9MDU: Human CXCR4 tetramer

Human CXCR4 tetramer. Determined by electron microscopy at 2.9 Å resolution. Released 10 Sept 2025.

Method: Electron microscopy
Resolution: 2.9 Å
Organism: Homo sapiens
Chains: 4
Atoms: 9,123
Mol. weight: 163.14 kDa
Released: 10 Sept 2025

Explore 9MDU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9MDU contains 68 α-helices and 8 β-strands across 4 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 A: 17 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	36-38	3
α-helix	40-62	23
α-helix	73-99	27
α-helix	106-138	33
α-helix	146-150	5
α-helix	151-155	5
α-helix	156	1
α-helix	157-161	5
α-helix	162-166	5
α-helix	169-173	5
β-strand	175-178	4	2
β-strand	185-188	4	2
α-helix	193-204	12
α-helix	205-209	5
α-helix	210-228	19
α-helix	240-266	27
α-helix	275-290	16
α-helix	291-296	6
α-helix	298-302	5

Chain B: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	37-64	28
α-helix	73-99	27
α-helix	105-138	34
α-helix	147-153	7
α-helix	155-156	2
α-helix	157-161	5
α-helix	162-166	5
α-helix	169-173	5
β-strand	175-178	4	1
β-strand	185-188	4	1
α-helix	193-204	12
α-helix	205-209	5
α-helix	210-226	17
α-helix	237-266	30
α-helix	274-291	18
α-helix	294-303	10

Chain C: 18 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	31-33	3
α-helix	41-60	20
α-helix	61-65	5
α-helix	74-99	26
α-helix	106-138	33
α-helix	146-150	5
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	3
β-strand	183-188	6	3
α-helix	193-204	12
α-helix	205-209	5
α-helix	210-223	14
α-helix	238-266	29
α-helix	282-291	10
α-helix	292-295	4
α-helix	297-303	7

Chain D: 19 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	30-33	4
α-helix	37-59	23
α-helix	60-65	6
α-helix	72-99	28
α-helix	106-138	33
α-helix	146-150	5
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	4
β-strand	183-188	6	4
α-helix	193-204	12
α-helix	205-209	5
α-helix	210-225	16
α-helix	233-237	5
α-helix	239-266	28
α-helix	274-291	18
α-helix	292-295	4
α-helix	297-304	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
C-X-C chemokine receptor type 4	A, B, C, D	protein	360	Homo sapiens	P61073 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>9MDU_1 C-X-C chemokine receptor type 4 (chains A, B, C, D)
MEGISIYTSDNYTEEMGSGDYDSMKEPCFREENANFNKIFLPTIYSIIFLTGIVGNGLVI
LVMGYQKKLRSMTDKYRLHLSVADLLFVITLPFWAVDAVANWYFGNFLCKAVHVIYTVNL
YSSVLILAFISLDRYLAIVHATNSQRPRKLLAEKVVYVGVWIPALLLTIPDFIFANVSEA
DDRYICDRFYPNDLWVVVFQFQHIMVGLILPGIVILSCYCIIISKLSHSKGHQKRKALKT
TVILILAFFACWLPYYIGISIDSFILLEIIKQGCEFENTVHKWISITEALAFFHCCLNPI
LYAFLGAKFKTSAQHALTSVSRGSSLKILSKGKRGGHSSVSTESESSSFHSSDYKDDDDK

Primary citation

human CXCR4 tetramer. Zhang, Z., Dinshaw, J.P., Junyu, X. To be published.

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…
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…
8U4R 3.1 Å, Structure of REGN7663-Fab bound CXCR4

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