8U4S: Trimeric CXCR4

Structure of trimeric CXCR4 in complex with REGN7663 Fab. Determined by electron microscopy at 3.35 Å resolution. Released 13 Mar 2024.

Method: Electron microscopy
Resolution: 3.35 Å
Organism: Homo sapiens
Chains: 9
Atoms: 12,684
Mol. weight: 367.49 kDa
Ligands: D21, CLR
Released: 13 Mar 2024

Explore 8U4S in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8U4S contains 57 α-helices and 72 β-strands across 9 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A, E and L: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5-7	3	6
β-strand	10-11	2	7
β-strand	19-24	6	6
β-strand	38-43	6	7
β-strand	50-55	6	7
β-strand	58-59	2	7
β-strand	67-72	6	6
β-strand	75-80	6	6
β-strand	90-95	6	7
β-strand	102	1	7
β-strand	107-109	3	7

Chains B, F and H: 2 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	8
β-strand	10-12	3	9
β-strand	18-25	8	8
α-helix	29-31	3
β-strand	33-39	7	9
β-strand	45-51	7	9
β-strand	59-60	2	9
β-strand	68-73	6	8
β-strand	78-83	6	8
α-helix	88-90	3
β-strand	92-99	8	9
β-strand	116	1	9
β-strand	120-124	5	9

Chains C, G and R: 17 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	34-60	27
α-helix	61-67	7
α-helix	72-89	18
α-helix	91-99	9
α-helix	105-138	34
α-helix	145-150	6
α-helix	151-155	5
α-helix	156	1
α-helix	157-161	5
α-helix	162-166	5
α-helix	169-174	6
β-strand	175-180	6	10
β-strand	183-188	6	10
α-helix	193-204	12
α-helix	205-209	5
α-helix	210-226	17
α-helix	233-266	34
α-helix	275-290	16
α-helix	293-301	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
REGN7663 Fab light chain	A, E, L	protein	219	Homo sapiens
REGN7663 Fab heavy chain	B, F, H	protein	240	Homo sapiens
C-X-C chemokine receptor type 4	C, G, R	protein	632	Homo sapiens	P42212 (AlphaFold model), P61073 (AlphaFold model)

Sequence of entity 1 (A, E, L), FASTA

>8U4S_1 REGN7663 Fab light chain (chains A, E, L)
DVVMTQSPLSLPVTLGQPASISCRSSQSLVYTDGNTYLNWFQQRPGQSPRRLIYKVSNRD
SGVPDRFSGSGSGTDFTLKISRVEAEDVGFYYCMQNTHWPLTFGGGTKVEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 2 (B, F, H), FASTA

>8U4S_2 REGN7663 Fab heavy chain (chains B, F, H)
QVQLVQSGAEVKKPGASVKVSCKASGYTFTSYGISWVRQAPGQGIEWMGWISTYNGNRNY
AQKVQGRVTMTTDRSTSTAYMDLRSLRSDDTAVYYCARHGITGARNYYYHYGMDVWGQGT
TVTVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFP
AVLQSSGLYSLSSVVTVPSSSLGTKTYTCNVDHKPSNTKVDKRVESKYGPPCPPCPAPPV

Sequence of entity 3 (C, G, R), FASTA

>8U4S_3 C-X-C chemokine receptor type 4 (chains C, G, R)
MKTIIALSYIFCLVFAGAPEGISIYTSDNYTEEMGSGDYDSMKEPCFREENANFNKIFLP
TIYSIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHLSVADLLFVITLPFWAVDAVANW
YFGNFLCKAVHVIYTVSLYSSVLILAFISLDRYLAIVHATNSQRPRKLLAEKVVYVGVWI
PALLLTIPDFIFANVSEADDRYICDRFYPNDLWVVVFQFQHIMVGLILPGIVILSCYCII
ISKLSHSKGHQKRKALKTTVILILAFFACWLPYYIGISIDSFILLEIIKQGCEFENTVHK
WISITEALAFFHCCLNPILYAFLGAKFKTSAQHALTSVSRGSSLKILSKGKRGGHSSVST
ESESSSFHSSGRPLEVLFQGPGGGGSVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGE
GDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQ
ERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMA
DKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEK
RDHMVLLEFVTAAGITLGMDELYKDYKDDDDK

Ligands and cofactors

ID	Name	Formula	Copies
D21	(2R)-1-(hexadecanoyloxy)-3-(phosphonooxy)propan-2-yl (9Z)-octadec-9-enoate	C37 H71 O8 P	3
CLR	Cholesterol	C27 H46 O	6

Primary citation

Structural insights into CXCR4 modulation and oligomerization. Saotome, K., McGoldrick, L.L., Ho, J.H. et al. Nat Struct Mol Biol (2025) 32:315-325. DOI 10.1038/s41594-024-01397-1 · PubMed

Other PDB entries of the same protein (UniProt P42212 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6L27 0.77 Å, X-ray crystal structure of the mutant green fluorescent protein
6JGJ 0.78 Å, Crystal structure of the F99S/M153T/V163A/E222Q variant of GFP at 0.78 A
6KL0 0.8 Å, Crystal structure of the S65T/F99S/M153T/V163A variant of perdeuterated GFP at pD 7.0
6JGI 0.85 Å, Crystal structure of the S65T/F99S/M153T/V163A variant of GFP at 0.85 A
6KL1 0.85 Å, Crystal structure of the S65T/F99S/M153T/V163A variant of non-deuterated GFP at pD 8.5
2WUR 0.9 Å, Atomic resolution structure of GFP measured on a rotating anode
6KKZ 0.9 Å, Crystal structure of the S65T/F99S/M153T/V163A variant of perdeuterated GFP at pD 8.5
6JGH 0.94 Å, Crystal structure of the F99S/M153T/V163A/T203I variant of GFP at 0.94 A
4AS8 1.02 Å, X-ray structure of the cyan fluorescent protein Cerulean cryoprotected with ethylene…
5OXC 1.02 Å, Structure of Cerulean Fluorescent Protein at 1.02 Angstrom resolution
7PCA 1.05 Å, Functional and structural characterization of redox sensitive superfolder green…
4GF6 1.1 Å, crystal structure of GFP with cuprum bound at the Incorporated metal Chelating Amino…

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