8IED: GPR156-miniGo-scFv16 complex

Cryo-EM structure of GPR156-miniGo-scFv16 complex. Determined by electron microscopy at 3.33 Å resolution. Released 14 Feb 2024.

Method: Electron microscopy
Resolution: 3.33 Å
Organisms: Homo sapiens, Mus musculus
Chains: 6
Atoms: 10,694
Mol. weight: 233.25 kDa
Ligands: A1LYA
Released: 14 Feb 2024

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

Secondary structure: helices and β-sheets

8IED contains 36 α-helices and 65 β-strands across 6 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, 2 β-strands

Element	Residues	Length	Sheet
α-helix	47-73	27
α-helix	78-81	4
α-helix	85-104	20
α-helix	116-150	35
α-helix	162-186	25
β-strand	191-201	11	1
β-strand	206-216	11	1
α-helix	221-245	25
α-helix	258-279	22
α-helix	285-316	32

Chain B: 11 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	47-73	27
α-helix	78-82	5
α-helix	85-104	20
α-helix	116-149	34
α-helix	162-186	25
β-strand	190-201	12	1
β-strand	206-217	12	1
α-helix	221-245	25
α-helix	257-280	24
α-helix	285-314	30
α-helix	316-318	3
α-helix	325-327	3
α-helix	330-332	3

Chain C: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	33-40	8	2
β-strand	54-55	2	2
β-strand	71-76	6	2
β-strand	79-84	6	2
α-helix	97-101	5
β-strand	105-111	7	2
α-helix	118-128	11
α-helix	132-134	3
β-strand	138-144	7	2
α-helix	146-152	7
α-helix	171-183	13
β-strand	193-197	5	2
α-helix	206-224	19

Chain D: 2 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	4-24	21
β-strand	49-51	3	3
β-strand	58-63	6	4
β-strand	69-74	6	4
β-strand	78-83	6	4
β-strand	88-94	7	4
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	120-125	6	5
β-strand	134-140	7	5
β-strand	146-151	6	6
β-strand	156-161	6	6
β-strand	165-170	6	6
β-strand	175-181	7	6
β-strand	187	1	7
β-strand	191-192	2	7
β-strand	198-203	6	7
β-strand	207-212	6	7
β-strand	218-222	5	7
β-strand	229-234	6	8
β-strand	240-245	6	8
β-strand	249-254	6	8
β-strand	259-265	7	8
α-helix	272-273	2
β-strand	276-278	3	9
β-strand	284-289	6	9
β-strand	293-298	6	9
β-strand	306-309	4	9
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	336-339	4	3

Chain N: 6 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	10-12	3	11
β-strand	17-25	9	10
α-helix	29-31	3
β-strand	35-39	5	12
β-strand	45-51	7	12
α-helix	53-55	3
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	93-98	6	12
β-strand	110-111	2	12
α-helix	112	1
β-strand	113	1	10
α-helix	114	1
β-strand	115-116	2	12
β-strand	117-119	3	11
β-strand	135	1	13
β-strand	142-147	6	14
β-strand	154	1	15
β-strand	160	1	15
β-strand	164-167	4	16
β-strand	174-178	5	16
β-strand	182-183	2	16
α-helix	184	1
β-strand	191-196	6	14
β-strand	199-205	7	14
β-strand	214-216	3	16
β-strand	231-232	2	16
β-strand	233	1	13

Chain Y: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	9-23	15
α-helix	35-43	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Probable G-protein coupled receptor 156	A, B	protein	598	Homo sapiens	Q8NFN8 (AlphaFold model)
Guanine nucleotide-binding protein G(o) subunit alpha	C	protein	228	Homo sapiens	P09471 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	D	protein	358	Homo sapiens	P62873 (AlphaFold model)
Single-chain variable fragment scFv16	N	protein	259	Mus musculus
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	Y	protein	71	Homo sapiens	P59768 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8IED_1 Probable G-protein coupled receptor 156 (chains A, B)
MEPEINCSELCDSFPGQELDRRPLHDLCKTTITSSHHSSKTISSLSPVLLGIVWTFLSCG
LLLILFFLAFTIHCRKNRIVKMSSPNLNIVTLLGSCLTYSSAYLFGIQDVLVGSSMETLI
QTRLSMLCIGTSLVFGPILGKSWRLYKVFTQRVPDKRVIIKDLQLLGLVAALLMADVILL
MTWVLTDPIQCLQILSVSMTVTGKDVSCTSTSTHFCASRYSDVWIALIWGCKGLLLLYGA
YLAGLTGHVSSPPVNQSLTIMVGVNLLVLAAGLLFVVTRYLHSWPNLVFGLTSGGIFVCT
TTINCFIFIPQLKQWKAFEEENQTIRRMAKYFSTPNKSFHTQYGEEENCHPRGEKSSMER
LLTEKNAVIESLQEQVNNAKEKIVRLMSAECTYDLPEGAAPPASSPNKDVQAVASVHTLA
AAQGPSGHLSDFQNDPGMAARDSQCTSGPSSYAQSLEGPGKDSSFSPGKEEKISDSKDFS
DHLDSGCSQKPWTEQSLGPERGDQVPMNPSQSLLPERGGSDPQRQRHLENSEEPPERRSR
VSSVIREKLQEVLQDLGSGSGSGRGRGGSENLYFQGGSGSGGDYKDDDDKDYKDDDDK

Sequence of entity 2 (C), FASTA

>8IED_2 Guanine nucleotide-binding protein G(o) subunit alpha (chains C)
MGCTLSAEDKAAVERSKMIEKNLKEDGISAAKDVKLLLLGADNSGKSTIVKQMKIIHGGS
GGSGGTTGIVETHFTFKNLHFRLFDVGGQRSERKKWIHCFEDVTAIIFCVDLSDYNRMHE
SLMLFDSICNNKFFIDTSIILFLNKKDLFGEKIKKSPLTICFPEYTGPNTYEDAAAYIQA
QFESKNRSPNKEIYCHMTCATDTNNAQVIFDAVTDIIIANNLRGCGLY

Sequence of entity 3 (D), FASTA

>8IED_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains D)
MHHHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGR
IQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMT
CAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSG
DTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTF
TGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSG
RLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (N), FASTA

>8IED_4 Single-chain variable fragment scFv16 (chains N)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLTSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVIPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAAHHHHHHHH

Sequence of entity 5 (Y), FASTA

>8IED_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains Y)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Ligands and cofactors

ID	Name	Formula	Copies
A1LYA	[(2R)-3-[(E)-hexadec-9-enoyl]oxy-2-octadecanoyloxy-propyl]…	C42 H82 N O8 P	2

Primary citation

Constitutive activation mechanism of a class C GPCR. Shin, J., Park, J., Jeong, J. et al. Nat Struct Mol Biol (2024) 31:678-687. DOI 10.1038/s41594-024-01224-7 · PubMed

Other PDB entries of the same protein (UniProt Q8NFN8 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8YK0 2.4 Å, Cryo-EM structure of human GPR156-Gi3 complex
8IEP 2.61 Å, Cryo-EM structure of GPR156C/D of G-protein free GPR156 (local refine)
8IEI 2.62 Å, Cryo-EM structure of GPR156A/B of G-protein free GPR156 (local refine)
8IEQ 2.73 Å, Cryo-EM structure of G-protein free GPR156
8IEB 3.03 Å, Cryo-EM structure of GPR156 of GPR156-miniGo-scFv16 complex (local refine)
8YJP 3.09 Å, Cryo-EM structure of human apo GPR156

Browse structure collections

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