9IZH: LPA1-G13 complex with LPA

Cryo-EM structure of LPA1-G13 complex with LPA. Determined by electron microscopy at 3.04 Å resolution. Released 1 Jan 2025.

Method: Electron microscopy
Resolution: 3.04 Å
Organisms: Escherichia coli, Homo sapiens, synthetic construct
Chains: 5
Atoms: 8,861
Mol. weight: 175.98 kDa
Ligands: NKP
Released: 1 Jan 2025

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

Secondary structure: helices and β-sheets

9IZH contains 33 α-helices and 65 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: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	9-30	22
β-strand	34-39	6	2
α-helix	46-51	6
β-strand	70-76	7	2
β-strand	79-85	7	2
α-helix	88-91	4
β-strand	105-111	7	2
α-helix	115-129	15
β-strand	138-144	7	2
α-helix	146-152	7
α-helix	172-184	13
β-strand	191	1	3
β-strand	193	1	3
β-strand	195-198	4	2
α-helix	207-226	20

Chain B: 4 helices, 29 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	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
α-helix	95	1
β-strand	100-105	6	6
β-strand	111-116	6	6
β-strand	121-125	5	6
β-strand	134-139	6	6
β-strand	146-153	8	7
β-strand	156-161	6	7
β-strand	165-170	6	7
β-strand	175-180	6	7
β-strand	187	1	8
β-strand	191-192	2	8
β-strand	198-203	6	8
β-strand	207-212	6	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	260-264	5	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	336-339	4	4

Chain C: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	30-43	14
α-helix	45-47	3
α-helix	54-55	2

Chain R: 14 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	30-36	7
α-helix	47-76	30
α-helix	78-80	3
α-helix	83-107	25
α-helix	118-148	31
α-helix	156-158	3
α-helix	162-180	19
α-helix	181-183	3
β-strand	195	1	1
β-strand	203	1	1
α-helix	204-238	35
α-helix	250-255	6
α-helix	257-283	27
α-helix	293-301	9
α-helix	303-306	4
α-helix	316-325	10

Chain S: 4 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	11
β-strand	11-12	2	12
β-strand	18-24	7	11
α-helix	29-31	3
β-strand	33-39	7	13
β-strand	45-51	7	13
β-strand	58-60	3	13
β-strand	65	1	11
β-strand	68-73	6	11
β-strand	78-83	6	11
β-strand	92-99	8	13
β-strand	110-111	2	13
β-strand	115-117	3	13
β-strand	118-119	2	12
β-strand	128-129	2	14
β-strand	134-135	2	15
β-strand	143-149	7	14
β-strand	154	1	16
β-strand	160	1	16
β-strand	162-167	6	15
β-strand	174-178	5	15
β-strand	182-183	2	15
α-helix	184	1
β-strand	191-195	5	14
β-strand	199-204	6	14
α-helix	209-211	3
β-strand	213-219	7	15
β-strand	227	1	15
α-helix	228-230	3
β-strand	232-233	2	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Soluble cytochrome b562,Lysophosphatidic acid receptor 1,LgBiT tag	R	protein	651	Escherichia coli, Homo sapiens, synthetic construct	P0ABE7 (AlphaFold model), Q92633 (AlphaFold model)
G protein subunit 13 (Gi2-mini-G13 chimera)	A	protein	228	Homo sapiens	Q14344 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	382	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	protein	70	Mus musculus	P63213
scFv16	S	protein	248	synthetic construct

Sequence of entity 1 (R), FASTA

>9IZH_1 Soluble cytochrome b562,Lysophosphatidic acid receptor 1,LgBiT tag (chains R)
MKTIIALSYIFCLVFADYKDDDDKADLEDNWETLNDNLKVIEKADNAAQVKDALTKMRAA
ALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKEAQAAAEQLKT
TRNAYIQKYLAAISTSIPVISQPQFTAMNEPQCFYNESIAFFYNRSGKHLATEWNTVSKL
VMGLGITVCIFIMLANLLVMVAIYVNRRFHFPIYYLMANLAAADFFAGLAYFYLMFNTGP
NTRRLTVSTWLLRQGLIDTSLTASVANLLAIAIERHITVFRMQLHTRMSNRRVVVVIVVI
WTMAIVMGAIPSVGWNCICDIENCSNMAPLYSDSYLVFWAIFNLVTFVVMVVLYAHIFGY
VRQRTMRMSRHSSGPRRNRDTMMSLLKTVVIVLGAFIICWTPGLVLLLLDVCCPQCDVLA
YEKFFLLLAEFNSAMNPIIYSYRDKEMSATFRQILCCQRSENPTGPTEGSDRSASSLNHT
ILAGVHSNDHSVVVFTLEDFVGDWEQTAAYNLDQVLEQGGVSSLLQNLAVSVTPIQRIVR
SGENALKIDIHVIIPYEGLSADQMAQIEEVFKVVYPVDDHHFKVILPYGTLVIDGVTPNM
LNYFGRPYEGIAVFDGKKITVTGTLWNGNKIIDERLITPDGSMLFRVTINS

Sequence of entity 2 (A), FASTA

>9IZH_2 G protein subunit 13 (Gi2-mini-G13 chimera) (chains A)
STVSAEDKAAAERSKEIDKCLSREKTYVKRLVKILLLGADNSGKSTFLKQMRIIHGGSGG
SGGTKGIHEYDFEIKNVPFKMVDVGGQRSERKRWFECFDSVTSILFLVDSSDFNRLTESL
NDFETIVNNRVFSNVSIILFLNKTDLLEEKVQIVSIKDYFLEFEGDPHCLRDVQKFLVEC
FRNKRRDQQQKPLYHHFTTAINTENARLIFRDVKDTILHDNLKQLMLQ

Sequence of entity 3 (B), FASTA

>9IZH_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHHHENLYFQGSSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQ
MRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCA
YAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDT
TCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTG
HESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRL
LLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNGGSG
GGGSGGSSSGGVSGWRLFKKIS

Sequence of entity 4 (C), FASTA

>9IZH_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF
REKKFFCAIL

Sequence of entity 5 (S), FASTA

>9IZH_5 scFv16 (chains S)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELK

Ligands and cofactors

ID	Name	Formula	Copies
NKP	(2R)-2-hydroxy-3-(phosphonooxy)propyl (9E)-octadec-9-enoate	C21 H41 O7 P	1

Primary citation

Structural insights into the engagement of lysophosphatidic acid receptor 1 with different G proteins. Suzuki, S., Tanaka, K., Kamegawa, A. et al. J Struct Biol (2024) 217:108164-108164. DOI 10.1016/j.jsb.2024.108164 · PubMed

Other PDB entries of the same protein (UniProt P0ABE7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DYF 1.1 Å, Cu(II)-bound structure of the engineered cyt cb562 variant, CH3Y
5YO6 1.2 Å, Crystal Structure of B562RIL with engineered disulfide bond T9C-A36C
4JEA 1.22 Å, Crystal structure of an engineered Zn-RIDC1 construct with four interfacial disulfide…
7LSJ 1.26 Å, Cu-bound crystal structure of the engineered cyt cb562 variant, DiCyt2 - H63A,…
7MK4 1.27 Å, Co-bound crystal structure of the engineered cyt cb562 variant, DiCyt2
6DYC 1.33 Å, Co(II)-bound structure of the engineered cyt cb562 variant, CH3
5YO4 1.37 Å, Crystal Structure of B562RIL with engineered disulfide bond K27C-A79C
256B 1.4 Å, Improvement of the 2.5 Å resolution model of cytochrome B562 by redetermining the…
6OT4 1.4 Å, Bimetallic dodecameric cage design 2 (BMC2) from cytochrome cb562
7LRV 1.4 Å, Ni-bound crystal structure of the engineered cyt cb562 variant, DiCyt2, crystallized in…
9PQ4 1.48 Å, Bi-bound structure of the H77C variant of TriCyt2
6DYG 1.49 Å, Fe(II)-bound structure of the engineered cyt cb562 variant, CH3Y

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