7VV5: PDB entry 7VV5

Cryo-EM structure of pseudoallergen receptor MRGPRX2 complex with C48/80, state1. Determined by electron microscopy at 2.76 Å resolution. Released 1 Dec 2021.

Method: Electron microscopy
Resolution: 2.76 Å
Organism: Homo sapiens
Chains: 5
Atoms: 8,829
Mol. weight: 154.6 kDa
Ligands: CLR, 6IB
Released: 1 Dec 2021

Explore 7VV5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7VV5 contains 41 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 A: 10 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	7-31	25
β-strand	33-39	7	1
α-helix	46-54	9
α-helix	184	1
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
α-helix	227-229	3
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	296-308	13
β-strand	319-323	5	1
α-helix	331-350	20

Chain B: 4 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	4-23	20
α-helix	30-33	4
α-helix	38-39	2
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
α-helix	95	1
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	176-181	6	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 G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	8-23	16
α-helix	30-42	13
α-helix	54-55	2

Chain R: 17 helices, 0 β-strands

Element	Residues	Length
α-helix	31-53	23
α-helix	54-58	5
α-helix	60-61	2
α-helix	63-93	31
α-helix	105-132	28
α-helix	134-135	2
α-helix	136-140	5
α-helix	145-167	23
α-helix	177-211	35
α-helix	218-231	14
α-helix	232-236	5
α-helix	237-244	8
α-helix	246-249	4
α-helix	257-276	20
α-helix	277-281	5
α-helix	282-284	3
α-helix	285-287	3

Chain S: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	10
β-strand	11-12	2	11
β-strand	17-25	9	10
α-helix	29-31	3
β-strand	33-39	7	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	92-99	8	12
β-strand	110-111	2	12
β-strand	115-117	3	12
β-strand	118-119	2	11
α-helix	126-127	2
β-strand	128-129	2	13
β-strand	134-136	3	14
β-strand	143-149	7	13
β-strand	154	1	15
β-strand	160	1	15
β-strand	162-167	6	14
β-strand	173-178	6	14
β-strand	182-183	2	14
α-helix	184	1
β-strand	191-195	5	13
β-strand	199-204	6	13
α-helix	209-211	3
β-strand	214-219	6	14
α-helix	225	1
β-strand	227	1	14
β-strand	231-234	4	14

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
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	358	Homo sapiens	P62873 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	58	Homo sapiens	P59768 (AlphaFold model)
scFv	S	protein	285	Homo sapiens
Mas-related G-protein coupled receptor member X2	R	protein	330	Homo sapiens	Q96LB1 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7VV5_1 Guanine nucleotide-binding protein G(i) subunit alpha-1 (chains A)
MGCTLSAEDKAAVERSKMIDRNLREDGEKAAREVKLLLLGAGESGKSTIVKQMKIIHEAG
YSEEECKQYKAVVYSNTIQSIIAIIRAMGRLKIDFGDSARADDARQLFVLAGAAEEGFMT
AELAGVIKRLWKDSGVQACFNRSREYQLNDSAAYYLNDLDRIAQPNYIPTQQDVLRTRVK
TTGIVETHFTFKDLHFKMFDVGGQRSERKKWIHCFEGVTAIIFCVALSDYDLVLAEDEEM
NRMHESMKLFDSICNNKWFTDTSIILFLNKKDLFEEKIKKSPLTICYPEYAGSNTYEEAA
AYIQCQFEDLNKRKDTKEIYTHFTCATDTKNVQFVFDAVTDVIIKNNLKDCGLF

Sequence of entity 2 (B), FASTA

>7VV5_2 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHLEVLFQGPGSSGSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGR
IQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMT
CAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSG
DTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTF
TGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSG
RLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWN

Sequence of entity 3 (G), FASTA

>7VV5_3 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
NTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENPFR

Sequence of entity 4 (S), FASTA

>7VV5_4 scFv (chains S)
MLLVNQSHQGFNKEHTSKMVSAIVLYVLLAAAAHSAFAVQLVESGGGLVQPGGSRKLSCS
ASGFAFSSFGMHWVRQAPEKGLEWVAYISSGSGTIYYADTVKGRFTISRDDPKNTLFLQM
TSLRSEDTAMYYCVRSIYYYGSSPFDFWGQGTTLTVSAGGGGSGGGGSGGGGSADIVMTQ
ATSSVPVTPGESVSISCRSSKSLLHSNGNTYLYWFLQRPGQSPQLLIYRMSNLASGVPDR
FSGSGSGTAFTLTISRLEAEDVGVYYCMQHLEYPLTFGAGTKLEL

Sequence of entity 5 (R), FASTA

>7VV5_5 Mas-related G-protein coupled receptor member X2 (chains R)
MDPTTPAWGTESTTVNGNDQALLLLCGKETLIPVFLILFIALVGLVGNGFVLWLLGFRMR
RNAFSVYVLSLAGADFLFLCFQIINCLVYLSNFFCSISINFPSFFTTVMTCAYLAGLSML
STVSTERCLSVLWPIWYRCRRPRHLSAVVCVLLWALSLLLSILEGKFCGFLFSDGDSGWC
QTFDFITAAWLIFLFMVLCGSSLALLVRILCGSRGLPLTRLYLTILLTVLVFLLCGLPFG
IQWFLILWIWKDSDVLFCHIHPVSVVLSSLNSSANPIIYFFVGSFRKQWRLQQPILKLAL
QRALQDIAEVDHSEGCFRQGTPEMSRSSLV

Ligands and cofactors

ID	Name	Formula	Copies
CLR	Cholesterol	C27 H46 O	1
6IB	2-[4-methoxy-3-[[2-methoxy-3-[[2-methoxy-5-[2-(methylamino)ethyl]phenyl]methyl]…	C32 H45 N3 O3	1

Primary citation

Structure, function and pharmacology of human itch receptor complexes. Yang, F., Guo, L., Li, Y. et al. Nature (2021) 600:164-169. DOI 10.1038/s41586-021-04077-y · PubMed

Other PDB entries of the same protein (UniProt P63096 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6CRK 2.0 Å, Heterotrimeric G-protein in complex with an antibody fragment
3UMR 2.04 Å, Crystal structure of the G202D mutant of human G-alpha-i1
9P7Z 2.1 Å, NTSR1-Gi-NTS(8-13) Complex in the Canonical, AHD Open State (C-Open-Apo)
2OM2 2.2 Å, Crystal Structure Of Human G[alpha]i1 Bound To The Goloco Motif Of Rgs14
8YN9 2.3 Å, Cryo-EM structure of histamine H4 receptor in complex with histamine and Gi
9HYI 2.3 Å, DP81-bound serotonin 5-HT1A receptor - Gi Protein Complex
9O36 2.3 Å, CryoEM structure of mu-opioid receptor - Gi protein complex bound to fluornitrazene (FNZ)
9P80 2.3 Å, NTSR1-Gi-NTS(8-13) Complex in the Non-Canonical, AHD Open State (NC-Open-Apo)
8XXV 2.33 Å, Cryo-EM Structure of the Prostaglandin D2 Receptor 2-indomethacin Coupled to G Protein
3UMS 2.34 Å, Crystal structure of the G202A mutant of human G-alpha-i1
3ONW 2.38 Å, Structure of a G-alpha-i1 mutant with enhanced affinity for the RGS14 GoLoco motif.
20ZG 2.4 Å, Cryo-EM structure of the human neurotensin receptor 1 (hNTSR1)-Gi1 complex in the…

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