7D76: PDB entry 7D76

Cryo-EM structure of the beclomethasone-bound adhesion receptor GPR97-Go complex. Determined by electron microscopy at 3.1 Å resolution. Released 3 Feb 2021.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 7,015
Mol. weight: 136.6 kDa
Ligands: CLR, GXR, Y01, PLM
Released: 3 Feb 2021

Explore 7D76 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7D76 contains 24 α-helices and 41 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: 8 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	33-39	7	1
α-helix	46-48	3
β-strand	186-188	3	1
β-strand	191	1	1
β-strand	196-201	6	1
α-helix	209-212	4
α-helix	213-216	4
β-strand	221-224	4	1
β-strand	227	1	2
α-helix	243-255	13
β-strand	264-267	4	1
β-strand	270	1	2
α-helix	272-281	10
α-helix	297-309	13
β-strand	319	1	1
α-helix	332-350	19

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	30-34	5
β-strand	47-51	5	3
β-strand	58-63	6	4
β-strand	69-74	6	4
β-strand	78-83	6	4
β-strand	91-94	4	4
α-helix	95	1
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	187-192	6	7
β-strand	198-203	6	7
β-strand	208-212	5	7
β-strand	218-222	5	7
β-strand	229-234	6	8
β-strand	240-245	6	8
β-strand	250-254	5	8
β-strand	260-264	5	8
α-helix	272-273	2
β-strand	275-278	4	9
β-strand	284-288	5	9
β-strand	294-298	5	9
β-strand	304-307	4	9
β-strand	319-320	2	3
β-strand	327-329	3	3
β-strand	336-339	4	3

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	8-23	16
α-helix	30-43	14
α-helix	45-47	3

Chain R: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	264-296	33
α-helix	305-328	24
α-helix	335-367	33
α-helix	378-399	22
β-strand	403	1	10
β-strand	406-408	3	11
β-strand	417-419	3	11
β-strand	422	1	10
α-helix	429-431	3
α-helix	432-436	5
α-helix	437-463	27
α-helix	472-495	24
α-helix	503-524	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Guanine nucleotide-binding protein G(o) subunit alpha	A	protein	226	Homo sapiens	P09471 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	346	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Homo sapiens	P59768 (AlphaFold model)
Adhesion G protein-coupled receptor G3; GPR97	R	protein	561	Homo sapiens	Q86Y34 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7D76_1 Guanine nucleotide-binding protein G(o) subunit alpha (chains A)
MTLSAEERAALERSKAIEKNLKEDGISAAKDVKLLLLGADNSGKSTIVKQMKIIHGGSGG
SGGTTGIVETHFTFKNLHFRLFDVGGQRSERKKWIHCFEDVTAIIFCVDLSDYNRMHESL
MLFDSICNNKFFIDTSIILFLNKKDLFGEKIKKSPLTICFPEYTGPNTYEDAAAYIQAQF
ESKNRSPNKEIYCHMTCATDTNNAQVIFDAVTDIIIANNLRGCGLY

Sequence of entity 2 (B), FASTA

>7D76_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYA
MHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNI
CSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTF
TGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDINAICFFPNGNA
FATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGYDDFNCNVWDAL
KADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNHHHHHH

Sequence of entity 3 (G), FASTA

>7D76_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 4 (R), FASTA

>7D76_4 Adhesion G protein-coupled receptor G3; GPR97 (chains R)
DYKDDDDAKLQTMHHHHHHHHHHENLYFQGGTQEKPTEGPRNTCLGSNNMYDIFNLNDKA
LCFTKCRQSGSDSCNVENLQRYWLNYEAHLMKEGLTQKVNTPFLKALVQNLSTNTAEDFY
FSLEPSQVPRQVMKDEDKPPDRVRLPKSLFRSLPGNRSVVRLAVTILDIGPGTLFKGPRL
GLGDGSGVLNNRLVGLSVGQMHVTKLAEPLEIVFSHQRPPPNMTLTCVFWDVTKGTTGDW
SSEGCSTEVRPEGTVCCCDALAFFALLLRPTLDQSTVHILTRISQAGCGVSMIFLAFTII
LYAFLRLSRERFKSEDAPKIHVALGGSLFLLNLAFLVNVGSGSKGSDAACWARGAVFHYF
LLCAFTWMGLEAFHLYLLAVRVFNTYFGHYFLKLSLVGWGLPALMVIGTGSANSYGLYTI
RDRENRTSLELCWFREGTTMYALYITVHGYFLITFLFGMVVLALVVWKIFTLSRATAVKE
RGKNRKKVLTLLGLSSLVGVTWGLAIFTPLGLSTVYIFALFNSLQGVFICCWFTILYLPS
QSTTVSSSTARLDQAHSASQE

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	2
GXR	(8~{S},9~{R},10~{S},11~{S},13~{S},14~{S},16~{S},17~{R})-9-chloranyl-10,13,16-tr…	C22 H29 Cl O5	1
Y01	Cholesterol hemisuccinate	C31 H50 O4	1
PLM	Palmitic acid	C16 H32 O2	3

Primary citation

Structures of the glucocorticoid-bound adhesion receptor GPR97-G o complex. Ping, Y.Q., Mao, C., Xiao, P. et al. Nature (2021) 589:620-626. DOI 10.1038/s41586-020-03083-w · PubMed

Other PDB entries of the same protein (UniProt P09471 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9BSB 2.32 Å, Global reconstruction of DRD2 bound to LSD in complex with a mini-GoA and scFv16…
9VJE 2.47 Å, Cryo-EM structure of 5-HT1AR-GoA in complex with buspirone
9K20 2.65 Å, Cryo-EM structure of ATP-bound P2Y purinoceptor 2-miniGo-scFv16 complex
9VJ5 2.69 Å, Cryo-EM structure of 5-HT1AR-GoA in complex with gepirone
8E9X 2.7 Å, CryoEM structure of miniGo-coupled hM4Di in complex with DCZ
9T88 2.74 Å, Cryo-EM structure of ESG-2-37-bound D3 dopamine receptor with mini-Go
9VNF 2.74 Å, Cryo-EM structure of 5-HT1AR-GoA in complex with (S)-pindolol
8YN7 2.77 Å, Cryo-EM structure of histamine H3 receptor in complex with immethridine and miniGo
8YN8 2.77 Å, Cryo-EM structure of histamine H3 receptor in complex with proxyfan and miniGo
9KVP 2.79 Å, Structure of SB290157 bound to human C3aR in complex with Go (Full map)
7W2Z 2.8 Å, Cryo-EM structure of the ghrelin-bound human ghrelin receptor-Go complex
8XXH 2.8 Å, Structure of CXCR2 bound to CXCL2 (CXCR2-CXCL2-Go Full map)

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