7S8O: PDB entry 7S8O

CryoEM structure of Gi-coupled MRGPRX2 with small molecule agonist (R)-Zinc-3573. Determined by electron microscopy at 2.58 Å resolution. Released 17 Nov 2021.

Method: Electron microscopy
Resolution: 2.58 Å
Organisms: Escherichia coli, Homo sapiens, Mus musculus
Chains: 5
Atoms: 8,331
Mol. weight: 170.72 kDa
Ligands: 8IU
Released: 17 Nov 2021

Explore 7S8O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7S8O contains 34 α-helices and 61 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 B: 9 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-30	24
β-strand	34-40	7	1
α-helix	47-52	6
β-strand	185-190	6	1
β-strand	195-200	6	1
α-helix	208-210	3
α-helix	212-215	4
β-strand	220-226	7	1
β-strand	233	1	2
β-strand	241	1	2
α-helix	242-254	13
β-strand	263-269	7	1
α-helix	271-277	7
α-helix	283-285	3
α-helix	296-308	13
β-strand	319-323	5	1
α-helix	331-349	19

Chain C: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	3-23	21
α-helix	30-33	4
α-helix	38-40	3
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	88-94	7	4
β-strand	100-105	6	5
β-strand	111-116	6	5
β-strand	121-125	5	5
β-strand	134-139	6	5
β-strand	146-151	6	6
β-strand	156-161	6	6
β-strand	165-170	6	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	259-264	6	8
β-strand	273-278	6	9
β-strand	284-289	6	9
β-strand	294-298	5	9
β-strand	303-308	6	9
β-strand	315-320	6	3
β-strand	327-331	5	3
β-strand	336-339	4	3

Chain D: 4 helices, 0 β-strands

Element	Residues	Length
α-helix	9-22	14
α-helix	30-42	13
α-helix	53-55	3
α-helix	56-58	3

Chain E: 3 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	10-12	3	11
β-strand	18-25	8	10
α-helix	29-31	3
β-strand	33-39	7	11
β-strand	45-51	7	11
β-strand	58-60	3	11
β-strand	68-73	6	10
β-strand	78-83	6	10
α-helix	88-90	3
β-strand	92-99	8	11
β-strand	110-111	2	11
β-strand	115-119	5	11
β-strand	128-129	2	12
β-strand	135-136	2	13
β-strand	143-149	7	12
β-strand	154	1	14
β-strand	160	1	14
β-strand	162-167	6	15
β-strand	174-177	4	15
β-strand	183	1	15
α-helix	184	1
β-strand	191-196	6	12
β-strand	199-204	6	12
β-strand	214-219	6	15
β-strand	227	1	15
β-strand	231-232	2	15
β-strand	233-234	2	13

Chain R: 15 helices, 0 β-strands

Element	Residues	Length
α-helix	31-53	23
α-helix	54-58	5
α-helix	65-94	30
α-helix	103-132	30
α-helix	134-135	2
α-helix	136-140	5
α-helix	145-166	22
α-helix	178-211	34
α-helix	218-235	18
α-helix	237-241	5
α-helix	242-246	5
α-helix	247-249	3
α-helix	255-258	4
α-helix	261-276	16
α-helix	277-281	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Soluble cytochrome b562,Mas-related G-protein coupled receptor member X2 chimera	R	protein	480	Escherichia coli, Homo sapiens	P0ABE7 (AlphaFold model), Q96LB1 (AlphaFold model)
Guanine nucleotide-binding protein G(i) subunit alpha-1	B	protein	354	Homo sapiens	P63096 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C	protein	358	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D	protein	71	Homo sapiens	P59768
scFv16	E	protein	267	Mus musculus

Sequence of entity 1 (R), FASTA

>7S8O_1 Soluble cytochrome b562,Mas-related G-protein coupled receptor member X2 chimera (chains R)
DYKDDDDAKLQTMHHHHHHHHHHENLYFQGGTTMADLEDNWETLNDNLKVIEKADNAAQV
KDALTKMRAAALDAQKATPPKLEDKSPDSPEMKDFRHGFDILVGQIDDALKLANEGKVKE
AQAAAEQLKTTRNAYIQKYLGSTLEVLFQGPDPTTPAWGTESTTVNGNDQALLLLCGKET
LIPVFLILFIALVGLVGNGFVLWLLGFRMRRNAFSVYVLSLAGADFLFLCFQIINCLVYL
SNFFCSISINFPSFFTTVMTCAYLAGLSMLSTVSTERCLSVLWPIWYRCRRPRHLSAVVC
VLLWALSLLLSILEGKFCGFLFSDGDSGWCQTFDFITAAWLIFLFMVLCGSSLALLVRIL
CGSRGLPLTRLYLTILLTVLVFLLCGLPFGIQWFLILWIWKDSDVLFCHIHPVSVVLSSL
NSSANPIIYFFVGSFRKQWRLQQPILKLALQRALQDIAEVDHSEGCFRQGTPEMSRSSLV

Sequence of entity 2 (B), FASTA

>7S8O_2 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains B)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKNTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGAQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHASMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCSTDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 3 (C), FASTA

>7S8O_3 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains C)
MHHHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGR
IQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMT
CAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSG
DTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTF
TGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSG
RLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 4 (D), FASTA

>7S8O_4 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains D)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 5 (E), FASTA

>7S8O_5 scFv16 (chains E)
DVQLVESGGGLVQPGGSRKLSCSASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYY
ADTVKGRFTISRDDPKNTLFLQMTSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVS
SGGGGSGGGGSGGGGSDIVMTQATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQR
PGQSPQLLIYRMSNLASGVPDRFSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFG
AGTKLELKAAALEVLFQGPHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
8IU	(3R)-N,N-dimethyl-1-[(8S)-5-phenylpyrazolo[1,5-a]pyrimidin-7-yl]pyrrolidin-3-am…	C18 H21 N5	1

Primary citation

Structure, function and pharmacology of human itch GPCRs. Cao, C., Kang, H.J., Singh, I. et al. Nature (2021) 600:170-175. DOI 10.1038/s41586-021-04126-6 · 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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