› 8zpl

Electron Microscopy
3.01Å resolution

Cryo-EM strucutre of CXCR4 complexed with antagonist HF51116

Released:
DOI: 10.2210/pdb8zpl/pdb
PDB entry 8zpl coloured by chain, front view.
PDB entry 8zpl coloured by chain, side view.
PDB entry 8zpl coloured by chain, top view.
Source organisms:
Primary publication:
Structural mechanisms underlying the modulation of CXCR4 by diverse small-molecule antagonists.
Sang X, Jiao H, Meng Q, Fang X, Pan Q, Zhou J, Qian T, Zhang W, Xu Y, An J, Huang Z, Hu H
Proc Natl Acad Sci U S A 122 e2425795122 (2025)
PMID: 40063796
Related structures: EMD-60348

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-290639 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Nb6 nanobody Chain: N
Molecule details ›
Chain: N
Length: 169 amino acids
Theoretical weight: 18.67 KDa
Source organism: Lama glama
Expression system: Spodoptera frugiperda
C-X-C chemokine receptor type 4 Chain: R
Molecule details ›
Chain: R
Length: 486 amino acids
Theoretical weight: 55.45 KDa
Source organism: Escherichia coli
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P61073 (Residues: 1-224, 241-319; Coverage: 86%)
Gene name: CXCR4
Sequence domains:

Ligands and Environments

2 bound ligands:
Ligand CLR 2 x CLR
Ligand A1D8K 1 x A1D8K
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this EM entry.
Resolution: 3.01Å
Relevant EMDB volumes: EMD-60348
Expression system: Spodoptera frugiperda

Quick links