› 5kvm

X-ray diffraction
2.45Å resolution

Extracellular region of mouse GPR56/ADGRG1 in complex with FN3 monobody

Released:
DOI: 10.2210/pdb5kvm/pdb
PDB entry 5kvm coloured by chain, front view.
PDB entry 5kvm coloured by chain, side view.
PDB entry 5kvm coloured by chain, top view.
Source organisms:
Primary publication:
Structural Basis for Regulation of GPR56/ADGRG1 by Its Alternatively Spliced Extracellular Domains.
Salzman GS, Ackerman SD, Ding C, Koide A, Leon K, Luo R, Stoveken HM, Fernandez CG, Tall GG, Piao X, Monk KR, Koide S, Araç D
Neuron 91 1292-1304 (2016)
PMID: 27657451

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-165912 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (5 distinct):
ADGRG1 N-terminal fragment Chain: A
Molecule details ›
Chain: A
Length: 355 amino acids
Theoretical weight: 40.33 KDa
Source organism: Mus musculus
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q8K209 (Residues: 28-382; Coverage: 54%)
Gene names: Adgrg1, Cyt28, Gpr56
Sequence domains:
ADGRG1 C-terminal fragment Chain: B
Molecule details ›
Chain: B
Length: 9 amino acids
Theoretical weight: 1.03 KDa
Source organism: Mus musculus
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q8K209 (Residues: 383-391; Coverage: 1%)
Gene names: Adgrg1, Cyt28, Gpr56
FN3 monobody alpha5 Chain: C
Molecule details ›
Chain: C
Length: 95 amino acids
Theoretical weight: 10.39 KDa
Source organism: synthetic construct
Expression system: Escherichia coli BL21(DE3)
Structure domains: Immunoglobulins

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG, BMA
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
2 bound ligands:
Ligand NAG 1 x NAG
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 23-ID-B
Spacegroup: P65
Unit cell:
a: 120.336Å b: 120.336Å c: 72.85Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.217 0.215 0.263
Expression systems:
  • Trichoplusia ni
  • Escherichia coli BL21(DE3)

Quick links

Citations

19 review citations

Monobodies and other synthetic binding proteins for expanding protein science.
Sha et al. (2017)
18 more

7 mentions without citation

Mechanisms of adhesion G protein-coupled receptor activation.
Vizurraga et al. (2020)
6 more