8U4S

Structure of trimeric CXCR4 in complex with REGN7663 Fab

PDB DOI: https://doi.org/10.2210/pdb8U4S/pdb
EM Map EMD-41893: EMDB EMDataResource

Classification: SIGNALING PROTEIN/IMMUNE SYSTEM
Organism(s): Homo sapiens
Expression System: Cricetulus griseus, Spodoptera frugiperda
Mutation(s): No

Deposited: 2023-09-11 Released: 2024-03-13
Deposition Author(s): Saotome, K., McGoldrick, L.L., Franklin, M.C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.35 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural insights into CXCR4 modulation and oligomerization

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

(2024) Biorxiv

DOI: https://doi.org/10.1101/2024.02.09.579708

Macromolecule Content

Total Structure Weight: 367.49 kDa
Atom Count: 12,684
Modelled Residue Count: 1,557
Deposited Residue Count: 3,273
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
REGN7663 Fab light chain	A [auth L], D [auth A], G [auth E]	219	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
REGN7663 Fab heavy chain	B [auth H], E [auth B], H [auth F]	240	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
C-X-C chemokine receptor type 4	C [auth R], F [auth C], I [auth G]	632	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P61073
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
D21 Query on D21 Download Ideal Coordinates CCD File SDF format, chain K [auth R] SDF format, chain N [auth C] SDF format, chain Q [auth G] MOL2 format, chain K [auth R] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth G]	K [auth R], N [auth C], Q [auth G]	(2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate C₃₇ H₇₁ O₈ P OPVZUEPSMJNLOM-PGUFJCEWSA-N		Interactions Focus chain K [auth R] Focus chain N [auth C] Focus chain Q [auth G] Interactions & Density Focus chain K [auth R] Focus chain N [auth C] Focus chain Q [auth G]
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain J [auth R] SDF format, chain L [auth R] SDF format, chain M [auth C] SDF format, chain O [auth C] SDF format, chain P [auth G] SDF format, chain R [auth G] MOL2 format, chain J [auth R] MOL2 format, chain L [auth R] MOL2 format, chain M [auth C] MOL2 format, chain O [auth C] MOL2 format, chain P [auth G] MOL2 format, chain R [auth G]	J [auth R] L [auth R] M [auth C] O [auth C] P [auth G] J [auth R], L [auth R], M [auth C], O [auth C], P [auth G], R [auth G]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain J [auth R] Focus chain L [auth R] Focus chain M [auth C] Focus chain O [auth C] Focus chain P [auth G] Focus chain R [auth G] Interactions & Density Focus chain J [auth R] Focus chain L [auth R] Focus chain M [auth C] Focus chain O [auth C] Focus chain P [auth G] Focus chain R [auth G]