9EJC: CXCL1-KSHV ORF74-Gi-scFv16 Complex

Cryo-EM Structure of CXCL1-KSHV ORF74-Gi-scFv16 Complex. Determined by electron microscopy at 2.98 Å resolution. Released 3 Sept 2025.

Method: Electron microscopy
Resolution: 2.98 Å
Organisms: Homo sapiens, Human gammaherpesvirus 8, Mus musculus
Chains: 6
Atoms: 9,492
Mol. weight: 168.57 kDa
Released: 3 Sept 2025

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

Secondary structure: helices and β-sheets

9EJC contains 42 α-helices and 63 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, 6 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	33-38	6	10
α-helix	48-53	6
β-strand	186-190	5	10
β-strand	195-200	6	10
α-helix	201-203	3
α-helix	208-212	5
α-helix	213-215	3
β-strand	220-226	7	10
α-helix	242-254	13
β-strand	263-269	7	10
α-helix	271-277	7
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-323	5	10
α-helix	331-350	20

Chain B: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	6-25	20
α-helix	30-34	5
α-helix	38-39	2
β-strand	47-51	5	1
β-strand	58-63	6	2
β-strand	69-74	6	2
β-strand	78-83	6	2
β-strand	88-94	7	2
α-helix	95	1
β-strand	100-105	6	3
β-strand	111-116	6	3
β-strand	121-125	5	3
β-strand	134-139	6	3
β-strand	146-153	8	4
β-strand	156-161	6	4
β-strand	165-170	6	4
β-strand	175-181	7	4
β-strand	187-192	6	5
β-strand	198-203	6	5
β-strand	207-212	6	5
β-strand	218-222	5	5
β-strand	229-234	6	6
β-strand	240-245	6	6
β-strand	250-254	5	6
β-strand	259-264	6	6
β-strand	273-278	6	7
β-strand	284-289	6	7
β-strand	294-298	5	7
β-strand	304-308	5	7
α-helix	309-310	2
β-strand	315-320	6	1
β-strand	327-331	5	1
β-strand	336-339	4	1

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	10-18	9
α-helix	21-23	3
α-helix	30-43	14
α-helix	53-55	3

Chain D: 5 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	10-12	3	12
β-strand	18-25	8	11
β-strand	33-39	7	12
β-strand	45-51	7	12
β-strand	58-60	3	12
β-strand	68-73	6	11
α-helix	74-76	3
β-strand	78-83	6	11
α-helix	88-90	3
β-strand	92-99	8	12
β-strand	110	1	12
β-strand	115-119	5	12
β-strand	128-129	2	13
β-strand	134-136	3	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	214-219	6	14
α-helix	225	1
β-strand	226-227	2	14
β-strand	231-234	4	14

Chain E: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	47-74	28
α-helix	76-78	3
α-helix	81-90	10
α-helix	92-108	17
α-helix	110-112	3
α-helix	117-148	32
α-helix	154-156	3
α-helix	158-179	22
α-helix	180-182	3
β-strand	183-186	4	8
β-strand	195-198	4	8
α-helix	204-216	13
α-helix	217-221	5
α-helix	222-240	19
α-helix	246-279	34
α-helix	283-284	2
α-helix	286-316	31
α-helix	320-329	10

Chain F: 2 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	2-4	3
β-strand	26-27	2	9
β-strand	40-43	4	9
β-strand	49-52	4	9
α-helix	59-71	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	360	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	71	Homo sapiens	P59768 (AlphaFold model)
viral G-protein coupled receptor	E	protein	348	Human gammaherpesvirus 8	Q98146 (AlphaFold model)
Growth-regulated alpha protein	F	protein	91	Homo sapiens	P09341 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Homo sapiens	P63096
scFv Recombinant Mouse Monoclonal Antibody (scFv16)	D	protein	287	Mus musculus

Sequence of entity 1 (B), FASTA

>9EJC_1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
HHHHHHHHLEVLFQGPPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPV
GRIQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWV
MTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTS
SGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQ
TFTGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSK
SGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 2 (C), FASTA

>9EJC_2 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 3 (E), FASTA

>9EJC_3 viral G-protein coupled receptor (chains E)
MAAEDFLTIFLDDDESWNETLNMSGYDYSCNFSLEVSVCEMTTVVPYTWNVGILSLIFLI
NVLGNGLVTYIFCKHRSRAGAIDILLLGICLNSLCLSISLLAEVLMFLFPNIISTGLCRL
EIFFYYLYVYLDIFSVVCVSLVRYLLVAYSTRSWPKKQSLGWVLTSAAWLIALVLSGDAC
RHRSRVVDPVSKQAMCYENAGNMTADWRLHVRTVSVTAGFLLPLALLILFYALTWCVVRR
TKLQARRKVRGVIVAVVVLFFVFCFPYHVLNLLDTLLRRRWIRDSCYTRGLINVGLAVTS
LLQALYSAVVPLIYSCLGSLFRQRMYGLFQSLRQSFMSGADYKDDDDK

Sequence of entity 4 (F), FASTA

>9EJC_4 Growth-regulated alpha protein (chains F)
ASVATELRCQCLQTLQGIHPKCIQSVNVKSPGPHCAQTEVIATLKNGRKACLNPASPIVK
KIIEKMLNSDKSNLEVLFQGPHHHHHHHHHH

Sequence of entity 5 (A), FASTA

>9EJC_5 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 6 (D), FASTA

>9EJC_6 scFv Recombinant Mouse Monoclonal Antibody (scFv16) (chains D)
METDTLLLWVLLLWVPGSTGDVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQA
PEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSI
YYYGSSPFDFWGQGTTLTVSSGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCR
SSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLE
AEDVGVYYCMQHLEYPLTFGAGTKLELKAAALEVLFQGPHHHHHHHH

Primary citation

Structural basis for ligand promiscuity and high signaling activity of Kaposi's Sarcoma-associated Herpesvirus-encoded GPCR. Park, J.B., Sahoo, B., Sahoo, A.R. et al. Nat Commun (2025) 16:8403-8403. DOI 10.1038/s41467-025-63457-4 · PubMed

Other PDB entries of the same protein (UniProt P62873 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8QEH 1.43 Å, Crystal structure of the G11 protein heterotrimer bound to FR900359 inhibitor
8QEG 1.7 Å, Crystal structure of the G11 protein heterotrimer bound to YM-254890 inhibitor
8F0K 1.9 Å, Human Amylin3 Receptor in complex with Gs and Pramlintide analogue peptide San385
9YDQ 1.94 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE and allosteric…
9YDP 1.95 Å, Human delta opioid receptor complex with mini-Gi and agonist DADLE
6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
8F0J 2.0 Å, Calcitonin Receptor in complex with Gs and Pramlintide analogue peptide San45
8F2B 2.0 Å, Amylin 3 Receptor in complex with Gs and Pramlintide analogue peptide San45
9XXT 2.0 Å, Cryo-EM structure of lysophosphatidylserine (18:0)-bound GPR174-Gs complex
6X18 2.1 Å, GLP-1 peptide hormone bound to Glucagon-Like peptide-1 (GLP-1) Receptor
6X19 2.1 Å, Non peptide agonist CHU-128, bound to Glucagon-Like peptide-1 (GLP-1) Receptor
9NTU 2.1 Å, Cryo-EM structure of BETP-GLP-1(9-36)-GLP-1R-Gs complex

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