9UPU: Cryo-EM strucutre of CXCR4

Cryo-EM strucutre of CXCR4 complexed with agonist SDV1a. Determined by electron microscopy at 2.8 Å resolution. Released 29 Apr 2026.

Method: Electron microscopy
Resolution: 2.8 Å
Organisms: Homo sapiens, Escherichia coli, Oplophorus gracilirostris
Chains: 6
Atoms: 8,837
Mol. weight: 192.12 kDa
Ligands: CLR
Released: 29 Apr 2026

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

Secondary structure: helices and β-sheets

9UPU contains 35 α-helices and 62 β-strands across 6 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: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	9-30	22
β-strand	34-40	7	8
α-helix	47-52	6
β-strand	185-190	6	8
β-strand	195-200	6	8
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	8
β-strand	233	1	9
β-strand	241	1	9
α-helix	242-254	13
β-strand	263-269	7	8
α-helix	271-278	8
α-helix	296-308	13
β-strand	319-323	5	8
α-helix	328-351	24

Chain B: 3 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	7-25	19
α-helix	30-33	4
α-helix	38-40	3
β-strand	47-51	5	1
β-strand	58-63	6	2
β-strand	69-74	6	2
β-strand	78-83	6	2
β-strand	89-94	6	2
β-strand	100-105	6	3
β-strand	111-116	6	3
β-strand	121-125	5	3
β-strand	134-139	6	3
β-strand	146-153	8	4
β-strand	156-161	6	4
β-strand	165-170	6	4
β-strand	176-180	5	4
β-strand	187-192	6	5
β-strand	198-203	6	5
β-strand	207-212	6	5
β-strand	218-223	6	5
β-strand	229-234	6	6
β-strand	240-245	6	6
β-strand	250-254	5	6
β-strand	260-264	5	6
β-strand	273-278	6	7
β-strand	284-289	6	7
β-strand	294-298	5	7
β-strand	304-308	5	7
β-strand	315-317	3	1
β-strand	320	1	1
β-strand	327-331	5	1
β-strand	336-339	4	1

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	13-23	11
α-helix	30-43	14
α-helix	53-55	3
α-helix	56-58	3

Chain J: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3

Chain R: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-65	31
α-helix	72-88	17
α-helix	91-99	9
α-helix	106-139	34
α-helix	146-150	5
α-helix	151-155	5
α-helix	157-161	5
α-helix	162-167	6
α-helix	169-173	5
β-strand	177-180	4	15
β-strand	183-186	4	15
α-helix	194-204	11
α-helix	205-209	5
α-helix	210-227	18
α-helix	232-266	35
α-helix	274-291	18
α-helix	294-302	9
α-helix	307-316	10

Chain S: 3 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	10-12	3	11
β-strand	17-25	9	10
α-helix	29-31	3
β-strand	33-39	7	11
β-strand	45-51	7	11
α-helix	53-55	3
β-strand	58-60	3	11
β-strand	68-73	6	10
β-strand	78-84	7	10
α-helix	88-90	3
β-strand	92-99	8	11
β-strand	110-111	2	11
β-strand	115-119	5	11
β-strand	140-141	2	12
β-strand	146-148	3	13
β-strand	155-161	7	12
β-strand	166	1	14
β-strand	172	1	14
β-strand	174-179	6	13
β-strand	186-190	5	13
β-strand	194-195	2	13
β-strand	203-208	6	12
β-strand	211-216	6	12
β-strand	225-231	7	13
β-strand	243-246	4	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	384	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	71	Homo sapiens	P59768 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Homo sapiens	P63096 (AlphaFold model)
single-chain variable fragment scFv16	S	protein	259	Homo sapiens
Stromal cell-derived factor 1	J	protein	8	Homo sapiens	P48061 (AlphaFold model)
Soluble cytochrome b562,C-X-C chemokine receptor type 4,Oplophorus-luciferin 2-monooxygenase…	R	protein	648	Escherichia coli, Homo sapiens, Oplophorus gracilirostris	P0ABE7, P61073, Q9GV45

Sequence of entity 1 (B), FASTA

>9UPU_1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
HHHHHHHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDP
VGRIQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSW
VMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVT
SSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCR
QTFTGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFS
KSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIW
NGASGASGASGASVSGWRLFKKIS

Sequence of entity 2 (C), FASTA

>9UPU_2 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 3 (A), FASTA

>9UPU_3 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 4 (S), FASTA

>9UPU_4 single-chain variable fragment scFv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAAHHHHHHHH

Sequence of entity 5 (J), FASTA

>9UPU_5 Stromal cell-derived factor 1 (chains J)
KPVSLSYR

Sequence of entity 6 (R), FASTA

>9UPU_6 Soluble cytochrome b562,C-X-C chemokine receptor type 4,Oplophorus-luciferin 2-monooxygenase catalytic subunit (chains R)
MKTIIALSYIFCLVFADYKDDDDKGSADLEDNWETLNDNLKVIEKADNAAQVKDALTKMR
AAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQL
KTTRNAYIQKYLLVPRGSMEGISIYTSDNYTEEMGSGDYDSMKEPCFREENANFNKIFLP
TIYSIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHLSVADLLFVITLPFWAVDAVANW
YFGNFLCKAVHVIYTVSLYSSVLILAFISLDRYLAIVHATNSQRPRKLLAEKVVYVGVWI
PALLLTIPDFIFANVSEADDRYICDRFYPNDLWVVVFQFQHIMVGLILPGIVILSCYCII
ISKLSHSKGHQKRKALKTTVILILAFFACWLPYYIGISIDSFILLEIIKQGCEFENTVHK
WISITEALAFFHCCLNPILYAFLGAKFKTSAQHALTSVSRGSSLKILSKGKRGGHSSVST
ESESSSFHSSVFTLEDFVGDWEQTAAYNLDQVLEQGGVSSLLQNLAVSVTPIQRIVRSGE
NALKIDIHVIIPYEGLSADQMAQIEEVFKVVYPVDDHHFKVILPYGTLVIDGVTPNMLNY
FGRPYEGIAVFDGKKITVTGTLWNGNKIIDERLITPDGSMLFRVTINS

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	1

Primary citation

The cryo-EM-delineated mechanism underlying mimicry of CXCR4 agonism enables widespread stem cell neuroprotection in a mouse model of ALS. Sang, X., Jiao, H., Meng, Q. et al. bioRxiv (2025). DOI 10.1101/2025.07.08.663251 · PubMed

Other PDB entries of the same protein (UniProt P62873 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8QEH 1.43 Å, Crystal structure of the G11 protein heterotrimer bound to FR900359 inhibitor
8QEG 1.7 Å, Crystal structure of the G11 protein heterotrimer bound to YM-254890 inhibitor
8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
9YDQ 1.94 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE and allosteric…
9YDP 1.95 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE
6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
8F0J 2.0 Å, Calcitonin Receptor in complex with Gs and Pramlintide analogue peptide San45
8F2B 2.0 Å, Amylin 3 Receptor in complex with Gs and Pramlintide analogue peptide San45
9XXT 2.0 Å, Cryo-EM structure of lysophosphatidylserine (18:0)-bound GPR174-Gs complex
6X18 2.1 Å, GLP-1 peptide hormone bound to Glucagon-Like peptide-1 (GLP-1) Receptor
6X19 2.1 Å, Non peptide agonist CHU-128, bound to Glucagon-Like peptide-1 (GLP-1) Receptor
9NTU 2.1 Å, Cryo-EM structure of BETP-GLP-1(9-36)-GLP-1R-Gs complex

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