9IZF: LPA1-Gi complex with LPA

Cryo-EM structure of LPA1-Gi complex with LPA. Determined by electron microscopy at 3.14 Å resolution. Released 1 Jan 2025.

Method: Electron microscopy
Resolution: 3.14 Å
Organisms: Escherichia coli, Homo sapiens, synthetic construct
Chains: 5
Atoms: 8,711
Mol. weight: 190.04 kDa
Ligands: NKP
Released: 1 Jan 2025

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

Secondary structure: helices and β-sheets

9IZF contains 32 α-helices and 70 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, 9 β-strands

Element	Residues	Length	Sheet
α-helix	9-30	22
β-strand	34-40	7	2
β-strand	185-187	3	2
β-strand	190	1	3
β-strand	195	1	3
β-strand	196-200	5	2
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	2
α-helix	242-254	13
β-strand	263-269	7	2
α-helix	271-280	10
α-helix	283-285	3
α-helix	297-307	11
β-strand	319	1	2
β-strand	322-323	2	2
α-helix	330-350	21

Chain B: 5 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
α-helix	30-33	4
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
β-strand	100-105	6	6
β-strand	111-116	6	6
β-strand	120-125	6	6
β-strand	134-140	7	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	198-203	6	8
β-strand	207-212	6	8
β-strand	218-223	6	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
α-helix	272-273	2
β-strand	275-278	4	10
α-helix	279	1
α-helix	280-282	3
β-strand	284-288	5	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: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	10-22	13
α-helix	30-43	14

Chain R: 12 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	31-37	7
α-helix	47-76	30
α-helix	78-80	3
α-helix	83-106	24
α-helix	110-112	3
α-helix	118-151	34
α-helix	162-180	19
β-strand	195	1	1
β-strand	203	1	1
α-helix	204-236	33
α-helix	257-269	13
α-helix	272-280	9
α-helix	291-310	20
α-helix	316-326	11

Chain S: 5 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	11
β-strand	11-12	2	12
β-strand	17-25	9	11
α-helix	29-31	3
β-strand	34-39	6	13
β-strand	45-51	7	13
α-helix	53-55	3
β-strand	58-60	3	13
β-strand	65	1	11
β-strand	68-73	6	11
β-strand	78-84	7	11
β-strand	93-94	2	14
β-strand	95	1	13
β-strand	97	1	15
β-strand	111	1	15
β-strand	115-116	2	14
β-strand	118-119	2	12
α-helix	125-127	3
β-strand	128-129	2	16
β-strand	135-136	2	17
β-strand	143-149	7	16
β-strand	154	1	18
β-strand	160	1	18
β-strand	162-166	5	19
β-strand	167	1	20
β-strand	174-177	4	19
β-strand	183	1	19
α-helix	184	1
β-strand	191-196	6	16
β-strand	199-204	6	16
β-strand	214-215	2	20
β-strand	217-219	3	19
α-helix	225	1
β-strand	227	1	19
β-strand	231-232	2	20
β-strand	233-234	2	17

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)
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	protein	354	Homo sapiens	P63096 (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

>9IZF_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

>9IZF_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVAAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYQEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (B), FASTA

>9IZF_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

>9IZF_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains C)
ASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPF
REKKFFCAIL

Sequence of entity 5 (S), FASTA

>9IZF_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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