8ZPN: Cryo-EM strucutre of CXCR4

Cryo-EM strucutre of CXCR4 complexed with antagonist AMD3100. Determined by electron microscopy at 3.31 Å resolution. Released 26 Feb 2025.

Method: Electron microscopy
Resolution: 3.31 Å
Organisms: Escherichia coli, Homo sapiens, Lama glama
Chains: 2
Atoms: 3,204
Mol. weight: 75.01 kDa
Ligands: VH6, CLR
Released: 26 Feb 2025

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

Secondary structure: helices and β-sheets

8ZPN contains 16 α-helices and 16 β-strands across 2 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.

Chain N: 1 helix, 14 β-strands

Element	Residues	Length	Sheet
β-strand	4-6	3	2
β-strand	9	1	3
β-strand	12-14	3	4
β-strand	21-22	2	5
β-strand	23	1	3
β-strand	26-28	3	2
β-strand	32-39	8	6
β-strand	49-54	6	6
β-strand	70-74	5	5
β-strand	79-83	5	5
α-helix	89-91	3
β-strand	93-95	3	4
β-strand	96-102	7	6
β-strand	110-113	4	6
β-strand	117-121	5	4

Chain R: 15 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-64	30
α-helix	72-99	28
α-helix	106-139	34
α-helix	146-153	8
α-helix	156	1
α-helix	157-161	5
α-helix	162-166	5
α-helix	169-174	6
β-strand	175-177	3	1
β-strand	186-188	3	1
α-helix	193-204	12
α-helix	205-209	5
α-helix	210-226	17
α-helix	236-274	39
α-helix	282-299	18
α-helix	300-304	5
α-helix	305-312	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Soluble cytochrome b562,C-X-C chemokine receptor type 4	R	protein	486	Escherichia coli, Homo sapiens	P61073 (AlphaFold model)
Nb6 nanobody	N	protein	169	Lama glama

Sequence of entity 1 (R), FASTA

>8ZPN_1 Soluble cytochrome b562,C-X-C chemokine receptor type 4 (chains R)
MKTIIALSYIFCLVFADYKDDDDKGSADLEDNWETLNDNLKVIEKADNAAQVKDALTKMR
AAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQL
KTTRNAYIQKYLLVPRGSMEGISIYTSDNYTEEMGSGDYDSMKEPCFREENANFNKIFLP
TIYSIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHLSVADLLFVITLPFWAVDAVANW
YFGNFLCKAVHVIYTVNLYSSVWILAFISLDRYLAIVHATNSQRPRKLLAEKVVYVGVWI
PALLLTIPDFIFANVSEADDRYICDRFYPNDLWVVVFQFQHIMVGLILPGIVILSCYCII
ISRLKSVRLLSGSREKDRNLRRITRPTVILILAFFACWLPYYIGISIDSFILLEIIKQGC
EFENTVHKWISITEALAFFHCCLNPILYAFLGAKFKTSAQHALTSGRPLEVLFQGPHHHH
HHHHHH

Sequence of entity 2 (N), FASTA

>8ZPN_2 Nb6 nanobody (chains N)
MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAMAQVQLQESGGGLVQAGESLRL
SCAASGTIFRLYDMGWYRRVSGNQRELVASITSGGSTKYGDSVKGRFTISRDNAKNTVYL
QMSSLKPEDTAVYYCNAEYRTGIWEELLDGWGQGTQVTVSSHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
VH6	Plerixafor	C28 H54 N8	1
CLR	Cholesterol	C27 H46 O	1

Primary citation

Structural mechanisms underlying the modulation of CXCR4 by diverse small-molecule antagonists. Sang, X., Jiao, H., Meng, Q. et al. Proc Natl Acad Sci U S A (2025) 122:e2425795122-e2425795122. DOI 10.1073/pnas.2425795122 · PubMed

Other PDB entries of the same protein (UniProt P61073 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3ODU 2.5 Å, The 2.5 A structure of the CXCR4 chemokine receptor in complex with small molecule…
9UPV 2.7 Å, Cryo-EM structure of CXCR4 complexed with agonist SDVX1
8U4N 2.72 Å, Structure of Apo CXCR4/Gi complex
9UPU 2.8 Å, Cryo-EM strucutre of CXCR4 complexed with agonist SDV1a
8K3Z 2.81 Å, Cryo-EM structure of CXCR4 in complex with CXCL12
3OE0 2.9 Å, Crystal structure of the CXCR4 chemokine receptor in complex with a cyclic peptide…
9MDU 2.9 Å, Human CXCR4 tetramer
8YU7 3.01 Å, Cryo-EM structure of CXCR4 tetramer
8ZPL 3.01 Å, Cryo-EM strucutre of CXCR4 complexed with antagonist HF51116
3OE8 3.1 Å, Crystal structure of the CXCR4 chemokine receptor in complex with a small molecule…
3OE9 3.1 Å, Crystal structure of the chemokine CXCR4 receptor in complex with a small molecule…
4RWS 3.1 Å, Crystal structure of CXCR4 and viral chemokine antagonist vMIP-II complex (PSI Community…

Browse structure collections

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