8U4P: AMD3100-bound CXCR4/Gi complex

Structure of AMD3100-bound CXCR4/Gi complex. Determined by electron microscopy at 3.15 Å resolution. Released 13 Mar 2024.

Method: Electron microscopy
Resolution: 3.15 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,006
Mol. weight: 159.94 kDa
Ligands: VH6, CLR
Released: 13 Mar 2024

Explore 8U4P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8U4P contains 33 α-helices and 40 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: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	34-39	6	1
α-helix	48-52	5
β-strand	185-190	6	1
β-strand	195-200	6	1
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	1
α-helix	227-229	3
β-strand	233	1	2
β-strand	241	1	2
α-helix	242-254	13
β-strand	263-269	7	1
α-helix	271-278	8
α-helix	296-308	13
β-strand	319-323	5	1
α-helix	331-350	20

Chain B: 4 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	7-24	18
α-helix	30-33	4
α-helix	38-43	6
β-strand	47-52	6	3
β-strand	58-63	6	4
β-strand	70-74	5	4
β-strand	78-82	5	4
β-strand	89-94	6	4
α-helix	95	1
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	120-125	6	5
β-strand	134-140	7	5
β-strand	146-153	8	6
β-strand	156-161	6	6
β-strand	165-170	6	6
β-strand	175-181	7	6
β-strand	187	1	7
β-strand	191-192	2	8
β-strand	198-202	5	8
β-strand	203	1	7
β-strand	207-212	6	8
β-strand	218-223	6	8
β-strand	229-234	6	9
β-strand	240-245	6	9
β-strand	250-254	5	9
β-strand	259-264	6	9
β-strand	273-278	6	10
β-strand	284-289	6	10
β-strand	294-298	5	10
β-strand	307-308	2	10
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	335-339	5	3

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 R: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	34-64	31
α-helix	74-89	16
α-helix	91-99	9
α-helix	107-139	33
α-helix	146-150	5
α-helix	151-161	11
α-helix	162-166	5
α-helix	169-174	6
β-strand	175-180	6	11
β-strand	183-188	6	11
α-helix	193-204	12
α-helix	205-209	5
α-helix	210-226	17
α-helix	233-266	34
α-helix	274-291	18
α-helix	294-298	5
α-helix	299-303	5
α-helix	307-317	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	365	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	350	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)
C-X-C chemokine receptor type 4	R	protein	632	Homo sapiens	P42212 (AlphaFold model), P61073

Sequence of entity 1 (A), FASTA

>8U4P_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MHHHHHHGGGGSGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKCTI
VKQMKIIHEAGYSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFV
LAGAAEEGFMTAELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIP
TQQDVLRTRVKTTGIVETHFTFKDLHFKMFDVTAQRSERKKWIHCFEGVTAIIFCVALSD
YDLVLAEDEEMNRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPE
YAGSNTYEEAAAYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLK
DCGLF

Sequence of entity 2 (B), FASTA

>8U4P_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRT
LRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGN
YVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWD
IETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDIN
AICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYD
DFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (C), FASTA

>8U4P_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (R), FASTA

>8U4P_4 C-X-C chemokine receptor type 4 (chains R)
MKTIIALSYIFCLVFAGAPEGISIYTSDNYTEEMGSGDYDSMKEPCFREENANFNKIFLP
TIYSIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHLSVADLLFVITLPFWAVDAVANW
YFGNFLCKAVHVIYTVSLYSSVLILAFISLDRYLAIVHATNSQRPRKLLAEKVVYVGVWI
PALLLTIPDFIFANVSEADDRYICDRFYPNDLWVVVFQFQHIMVGLILPGIVILSCYCII
ISKLSHSKGHQKRKALKTTVILILAFFACWLPYYIGISIDSFILLEIIKQGCEFENTVHK
WISITEALAFFHCCLNPILYAFLGAKFKTSAQHALTSVSRGSSLKILSKGKRGGHSSVST
ESESSSFHSSGRPLEVLFQGPGGGGSVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGE
GDATYGKLTLKFICTTGKLPVPWPTLVTTLTYGVQCFSRYPDHMKQHDFFKSAMPEGYVQ
ERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMA
DKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSKLSKDPNEK
RDHMVLLEFVTAAGITLGMDELYKDYKDDDDK

Ligands and cofactors

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

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 P63096 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
3UMR 2.04 Å, Crystal structure of the G202D mutant of human G-alpha-i1
9P7Z 2.1 Å, NTSR1-Gi-NTS(8-13) Complex in the Canonical, AHD Open State (C-Open-Apo)
2OM2 2.2 Å, Crystal Structure Of Human G[alpha]i1 Bound To The Goloco Motif Of Rgs14
8YN9 2.3 Å, Cryo-EM structure of histamine H4 receptor in complex with histamine and Gi
9HYI 2.3 Å, DP81-bound serotonin 5-HT1A receptor - Gi Protein Complex
9O36 2.3 Å, CryoEM structure of mu-opioid receptor - Gi protein complex bound to fluornitrazene (FNZ)
9P80 2.3 Å, NTSR1-Gi-NTS(8-13) Complex in the Non-Canonical, AHD Open State (NC-Open-Apo)
8XXV 2.33 Å, Cryo-EM Structure of the Prostaglandin D2 Receptor 2-indomethacin Coupled to G Protein
3UMS 2.34 Å, Crystal structure of the G202A mutant of human G-alpha-i1
3ONW 2.38 Å, Structure of a G-alpha-i1 mutant with enhanced affinity for the RGS14 GoLoco motif.
20ZG 2.4 Å, Cryo-EM structure of the human neurotensin receptor 1 (hNTSR1)-Gi1 complex in the…

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