9XIY: CX3CL1.44-US28-GqiN18-scFv16 in the T2C-state

Structure of the CX3CL1.44-US28-GqiN18-scFv16 in the T2C-state. Determined by electron microscopy at 2.86 Å resolution. Released 23 Sept 2026.

Method: Electron microscopy
Resolution: 2.86 Å
Organisms: Homo sapiens, Mus musculus, Cytomegalovirus
Chains: 6
Atoms: 10,005
Mol. weight: 166.31 kDa
Ligands: GDP
Released: 23 Sept 2026

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

Secondary structure: helices and β-sheets

9XIY contains 43 α-helices and 64 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: 19 helices, 6 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	69-97	29
α-helix	107-112	6
α-helix	126-136	11
α-helix	139-145	7
α-helix	148-150	3
α-helix	157-162	6
α-helix	165-168	4
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
α-helix	247-259	13
β-strand	268-274	7	1
α-helix	276-285	10
α-helix	288-290	3
α-helix	303-314	12
β-strand	324-328	5	1
α-helix	333-335	3
α-helix	338-355	18

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-33	4
α-helix	38-39	2
β-strand	47-51	5	2
β-strand	58-63	6	3
β-strand	69-74	6	3
β-strand	78-83	6	3
β-strand	89-94	6	3
β-strand	100-105	6	4
β-strand	111-116	6	4
β-strand	121-125	5	4
β-strand	134-139	6	4
β-strand	146-153	8	5
β-strand	156-161	6	5
β-strand	165-170	6	5
β-strand	175-181	7	5
α-helix	186	1
β-strand	187-192	6	6
β-strand	198-203	6	6
β-strand	207-212	6	6
β-strand	218-223	6	6
β-strand	229-234	6	7
β-strand	240-245	6	7
β-strand	249-254	6	7
β-strand	259-265	7	7
β-strand	275-278	4	8
β-strand	284-288	5	8
β-strand	294-298	5	8
β-strand	304-308	5	8
β-strand	319-320	2	2
β-strand	327-329	3	2
β-strand	336-339	4	2

Chain C: 2 helices, 0 β-strands

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

Chain D: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	11-12	2	10
β-strand	18-25	8	9
α-helix	29-31	3
β-strand	35-39	5	11
β-strand	45-51	7	11
α-helix	52	1
β-strand	58-60	3	11
β-strand	68-69	2	9
β-strand	72-73	2	9
α-helix	74-76	3
β-strand	78-83	6	9
β-strand	92-95	4	11
β-strand	97	1	12
β-strand	111	1	12
β-strand	115-117	3	11
β-strand	118-119	2	10
β-strand	129	1	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	214	1	14
β-strand	217-219	3	14
β-strand	226	1	14
β-strand	232-234	3	14

Chain L: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-6	5

Chain R: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	26-57	32
α-helix	63-64	2
α-helix	67-84	18
α-helix	86-95	10
α-helix	101-130	30
α-helix	131-135	5
α-helix	141-163	23
β-strand	167	1	16
β-strand	175	1	16
α-helix	184-196	13
α-helix	198-217	20
α-helix	223-254	32
α-helix	263-281	19
α-helix	287-288	2
α-helix	289-293	5
α-helix	299-305	7

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)
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 (AlphaFold model)
G-protein coupled receptor homolog US28	R	protein	362	Cytomegalovirus	P69332

Sequence of entity 1 (A), FASTA

>9XIY_1 Guanine nucleotide-binding protein G(i) subunit alpha-1,Guanine nucleotide-binding protein G(q) subunit alpha,Guanine nucleotide-binding protein G(q) subunit alpha (chains A)
GCTLSAEDKAAVERSKMIERQLRRDKRDARRELKLLLLGTGESGKSTFIKQMRIIHGSGY
SDEDKRGFTKLVYQNIFTAMQAMIRAMDTLKIPYKYEHNKAHAQLVREVDVEKVSAFENP
YVDAIKSLWNDPGIQECYDRRREYQLSDSTKYYLNDLDRVADPAYLPTQQDVLRVRVPTT
GIIEYPFDLQSVIFRMVDVGGQRSERRKWIHCFENVTSIMFLVALSEYDQVLVESDNENR
MEESKALFRTIITYPWFQNSSVILFLNKKDLLEEKIMYSHLVDYFPEYDGPQRDAQAARE
FILKMFVDLNPDSDKIIYSHFTCATDTENIRFVFAAVKDTILQLNLKEYNLV

Sequence of entity 2 (B), FASTA

>9XIY_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

>9XIY_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF
REKKFFC

Sequence of entity 4 (D), FASTA

>9XIY_4 antibody fragment scFv16 (chains D)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKGSLEVLFQ

Sequence of entity 5 (L), FASTA

>9XIY_5 Processed fractalkine (chains L)
VRPHINNCNITCSKMTSKIPVALLIHYQQNQASCGKRAIILETRQHRLFCADPKEQWVKD
AMQHLDRQAAALTRNGGSGSGSAAALEVLFQ

Sequence of entity 6 (R), FASTA

>9XIY_6 G-protein coupled receptor homolog US28 (chains R)
DYKDDDDAMTPTTTTAELTTEFDYDEDATPCVFTDVLNQSKPVTLFLYGVVFLFGSIGNF
LVIFTITWRRRIQCSGDVYFINLAAADLLFVCTLPLWMQYLLDHNSLASVPCTLLTACFY
VAMFASLCFITEIALDRYYAIVYMRYRPVKQACLFSIFWWIFAVIIAIPHFMVVTKKDNQ
CMTDYDYLEVSYPIILNVELMLGAFVIPLSVISYCYYRISRIVAVSQSRHKGRIVRVLIA
VVLVFIIFWLPYHLTLFVDTLKLLKWISSSCEFERSLKRALILTESLAFCHCCLNPLLYV
FVGTKFRQELHCLLAEFRQRLFSRDVSWYHSMSFSRRSSPSRRETSSDTLSDEVCRVSQI
IP

Ligands and cofactors

ID	Name	Formula	Copies
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., 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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