› 6nmr

X-ray diffraction
2.42Å resolution

Blocking Fab 119 anti-SIRP-alpha antibody in complex with SIRP-alpha Variant 1

Released:
DOI: 10.2210/pdb6nmr/pdb
PDB entry 6nmr coloured by chain, front view.
PDB entry 6nmr coloured by chain, side view.
PDB entry 6nmr coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of high affinity, pan-allelic, and pan-mammalian reactive antibodies against the myeloid checkpoint receptor SIRPα.
Sim J, Sockolosky JT, Sangalang E, Izquierdo S, Pedersen D, Harriman W, Wibowo AS, Carter J, Madan A, Doyle L, Harrabi O, Kauder SE, Chen A, Kuo TC, Wan H, Pons J
MAbs 11 1036-1052
PMID: 31257988

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-211515 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Fab 119 anti-SIRP-alpha antibody Variable Light Chain Chains: B, G, K, L
Molecule details ›
Chains: B, G, K, L
Length: 215 amino acids
Theoretical weight: 23.82 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Fab 119 anti-SIRP-alpha antibody Variable Heavy Chain Chains: A, F, H, J
Molecule details ›
Chains: A, F, H, J
Length: 229 amino acids
Theoretical weight: 24.39 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
Tyrosine-protein phosphatase non-receptor type substrate 1 Chains: E, I, M, S
Molecule details ›
Chains: E, I, M, S
Length: 127 amino acids
Theoretical weight: 14.03 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: P78324 (Residues: 31-149; Coverage: 25%)
Gene names: BIT, MFR, MYD1, PTPNS1, SHPS1, SIRP, SIRPA
Sequence domains: Immunoglobulin V-set domain

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P21
Unit cell:
a: 63.07Å b: 113.56Å c: 152.08Å
α: 90° β: 91.35° γ: 90°
R-values:
R R work R free
0.29 0.288 0.323
Expression system: Homo sapiens

Quick links

Citations

13 review citations

Emerging strategies in targeting tumor-resident myeloid cells for cancer immunotherapy.
Wang et al. (2022)
12 more

2 mentions without citation

Macrophage checkpoint blockade: results from initial clinical trials, binding analyses, and CD47-SIRPα structure-function.
Jalil et al. (2020)
1 more