8K4O: G protein-coupled receptor

Cryo-EM structure of Kaposi's Sarcoma-Associated Herpesvirus-G Protein-Coupled Receptor (KSHV-GPCR)in complex with CXC chemokine CXCL1. Determined by electron microscopy at 3.01 Å resolution. Released 24 Jul 2024.

Method: Electron microscopy
Resolution: 3.01 Å
Organisms: Human gammaherpesvirus 8, Homo sapiens
Chains: 5
Atoms: 7,946
Mol. weight: 127.48 kDa
Released: 24 Jul 2024

Explore 8K4O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8K4O contains 32 α-helices and 46 β-strands across 5 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 B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	14-20	7
α-helix	38-39	2
β-strand	47-52	6	4
β-strand	58-63	6	5
β-strand	69-74	6	5
β-strand	78-83	6	5
β-strand	88-94	7	5
β-strand	100-105	6	6
β-strand	112-116	5	6
β-strand	121-125	5	6
β-strand	134-139	6	6
β-strand	146-151	6	7
β-strand	157-161	5	7
β-strand	166-168	3	7
β-strand	178-180	3	7
β-strand	187-192	6	8
β-strand	199-203	5	8
β-strand	207-210	4	8
β-strand	220-223	4	8
β-strand	229-234	6	9
β-strand	240-245	6	9
β-strand	250-254	5	9
β-strand	259-264	6	9
β-strand	273-278	6	10
β-strand	284-289	6	10
β-strand	294-298	5	10
β-strand	304-307	4	10
β-strand	315-320	6	4
β-strand	327-331	5	4
β-strand	335-339	5	4

Chain C: 9 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	10-12	3
α-helix	14-29	16
β-strand	34-38	5	11
β-strand	40	1	11
α-helix	46-53	8
β-strand	184-185	2	11
β-strand	188-190	3	11
β-strand	195-201	7	11
α-helix	212-215	4
β-strand	220-221	2	11
β-strand	224-226	3	11
β-strand	233	1	12
β-strand	241	1	12
α-helix	242-254	13
β-strand	263-269	7	11
α-helix	271-280	10
α-helix	283-285	3
α-helix	300-308	9
β-strand	319-323	5	11
α-helix	332-351	20

Chain E: 16 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	38	1	1
α-helix	47-74	28
α-helix	81-89	9
α-helix	93-100	8
α-helix	104-108	5
α-helix	110-112	3
α-helix	115-148	34
α-helix	154-156	3
α-helix	158-179	22
β-strand	183-187	5	2
β-strand	194-198	5	2
α-helix	201-203	3
α-helix	209-216	8
α-helix	217-221	5
α-helix	222-238	17
α-helix	250-278	29
α-helix	292-308	17
α-helix	310-316	7
α-helix	319-334	16

Chain F: 2 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	11	1	1
β-strand	25-28	4	3
β-strand	40-45	6	3
β-strand	48-50	3	3
α-helix	56-60	5
α-helix	61-62	2

Chain G: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	10-23	14
α-helix	30-43	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
G protein-coupled receptor	E	protein	333	Human gammaherpesvirus 8	Q98146 (AlphaFold model)
Growth-regulated alpha protein	F	protein	63	Homo sapiens	P09341 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	336	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I) subunit alpha-1	C	protein	350	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein subunit gamma	G	protein	54	Homo sapiens	P59768

Sequence of entity 1 (E), FASTA

>8K4O_1 G protein-coupled receptor (chains E)
DFLTIFLDDDESWNETLNMSGYDYSGNFSLEVSVCEMTTVVPYTWNVGILSLIFLINVLG
NGLVTYIFCKHRSRAGAIDILLLGICLNSLCLSISLLAEVLMFLFPNIISTGLCRLEIFF
YYLYVYLDIFSVVCVSLVRYLLVAYSTRSWPKKQSLGWVLTSAALLIALVLSGDACRHRS
RVVDPVSKQAMCYENAGNMTADWRLHVRTVSVTAGFLLPLALLILFYALTWCVVRRTKLQ
ARRKVRGVIVAVVLLFFVFCFPYHVLNLLDTLLRRRWIRDSCYTRGLINVGLAVTSLLQA
LYSAVVPLIYSCLGSLFRQRMYGLFQSLRQSFM

Sequence of entity 2 (F), FASTA

>8K4O_2 Growth-regulated alpha protein (chains F)
ASVATELRCQCLQTLQGIHPKNIQSVNVKSPGPHCAQTEVIATLKNGRKACLNPASPIVK
KII

Sequence of entity 3 (B), FASTA

>8K4O_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
DQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHWG
TDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIY
NLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHT
GDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFATG
SDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKADR
AGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (C), FASTA

>8K4O_4 Guanine nucleotide-binding protein G(I) subunit alpha-1 (chains C)
LSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAGYSEE
ECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDAARADDARQLFVLAGSAEEGFMTAELA
GVIKRLWKDGGVQACFSRSREYQLNDSAAYYLNDLDRISQGSYIPTQQDVLRTRVKTTGI
VETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEMNRMH
ESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAAAYIQ
CQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 5 (G), FASTA

>8K4O_5 Guanine nucleotide-binding protein subunit gamma (chains G)
IAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFR

Primary citation

Structural insights into KSHV-GPCR constitutive activation and CXCL1 chemokine recognition. Liu, A., Liu, Y., Llinas Del Torrent Masachs, C. et al. Proc Natl Acad Sci U S A (2024) 121:e2403217121-e2403217121. DOI 10.1073/pnas.2403217121 · PubMed

Other PDB entries of the same protein (UniProt Q98146 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8K4P 2.81 Å, Cryo-EM structure of an active Kaposi's Sarcoma-Associated Herpesvirus-G Protein-Coupled…
8W1A 2.89 Å, Cryo-EM Structure of KSHV ORF74 Apo Dimer at 2.8A
9EJC 2.98 Å, Cryo-EM Structure of CXCL1-KSHV ORF74-Gi-scFv16 Complex

Browse structure collections

About this viewer

MolViewer shows 8K4O 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.