8U4T | pdb_00008u4t

Structure of tetrameric CXCR4 in complex with REGN7663 Fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.38 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8U4T

This is version 1.3 of the entry. See complete history

Literature

Structural insights into CXCR4 modulation and oligomerization.

Saotome, K.McGoldrick, L.L.Ho, J.H.Ramlall, T.F.Shah, S.Moore, M.J.Kim, J.H.Leidich, R.Olson, W.C.Franklin, M.C.

(2025) Nat Struct Mol Biol 32: 315-325

  • DOI: https://doi.org/10.1038/s41594-024-01397-1
  • Primary Citation Related Structures: 
    8U4N, 8U4O, 8U4P, 8U4Q, 8U4R, 8U4S, 8U4T

  • PubMed Abstract: 

    Activation of the chemokine receptor CXCR4 by its chemokine ligand CXCL12 regulates diverse cellular processes. Previously reported crystal structures of CXCR4 revealed the architecture of an inactive, homodimeric receptor. However, many structural aspects of CXCR4 remain poorly understood. Here, we use cryo-electron microscopy to investigate various modes of human CXCR4 regulation. CXCL12 activates CXCR4 by inserting its N terminus deep into the CXCR4 orthosteric pocket. The binding of US Food and Drug Administration-approved antagonist AMD3100 is stabilized by electrostatic interactions with acidic residues in the seven-transmembrane-helix bundle. A potent antibody blocker, REGN7663, binds across the extracellular face of CXCR4 and inserts its complementarity-determining region H3 loop into the orthosteric pocket. Trimeric and tetrameric structures of CXCR4 reveal modes of G-protein-coupled receptor oligomerization. We show that CXCR4 adopts distinct subunit conformations in trimeric and tetrameric assemblies, highlighting how oligomerization could allosterically regulate chemokine receptor function.


  • Organizational Affiliation
    • Regeneron Pharmaceuticals, Inc., Tarrytown, NY, USA. kei.saotome@regeneron.com.

Macromolecule Content 

  • Total Structure Weight: 493.08 kDa 
  • Atom Count: 16,968 
  • Modeled Residue Count: 2,056 
  • Deposited Residue Count: 4,364 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
REGN7663 Fab light chainA [auth L],
D [auth F],
G [auth O],
J [auth Y]
219Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
REGN7663 Fab heavy chainB [auth H],
E [auth G],
H [auth P],
K [auth Z]
240Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
C-X-C chemokine receptor type 4C [auth R],
F [auth I],
I [auth Q],
L [auth AA]
632Homo sapiensMutation(s): 0 
Gene Names: CXCR4
UniProt & NIH Common Fund Data Resources
Find proteins for P61073 (Homo sapiens)
Explore P61073 
Go to UniProtKB:  P61073
PHAROS:  P61073
GTEx:  ENSG00000121966 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61073
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
D21

Query on D21



Download:Ideal Coordinates CCD File
EA [auth AA],
P [auth R],
U [auth I],
Z [auth Q]
(2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate
C37 H71 O8 P
OPVZUEPSMJNLOM-PGUFJCEWSA-N
CLR

Query on CLR



Download:Ideal Coordinates CCD File
AA [auth Q]
BA [auth AA]
CA [auth AA]
DA [auth AA]
FA [auth AA]
AA [auth Q],
BA [auth AA],
CA [auth AA],
DA [auth AA],
FA [auth AA],
M [auth R],
N [auth R],
O [auth R],
Q [auth R],
R [auth I],
S [auth I],
T [auth I],
V [auth I],
W [auth Q],
X [auth Q],
Y [auth Q]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.38 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-13
    Type: Initial release
  • Version 1.1: 2024-10-02
    Changes: Data collection, Database references
  • Version 1.2: 2024-10-23
    Changes: Data collection, Structure summary
  • Version 1.3: 2025-02-26
    Changes: Data collection, Database references