› 6ir2

X-ray diffraction
1.39Å resolution

Crystal structure of red fluorescent protein mCherry complexed with the nanobody LaM2 at 1.4 Angstron resolution

Released:
DOI: 10.2210/pdb6ir2/pdb
PDB entry 6ir2 coloured by chain, front view.
PDB entry 6ir2 coloured by chain, side view.
PDB entry 6ir2 coloured by chain, top view.
Source organisms:
Primary publication:
Structural insights into the binding of nanobodies LaM2 and LaM4 to the red fluorescent protein mCherry.
Wang Z, Li L, Hu R, Zhong P, Zhang Y, Cheng S, Jiang H, Liu R, Ding Y
Protein Sci 30 2298-2309 (2021)
PMID: 34562299

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-212966 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
MCherry fluorescent protein Chain: A
Molecule details ›
Chain: A
Length: 225 amino acids
Theoretical weight: 25.71 KDa
Source organism: Anaplasma marginale
Expression system: Escherichia coli
UniProt:
  • Canonical: X5DSL3 (Residues: 1-226; Coverage: 96%)
Gene name: mCherry
Sequence domains: Green fluorescent protein
mCherry's nanobody LaM2 Chain: B
Molecule details ›
Chain: B
Length: 127 amino acids
Theoretical weight: 13.81 KDa
Source organism: Camelus bactrianus
Expression system: Escherichia coli

Ligands and Environments

No bound ligands
1 modified residue:
Ligand CH6 1 x CH6

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P212121
Unit cell:
a: 49.817Å b: 61.046Å c: 109.21Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.195 0.216
Expression system: Escherichia coli

Quick links

Citations

2 citation in other articles

Single-domain near-infrared protein provides a scaffold for antigen-dependent fluorescent nanobodies.
Oliinyk et al. (2022)
1 more

2 mentions without citation

Structural insights into the binding of nanobodies LaM2 and LaM4 to the red fluorescent protein mCherry.
Wang et al. (2021)
1 more