8K3Z: CXCR4

Cryo-EM structure of CXCR4 in complex with CXCL12. Determined by electron microscopy at 2.81 Å resolution. Released 17 Jul 2024.

Method: Electron microscopy
Resolution: 2.81 Å
Organisms: Homo sapiens, Vicugna pacos
Chains: 6
Atoms: 9,536
Mol. weight: 151.2 kDa
Released: 17 Jul 2024

Explore 8K3Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8K3Z contains 37 α-helices and 71 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: 18 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	32-64	33
α-helix	73-89	17
α-helix	91-96	6
α-helix	105-139	35
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	175-177	3	1
β-strand	180	1	2
β-strand	183	1	2
β-strand	186-188	3	1
α-helix	193-204	12
α-helix	205-209	5
α-helix	210-226	17
α-helix	234-266	33
α-helix	274-291	18
α-helix	294-299	6
α-helix	300-304	5
α-helix	307-316	10

Chain B: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	10-23	14
α-helix	30-33	4
β-strand	47-51	5	3
β-strand	58-63	6	4
β-strand	69-74	6	4
β-strand	78-83	6	4
β-strand	88-94	7	4
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	187-192	6	7
β-strand	198-203	6	7
β-strand	207-212	6	7
β-strand	218-223	6	7
β-strand	229-234	6	8
β-strand	240-245	6	8
β-strand	250-254	5	8
β-strand	260-264	5	8
β-strand	273-278	6	9
β-strand	284-289	6	9
β-strand	294-298	5	9
β-strand	303-308	6	9
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	336-339	4	3

Chain C: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	34-39	6	10
α-helix	46-50	5
β-strand	185-191	7	10
β-strand	194-200	7	10
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	10
β-strand	233	1	11
β-strand	241	1	11
α-helix	242-254	13
β-strand	263-269	7	10
α-helix	271-280	10
α-helix	296-308	13
β-strand	319-322	4	10
α-helix	330-350	21

Chain D: 2 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	3-5	3
β-strand	25	1	12
β-strand	28-29	2	13
β-strand	37-38	2	13
β-strand	40	1	14
β-strand	41	1	12
β-strand	49	1	14
α-helix	56-61	6

Chain G: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	10-23	14
α-helix	30-44	15
α-helix	45-47	3
α-helix	53-55	3
α-helix	56-58	3

Chain S: 2 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	15
β-strand	11-12	2	16
β-strand	17-25	9	15
α-helix	29-31	3
β-strand	33-39	7	17
β-strand	45-51	7	17
β-strand	58-60	3	17
β-strand	68-73	6	15
β-strand	78-84	7	15
β-strand	92-99	8	17
β-strand	110-111	2	17
β-strand	115-117	3	17
β-strand	118-119	2	16
β-strand	140-141	2	18
β-strand	146-148	3	19
β-strand	156-161	6	18
β-strand	166	1	20
β-strand	172	1	20
β-strand	174-179	6	19
β-strand	186-190	5	19
β-strand	194-195	2	19
α-helix	196	1
β-strand	204-207	4	18
β-strand	211-215	5	18
β-strand	225-231	7	19
β-strand	239	1	19
β-strand	243-246	4	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
C-X-C chemokine receptor type 4	A	protein	296	Homo sapiens	P61073 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	338	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	C	protein	354	Homo sapiens	P63096 (AlphaFold model)
Stromal cell-derived factor 1	D	protein	62	Homo sapiens	P48061 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	55	Homo sapiens	P59768
scFv16	S	protein	247	Vicugna pacos

Sequence of entity 1 (A), FASTA

>8K3Z_1 C-X-C chemokine receptor type 4 (chains A)
KEPCFREENANFNKIFLPTIYSIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHLSVAD
LLFVITLPFWAVDAVANWYFGNFLCKAVHVIYTVNLYSSVLILAFISLDRYLAIVHATNS
QRPRKLLAEKVVYVGVWIPALLLTIPDFIFANVSEADDRYICDRFYPNDLWVVVFQFQHI
MVGLILPGIVILSCYCIIISKLSHSKGHQKRKALKTTVILILAFFACWLPYYIGISIDSF
ILLEIIKQGCEFENTVHKWISITEALAFFHCCLNPILYAFLGAKFKTSAQHALTSV

Sequence of entity 2 (B), FASTA

>8K3Z_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
ELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMH
WGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICS
IYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTG
HTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFA
TGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKA
DRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (C), FASTA

>8K3Z_3 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains C)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 4 (D), FASTA

>8K3Z_4 Stromal cell-derived factor 1 (chains D)
KPVSLSYRCPCRFFESHVARANVKHLKILNTPNCALQIVARLKNNNRQVCIDPKLKWIQE
YL

Sequence of entity 5 (G), FASTA

>8K3Z_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
IAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFRE

Sequence of entity 6 (S), FASTA

>8K3Z_6 scFv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLEL

Primary citation

Cryo-EM structure of monomeric CXCL12-bound CXCR4 in the active state. Liu, Y., Liu, A., Li, X. et al. Cell Rep (2024) 43:114578-114578. DOI 10.1016/j.celrep.2024.114578 · 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
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…
8U4R 3.1 Å, Structure of REGN7663-Fab bound CXCR4

Browse structure collections

About this viewer

MolViewer shows 8K3Z directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.