8K4P: PDB entry 8K4P

Cryo-EM structure of an active Kaposi's Sarcoma-Associated Herpesvirus-G Protein-Coupled Receptor (KSHV-GPCR) in complex with Gi protein. Determined by electron microscopy at 2.81 Å resolution. Released 24 Jul 2024.

Method: Electron microscopy
Resolution: 2.81 Å
Organisms: Homo sapiens, Human gammaherpesvirus 8
Chains: 4
Atoms: 7,231
Mol. weight: 117.03 kDa
Released: 24 Jul 2024

Explore 8K4P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8K4P contains 29 α-helices and 39 β-strands across 4 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: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	48-74	27
α-helix	81-90	10
α-helix	93-104	12
α-helix	115-148	34
α-helix	158-182	25
β-strand	184	1	8
β-strand	197	1	8
α-helix	209-216	8
α-helix	217-221	5
α-helix	222-238	17
α-helix	246-278	33
α-helix	288-317	30
α-helix	319-335	17

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-23	20
α-helix	30-33	4
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	89-94	6	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	146-151	6	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	218-223	6	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	293-298	6	7
β-strand	304-309	6	7
β-strand	315-320	6	1
β-strand	327-331	5	1
β-strand	336-339	4	1

Chain C: 9 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	34-40	7	9
α-helix	49-52	4
β-strand	56	1	9
β-strand	184-190	7	9
β-strand	195-201	7	9
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-225	6	9
β-strand	233	1	10
β-strand	241	1	10
α-helix	242-254	13
β-strand	263-268	6	9
α-helix	273-275	3
α-helix	277-280	4
α-helix	296-308	13
β-strand	319-322	4	9
α-helix	331-350	20

Chain G: 5 helices, 0 β-strands

Element	Residues	Length
α-helix	10-23	14
α-helix	30-43	14
α-helix	45-47	3
α-helix	53-55	3
α-helix	56-58	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	338	Homo sapiens	P62873 (AlphaFold model)
G protein-coupled receptor	A	protein	294	Human gammaherpesvirus 8	Q98146 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	C	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein subunit gamma	G	protein	55	Homo sapiens	P59768 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>8K4P_1 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
ELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMH
WGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICS
IYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTG
HTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFA
TGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKA
DRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 2 (A), FASTA

>8K4P_2 G protein-coupled receptor (chains A)
YTWNVGILSLIFLINVLGNGLVTYIFCKHRSRAGAIDILLLGICLNSLCLSISLLAEVLM
FLFPNIISTGLCRLEIFFYYLYVYLDIFSVVCVSLVRYLLVAYSTRSWPKKQSLGWVLTS
AALLIALVLSGDACRHRSRVVDPVSKQAMCYENAGNMTADWRLHVRTVSVTAGFLLPLAL
LILFYALTWCVVRRTKLQARRKVRGVIVAVVLLFFVFCFPYHVLNLLDTLLRRRWIRDSC
YTRGLINVGLAVTSLLQALYSAVVPLIYSCLGSLFRQRMYGLFQSLRQSFMSGA

Sequence of entity 3 (C), FASTA

>8K4P_3 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains C)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 4 (G), FASTA

>8K4P_4 Guanine nucleotide-binding protein subunit gamma (chains G)
SIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFR

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 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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