› 3rzw

X-ray diffraction
2.15Å resolution

Crystal Structure of the Monobody ySMB-9 bound to human SUMO1

Released:
DOI: 10.2210/pdb3rzw/pdb
PDB entry 3rzw coloured by chain, front view.
PDB entry 3rzw coloured by chain, side view.
PDB entry 3rzw coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Teaching an old scaffold new tricks: monobodies constructed using alternative surfaces of the FN3 scaffold.
Koide A, Wojcik J, Gilbreth RN, Hoey RJ, Koide S
J Mol Biol 415 393-405 (2012)
PMID: 22198408

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-159006 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Monobody ySMB-9 Chains: A, B
Molecule details ›
Chains: A, B
Length: 95 amino acids
Theoretical weight: 10.31 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
Structure domains: Immunoglobulins
Small ubiquitin-related modifier 1 Chains: C, D
Molecule details ›
Chains: C, D
Length: 99 amino acids
Theoretical weight: 11.26 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P63165 (Residues: 1-97; Coverage: 96%)
Gene names: OK/SW-cl.43, SMT3C, SMT3H3, SUMO1, UBL1
Sequence domains: Ubiquitin-2 like Rad60 SUMO-like
Structure domains: Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1

Ligands and Environments

1 bound ligand:
Ligand GOL 2 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: C2221
Unit cell:
a: 93.347Å b: 97.829Å c: 96.578Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.189 0.186 0.237
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

29 review citations

Nanobodies and recombinant binders in cell biology.
Helma et al. (2015)
28 more

11 mentions without citation

Nanobodies: Chemical Functionalization Strategies and Intracellular Applications.
Schumacher et al. (2018)
10 more