8H8J: Lodoxamide-bound GPR35

Lodoxamide-bound GPR35 in complex with G13. Determined by electron microscopy at 3.2 Å resolution. Released 8 Feb 2023.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Homo sapiens, Mus musculus
Chains: 5
Atoms: 8,842
Mol. weight: 152.27 kDa
Ligands: CLR, CA, WYB
Released: 8 Feb 2023

Explore 8H8J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8H8J contains 30 α-helices and 58 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 A: 8 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-47	26
β-strand	49-54	6	1
α-helix	61-72	12
β-strand	208-214	7	1
β-strand	217-223	7	1
α-helix	236-238	3
β-strand	243-249	7	1
β-strand	256	1	2
β-strand	264	1	2
α-helix	265-277	13
α-helix	280-282	3
β-strand	286-292	7	1
α-helix	294-301	8
α-helix	321-334	14
β-strand	343-347	5	1
α-helix	355-374	20

Chain B: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-34	5
α-helix	38-39	2
β-strand	47-52	6	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	121-125	5	5
β-strand	135-139	5	5
β-strand	148-151	4	6
β-strand	156-160	5	6
β-strand	166-170	5	6
β-strand	176-180	5	6
β-strand	189-192	4	7
β-strand	198-202	5	7
β-strand	207-212	6	7
β-strand	218-223	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
β-strand	273-278	6	9
β-strand	284-289	6	9
β-strand	294-298	5	9
β-strand	304-308	5	9
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	335-339	5	3

Chain C: 14 helices, 0 β-strands

Element	Residues	Length
α-helix	17-43	27
α-helix	44-48	5
α-helix	54-78	25
α-helix	87-118	32
α-helix	122-124	3
α-helix	130-157	28
α-helix	174-178	5
α-helix	181-197	17
α-helix	202-203	2
α-helix	206-240	35
α-helix	250-266	17
α-helix	268-271	4
α-helix	273-277	5
α-helix	281-287	7

Chain G: 3 helices, 0 β-strands

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

Chain H: 2 helices, 22 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	92-99	8	12
β-strand	110-111	2	12
β-strand	115-117	3	12
β-strand	118-119	2	11
β-strand	140-142	3	13
β-strand	146-148	3	14
β-strand	154-161	8	13
β-strand	174-179	6	14
β-strand	186-190	5	14
β-strand	194-195	2	14
β-strand	203-207	5	13
β-strand	211-217	7	13
β-strand	225-231	7	14
β-strand	243-246	4	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein subunit alpha-13	A	protein	362	Homo sapiens	Q14344 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	371	Homo sapiens	P62873 (AlphaFold model)
G-protein coupled receptor 35	C	protein	308	Homo sapiens	Q9HC97 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Homo sapiens	P59768 (AlphaFold model)
scFv16	H	protein	247	Mus musculus

Sequence of entity 1 (A), FASTA

>8H8J_1 Guanine nucleotide-binding protein subunit alpha-13 (chains A)
MGCTLSAEDKAAVERSKMIDKCLSREKTYVKRLVKILLLGAGESGKSTFLKQMRIIHGQD
FDQRAREEFRPTIYSNVIKGMRVLVDAREKLHIPWGDNSNQQHGDKMMSFDTRAPMAAQG
MVETRVFLQYLPAIRALWADSGIQNAYDRRREFQLGESVKYFLDNLDKLGEPDYIPSQQD
ILLARRPTKGIHEYDFEIKNVPFKMVDVGGQRSERKRWFECFDSVTSILFLVSSSEFDQV
LMEDRLTNRLTESLNIFETIVNNRVFSNVSIILFLNKTDLLEEKVQIVSIKDYFLEFEGD
PHCLRDVQKFLVECFRNKRRDQQQKPLYHHFTTAINTENIRLVFRDVKDTILHDNLKQLM
LQ

Sequence of entity 2 (B), FASTA

>8H8J_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHL
AKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACG
GLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQ
QTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFF
PNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCN
VWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNGSSGGGGSGGGGSSG
VSGWRLFKKIS

Sequence of entity 3 (C), FASTA

>8H8J_3 G-protein coupled receptor 35 (chains C)
NGTYNTCGSSDLTWPPAIKLGFYAYLGVLLVLGLLLNSLALWVFCCRMQQWTETRIYMTN
LAVADLCLLCTLPFVLHSLRDTSDTPLCQLSQGIYLTNRYMSISLVTAIAVDRYVAVRHP
LRARGLRSPRQAAAVCAVLWVLVIGSLVARWLLGIQEGGFCFRSTRHNFNSMAFPLLGFY
LPLAVVVFCSLKVVTALAQRPPTDVGQAEATRKAARMVWANLLVFVVCFLPLHVGLTVRL
AVGWNACALLETIRRALYITSKLSDANCCLDAICYYYMAKEFQEASALAVAPSAKAHKSQ
DSLCVTLA

Sequence of entity 4 (G), FASTA

>8H8J_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (H), FASTA

>8H8J_5 scFv16 (chains H)
VQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYA
DTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSA
GGGGSGGGGSGGGGSADIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLEL

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	3
CA	Calcium ion	Ca	1
WYB	2,2'-[(2-chloro-5-cyano-1,3-phenylene)bis(azanediyl)]bis(oxoacetic acid)	C11 H6 Cl N3 O6	1

Primary citation

Insights into divalent cation regulation and G 13 -coupling of orphan receptor GPR35. Duan, J., Liu, Q., Yuan, Q. et al. Cell Discov (2022) 8:135-135. DOI 10.1038/s41421-022-00499-8 · PubMed

Other PDB entries of the same protein (UniProt Q14344 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8IKL 2.33 Å, Cryo-EM structure of the CD97-G13 complex
9GE2 2.51 Å, Structure of GPR55 in complex with G13 and synthetic agonist ML184
7SF8 2.7 Å, GPR56 (ADGRG1) 7TM domain bound to tethered agonist in complex with G protein heterotrimer
8ZX4 2.85 Å, LPI-bound GPR55 in complex with G13
9GE3 2.87 Å, Structure of GPR55 in complex with G13 and endogenous lipid agonist…
7SF7 2.9 Å, LPHN3 (ADGRL3) 7TM domain bound to tethered agonist in complex with G protein heterotrimer
9E51 2.9 Å, Cryo-EM structure of human LPHN2 (ADGRL2)/G13 complex in lipid nanodiscs
9ECJ 2.9 Å, Human P2RY8 bound to S-geranylgeranyl-L-glutathione in complex with miniG13
9IY8 3.01 Å, Cryo-EM structure of apo-GPR55-G13 complex
8ZX5 3.03 Å, AM251-bound GPR55 in complex with G13
9IZH 3.04 Å, Cryo-EM structure of LPA1-G13 complex with LPA
8KGG 3.06 Å, LPS-bound P2Y10 in complex with G13

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