› 3dvg

X-ray diffraction
2.6Å resolution

Crystal structure of K63-specific fab Apu.3A8 bound to K63-linked di-ubiquitin

Released:
DOI: 10.2210/pdb3dvg/pdb
PDB entry 3dvg coloured by chain, front view.
PDB entry 3dvg coloured by chain, side view.
PDB entry 3dvg coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Ubiquitin chain editing revealed by polyubiquitin linkage-specific antibodies.
Newton K, Matsumoto ML, Wertz IE, Kirkpatrick DS, Lill JR, Tan J, Dugger D, Gordon N, Sidhu SS, Fellouse FA, Komuves L, French DM, Ferrando RE, Lam C, Compaan D, Yu C, Bosanac I, Hymowitz SG, Kelley RF, Dixit VM
Cell 134 668-78 (2008)
PMID: 18724939

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero tetramer (preferred)
PDBe Complex ID:
PDB-CPX-209608 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Ig-like domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 217 amino acids
Theoretical weight: 23.73 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6PIL8 (Residues: 24-114, 115-236; Coverage: 98%)
Gene name: IGK@
Sequence domains:
Structure domains: Immunoglobulins
Human IgG1 fab fragment heavy chain Chain: B
Molecule details ›
Chain: B
Length: 230 amino acids
Theoretical weight: 24.59 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
Structure domains: Immunoglobulins
Ubiquitin Chain: X
Molecule details ›
Chain: X
Length: 80 amino acids
Theoretical weight: 8.97 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Ubiquitin Chain: Y
Molecule details ›
Chain: Y
Length: 79 amino acids
Theoretical weight: 8.89 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL7-1
Spacegroup: C2
Unit cell:
a: 106.806Å b: 88.117Å c: 90.226Å
α: 90° β: 108.28° γ: 90°
R-values:
R R work R free
0.224 0.219 0.261
Expression system: Escherichia coli

Quick links

Citations

104 review citations

The ubiquitin code.
Komander et al. (2012)
103 more

9 mentions without citation

OptMAVEn--a new framework for the de novo design of antibody variable region models targeting specific antigen epitopes.
Li et al. (2014)
8 more