9XJ5: PDB entry 9XJ5

Structure of the CX3CL1.44-US28-GqiN18-scFv16 in the C-state, full chemokine domain modeled. Determined by electron microscopy at 2.81 Å resolution. Released 23 Sept 2026.

Method: Electron microscopy
Resolution: 2.81 Å
Organisms: Homo sapiens, Mus musculus, Human betaherpesvirus 5
Chains: 6
Atoms: 9,554
Mol. weight: 165.86 kDa
Released: 23 Sept 2026

Explore 9XJ5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9XJ5 contains 42 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: 10 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	6-36	24
β-strand	40-46	7	1
α-helix	52-62	11
β-strand	190-191	2	1
β-strand	194-195	2	1
β-strand	200-205	6	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	247-259	13
α-helix	262-264	3
β-strand	268-274	7	1
α-helix	276-284	9
α-helix	288-290	3
α-helix	302-314	13
β-strand	324-328	5	1
α-helix	334-355	22

Chain B: 4 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	30-33	4
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	146-153	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	208-212	5	7
β-strand	217-222	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
α-helix	272	1
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	315-317	3	3
β-strand	320	1	3
β-strand	327-331	5	3
β-strand	336-339	4	3

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	8-22	15
α-helix	30-42	13
α-helix	45-47	3
α-helix	53-55	3

Chain D: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	11-12	2	11
β-strand	17-25	9	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	78-84	7	10
α-helix	88-90	3
β-strand	92-94	3	13
β-strand	95-99	5	12
β-strand	110-111	2	12
β-strand	115-117	3	13
β-strand	118-119	2	11
α-helix	126-127	2
β-strand	128-130	3	14
β-strand	134-136	3	15
β-strand	143-149	7	14
β-strand	154	1	16
β-strand	160	1	16
β-strand	162-167	6	15
β-strand	174-178	5	15
β-strand	182-183	2	15
α-helix	184	1
β-strand	191-195	5	14
β-strand	199-204	6	14
β-strand	213-219	7	15
α-helix	225	1
β-strand	227	1	15
β-strand	231-234	4	15

Chain L: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	2-5	4
β-strand	10-11	2	17
β-strand	24-28	5	18
α-helix	38	1
β-strand	39-43	5	18
β-strand	48-51	4	18
α-helix	57-67	11

Chain R: 16 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	23-24	2	17
α-helix	27-58	32
α-helix	67-84	18
α-helix	86-94	9
α-helix	101-134	34
α-helix	141-159	19
α-helix	160-162	3
β-strand	165-168	4	19
β-strand	172-175	4	19
α-helix	184-193	10
α-helix	194-198	5
α-helix	199-216	18
α-helix	223-239	17
α-helix	242-255	14
α-helix	263-279	17
α-helix	280-282	3
α-helix	283-288	6
α-helix	289-293	5
α-helix	300-308	9

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

>9XJ5_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

>9XJ5_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

>9XJ5_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF
REKKFFC

Sequence of entity 4 (D), FASTA

>9XJ5_4 antibody fragment scFv16 (chains D)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKGSLEVLFQ

Sequence of entity 5 (L), FASTA

>9XJ5_5 Processed fractalkine (chains L)
VRPHINNCNITCSKMTSKIPVALLIHYQQNQASCGKRAIILETRQHRLFCADPKEQWVKD
AMQHLDRQAAALTRNGGSGSGSAAALEVLFQ

Sequence of entity 6 (R), FASTA

>9XJ5_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

Browse structure collections

About this viewer

MolViewer shows 9XJ5 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.