9XJP: PDB entry 9XJP

Structure of the CX3CL1.44-US28-GqiN18-scFv16 in the E-state, chemokine domain fully modeled. Determined by electron microscopy at 2.74 Å resolution. Released 23 Sept 2026.

Method: Electron microscopy
Resolution: 2.74 Å
Organisms: Homo sapiens, Mus musculus, Human betaherpesvirus 5
Chains: 6
Atoms: 10,700
Mol. weight: 167.08 kDa
Ligands: CLR, GDP
Released: 23 Sept 2026

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

Secondary structure: helices and β-sheets

9XJP contains 51 α-helices and 66 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: 22 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-35	23
α-helix	36-38	3
β-strand	39-46	8	1
α-helix	52-63	12
α-helix	69-73	5
α-helix	76-96	21
α-helix	106-114	9
α-helix	118-120	3
α-helix	126-136	11
α-helix	139-146	8
α-helix	148-150	3
α-helix	157-161	5
α-helix	164-168	5
α-helix	176-179	4
β-strand	190-196	7	1
β-strand	199-205	7	1
α-helix	213-215	3
α-helix	217-220	4
β-strand	225-231	7	1
β-strand	238	1	2
β-strand	246	1	2
α-helix	247-260	14
α-helix	262-264	3
β-strand	268-274	7	1
α-helix	276-282	7
α-helix	288-290	3
α-helix	302-314	13
α-helix	323-324	2
β-strand	325-328	4	1
α-helix	334-351	18

Chain B: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-23	20
α-helix	30-34	5
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	166-170	5	6
β-strand	175-180	6	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	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: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	8-23	16
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3
α-helix	56-58	3

Chain D: 5 helices, 25 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
α-helix	88-90	3
β-strand	92-99	8	12
β-strand	110-111	2	12
β-strand	115-117	3	12
β-strand	118-119	2	11
β-strand	128-129	2	13
β-strand	134-137	4	14
β-strand	143-149	7	13
β-strand	154	1	15
β-strand	160	1	15
β-strand	162-167	6	14
β-strand	174-178	5	14
β-strand	182-183	2	14
α-helix	184	1
β-strand	191-195	5	13
β-strand	199-204	6	13
α-helix	209-211	3
β-strand	213-219	7	14
α-helix	225	1
β-strand	226-227	2	14
β-strand	231-235	5	14

Chain L: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	24-28	5	17
α-helix	38	1
β-strand	39-43	5	17
β-strand	48-51	4	17
α-helix	56-66	11

Chain R: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	26-31	6
α-helix	33-59	27
α-helix	67-94	28
α-helix	101-134	34
α-helix	141-159	19
α-helix	160-162	3
β-strand	165	1	16
β-strand	175	1	16
α-helix	184-193	10
α-helix	194-198	5
α-helix	199-216	18
α-helix	223-255	33
α-helix	263-280	18
α-helix	283-287	5
α-helix	288-292	5
α-helix	296-309	14

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
G-protein coupled receptor homolog US28	R	protein	362	Human betaherpesvirus 5	P69332
Processed fractalkine	L	protein	91	Homo sapiens	P78423

Sequence of entity 1 (A), FASTA

>9XJP_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

>9XJP_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

>9XJP_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF
REKKFFC

Sequence of entity 4 (D), FASTA

>9XJP_4 Antibody fragment scFv16 (chains D)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKGSLEVLFQ

Sequence of entity 5 (R), FASTA

>9XJP_5 G-protein coupled receptor homolog US28 (chains R)
DYKDDDDAMTPTTTTAELTTEFDYDEDATPCVFTDVLNQSKPVTLFLYGVVFLFGSIGNF
LVIFTITWRRRIQCSGDVYFINLAAADLLFVCTLPLWMQYLLDHNSLASVPCTLLTACFY
VAMFASLCFITEIALDRYYAIVYMRYRPVKQACLFSIFWWIFAVIIAIPHFMVVTKKDNQ
CMTDYDYLEVSYPIILNVELMLGAFVIPLSVISYCYYRISRIVAVSQSRHKGRIVRVLIA
VVLVFIIFWLPYHLTLFVDTLKLLKWISSSCEFERSLKRALILTESLAFCHCCLNPLLYV
FVGTKFRQELHCLLAEFRQRLFSRDVSWYHSMSFSRRSSPSRRETSSDTLSDEVCRVSQI
IP

Sequence of entity 6 (L), FASTA

>9XJP_6 Processed fractalkine (chains L)
VRPHINNCNITCSKMTSKIPVALLIHYQQNQASCGKRAIILETRQHRLFCADPKEQWVKD
AMQHLDRQAAALTRNGGSGSGSAAALEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	2
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	1

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
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
9XJ5 2.81 Å, Structure of the CX3CL1.44-US28-GqiN18-scFv16 in the C-state, full chemokine domain…

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