ID-C
Unit cell:
a: 55.509Å b: 51.534Å c: 149.72Å
α: 90° β: 92.72° γ: 90°
R-values:
R R work R free
0.195 0.194 0.216
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 review citations

DNA-protein crosslinks from environmental exposure: Mechanisms of formation and repair.
Kojima et al. (2020)
4 more

3 mentions without citation

Structural biology of DNA abasic site protection by SRAP proteins.
Amidon et al. (2020)
2 more