9XJ7: PDB entry 9XJ7

Structure of the CX3CL1.44-US28-GqiN18-scFv16 in the C'-state with AHD visible. Determined by electron microscopy at 2.89 Å resolution. Released 23 Sept 2026.

Method: Electron microscopy
Resolution: 2.89 Å
Organisms: Homo sapiens, Mus musculus, Human betaherpesvirus 5
Chains: 6
Atoms: 10,068
Mol. weight: 165.86 kDa
Released: 23 Sept 2026

Explore 9XJ7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9XJ7 contains 40 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: 18 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-36	24
β-strand	39-46	8	1
α-helix	52-62	11
α-helix	69-97	29
α-helix	104-113	10
α-helix	126-137	12
α-helix	139-145	7
α-helix	157-161	5
α-helix	164-167	4
α-helix	176-180	5
β-strand	190-196	7	1
β-strand	199-205	7	1
α-helix	213-217	5
α-helix	218-220	3
β-strand	225-231	7	1
α-helix	234-236	3
β-strand	238-239	2	2
β-strand	245-246	2	2
α-helix	247-259	13
α-helix	262-264	3
β-strand	268-274	7	1
α-helix	276-285	10
α-helix	288-291	4
α-helix	302-314	13
β-strand	324-328	5	1
α-helix	334-355	22

Chain B: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-33	4
α-helix	34-36	3
α-helix	38-39	2
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	89-94	6	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	146-151	6	6
β-strand	156-161	6	6
β-strand	165-170	6	6
β-strand	175-181	7	6
α-helix	186	1
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	249-254	6	8
β-strand	259-264	6	8
β-strand	273-278	6	9
β-strand	284-289	6	9
β-strand	294-298	5	9
β-strand	304-308	5	9
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	336-339	4	3

Chain C: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	8-23	16
α-helix	30-43	14

Chain D: 1 helix, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	11-12	2	11
β-strand	18-25	8	10
α-helix	29-31	3
β-strand	33-39	7	12
β-strand	45-51	7	12
β-strand	58-60	3	12
β-strand	68-73	6	10
β-strand	78-83	6	10
β-strand	92-99	8	12
β-strand	111	1	12
β-strand	115-117	3	12
β-strand	118-119	2	11
β-strand	129-130	2	13
β-strand	134-136	3	14
β-strand	143-148	6	13
β-strand	154	1	15
β-strand	160	1	15
β-strand	162-167	6	14
β-strand	173-178	6	14
β-strand	182-183	2	14
β-strand	191-195	5	13
β-strand	199-204	6	13
β-strand	213-219	7	14
β-strand	231-234	4	14

Chain L: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-6	5

Chain R: 13 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	26-58	33
α-helix	67-95	29
α-helix	102-104	3
α-helix	105-130	26
α-helix	131-135	5
α-helix	141-163	23
β-strand	167	1	16
β-strand	175	1	16
α-helix	184-195	12
α-helix	198-216	19
α-helix	223-255	33
α-helix	263-279	17
α-helix	282-288	7
α-helix	289-293	5
α-helix	299-309	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(q)…	A	protein	352	Homo sapiens	P50148 (AlphaFold model), P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	345	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	67	Homo sapiens	P59768 (AlphaFold model)
antibody fragment scFv16	D	protein	256	Mus musculus
Processed fractalkine	L	protein	91	Homo sapiens	P78423
G-protein coupled receptor homolog US28	R	protein	362	Human betaherpesvirus 5	P69332

Sequence of entity 1 (A), FASTA

>9XJ7_1 Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(q) subunit alpha (chains A)
GCTLSAEDKAAVERSKMIERQLRRDKRDARRELKLLLLGTGESGKSTFIKQMRIIHGSGY
SDEDKRGFTKLVYQNIFTAMQAMIRAMDTLKIPYKYEHNKAHAQLVREVDVEKVSAFENP
YVDAIKSLWNDPGIQECYDRRREYQLSDSTKYYLNDLDRVADPAYLPTQQDVLRVRVPTT
GIIEYPFDLQSVIFRMVDVGGQRSERRKWIHCFENVTSIMFLVALSEYDQVLVESDNENR
MEESKALFRTIITYPWFQNSSVILFLNKKDLLEEKIMYSHLVDYFPEYDGPQRDAQAARE
FILKMFVDLNPDSDKIIYSHFTCATDTENIRFVFAAVKDTILQLNLKEYNLV

Sequence of entity 2 (B), FASTA

>9XJ7_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
GPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (C), FASTA

>9XJ7_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF
REKKFFC

Sequence of entity 4 (D), FASTA

>9XJ7_4 antibody fragment scFv16 (chains D)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKGSLEVLFQ

Sequence of entity 5 (L), FASTA

>9XJ7_5 Processed fractalkine (chains L)
VRPHINNCNITCSKMTSKIPVALLIHYQQNQASCGKRAIILETRQHRLFCADPKEQWVKD
AMQHLDRQAAALTRNGGSGSGSAAALEVLFQ

Sequence of entity 6 (R), FASTA

>9XJ7_6 G-protein coupled receptor homolog US28 (chains R)
DYKDDDDAMTPTTTTAELTTEFDYDEDATPCVFTDVLNQSKPVTLFLYGVVFLFGSIGNF
LVIFTITWRRRIQCSGDVYFINLAAADLLFVCTLPLWMQYLLDHNSLASVPCTLLTACFY
VAMFASLCFITEIALDRYYAIVYMRYRPVKQACLFSIFWWIFAVIIAIPHFMVVTKKDNQ
CMTDYDYLEVSYPIILNVELMLGAFVIPLSVISYCYYRISRIVAVSQSRHKGRIVRVLIA
VVLVFIIFWLPYHLTLFVDTLKLLKWISSSCEFERSLKRALILTESLAFCHCCLNPLLYV
FVGTKFRQELHCLLAEFRQRLFSRDVSWYHSMSFSRRSSPSRRETSSDTLSDEVCRVSQI
IP

Primary citation

Structural basis of a stepwise Gq activation by a chemokine receptor US28. Jude, K.M., Garcia, K.C., Tsutsumi, N. To be published.

Other PDB entries of the same protein (UniProt P50148 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9VAW 2.24 Å, Cryo-EM structure of human Neurotensin Receptor 1 (hNTSR1)-Gq (delipidated) complex in…
9M1H 2.55 Å, Cryo-EM structure of PGE2-EP1-Gq complex
9XIX 2.58 Å, Structure of the CX3CL1.44-US28-GqiN18-scFv16 in the C-state
8THK 2.6 Å, Cryo-EM structure of A61603-bound alpha-1A-adrenergic receptor in complex with…
9XH2 2.6 Å, Structure of the CX3CL1.44-US28-GqiN18-scFv16 in the E-state
8G59 2.64 Å, Cryo-EM structure of the TUG891 bound GPR120-Giq complex
24XB 2.65 Å, Cryo-EM Structure of the Apo FFAR4-Gq Complex
8XGO 2.68 Å, a peptide receptor complex structure
9K27 2.68 Å, PrRP31 bound prolactin-releasing peptide receptor coupled with Gq protein complex
9XJP 2.74 Å, Structure of the CX3CL1.44-US28-GqiN18-scFv16 in the E-state, chemokine domain fully…
9LL9 2.76 Å, DOI-bound Serotonin 2A (5-HT2A) receptor-Gq complex
7F6I 2.8 Å, Cryo-EM structure of human bradykinin receptor BK2R in complex Gq proteins and kallidin

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