7WBJ: Vasoactive intestinal polypeptide receptor 2

Cryo-EM structure of N-terminal modified human vasoactive intestinal polypeptide receptor 2 (VIP2R) in complex with PACAP27 and Gs. Determined by electron microscopy at 3.42 Å resolution. Released 18 May 2022.

Method: Electron microscopy
Resolution: 3.42 Å
Organisms: Homo sapiens, Bos taurus, Rattus norvegicus
Chains: 6
Atoms: 8,989
Mol. weight: 164.98 kDa
Released: 18 May 2022

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

Secondary structure: helices and β-sheets

7WBJ contains 33 α-helices and 58 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, 9 β-strands

Element	Residues	Length	Sheet
α-helix	10-39	30
β-strand	41-47	7	5
α-helix	53-61	9
β-strand	207-208	2	6
β-strand	211-214	4	5
β-strand	217-221	5	5
β-strand	223-224	2	6
β-strand	243-249	7	5
α-helix	266-277	12
β-strand	286-292	7	5
α-helix	294-300	7
α-helix	301-303	3
α-helix	313-317	5
α-helix	332-351	20
β-strand	359-360	2	5
β-strand	363	1	5
α-helix	370-390	21

Chain B: 2 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	4-25	22
α-helix	32-34	3
β-strand	47-51	5	7
β-strand	58-63	6	8
β-strand	70-74	5	8
β-strand	78-81	4	8
β-strand	91-94	4	8
β-strand	102-105	4	9
β-strand	111-115	5	9
β-strand	123-125	3	9
β-strand	134-137	4	9
β-strand	146-153	8	10
β-strand	156-161	6	10
β-strand	165-166	2	10
β-strand	180	1	10
β-strand	187-189	3	11
β-strand	192	1	12
β-strand	199	1	12
β-strand	202-203	2	11
β-strand	207-209	3	11
β-strand	221-222	2	11
β-strand	229-232	4	13
β-strand	240-245	6	13
β-strand	249-254	6	13
β-strand	264	1	13
β-strand	273-277	5	14
β-strand	284-289	6	14
β-strand	294-298	5	14
β-strand	315-317	3	7
β-strand	320	1	7
β-strand	327-331	5	7
β-strand	336-339	4	7

Chain G: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	9-23	15
α-helix	30-34	5
α-helix	37-43	7

Chain L: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	2-26	25

Chain N: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	15
β-strand	12	1	16
β-strand	19-25	7	15
β-strand	34-39	6	17
β-strand	45-51	7	17
β-strand	58-60	3	17
β-strand	69-73	5	15
β-strand	78-82	5	15
β-strand	92-98	7	17
β-strand	122-124	3	17
β-strand	126	1	16

Chain R: 19 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	32-37	6
β-strand	52	1	1
β-strand	56-57	2	2
β-strand	60-61	2	2
β-strand	65	1	1
β-strand	73	1	3
β-strand	89	1	3
β-strand	91-93	3	4
β-strand	98-101	4	4
α-helix	105-109	5
α-helix	116-150	35
α-helix	152-154	3
α-helix	157-181	25
α-helix	197-218	22
α-helix	221-229	9
α-helix	240-245	6
α-helix	246-250	5
α-helix	251-260	10
α-helix	279-310	32
α-helix	324-337	14
α-helix	339-342	4
α-helix	355-357	3
α-helix	358-363	6
α-helix	364-368	5
α-helix	369-372	4
α-helix	373-377	5
α-helix	380-392	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Vasoactive intestinal polypeptide receptor 2	R	protein	432	Homo sapiens	P41587 (AlphaFold model)
Pituitary adenylate cyclase-activating polypeptide 27	L	protein	27	Homo sapiens	P18509 (AlphaFold model)
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	A	protein	394	Bos taurus	P04896 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	protein	400	Rattus norvegicus	P54311 (AlphaFold model)
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	G	protein	71	Bos taurus	P63212
Nanobody-35	N	protein	140	synthetic construct

Sequence of entity 1 (R), FASTA

>7WBJ_1 Vasoactive intestinal polypeptide receptor 2 (chains R)
DYKDDDDVDHHHHHHHHECRFHLEIQEEETKCAELLRSQTEKHKACSGVWDNITCWRPAN
VGETVTVPCPKVFSNFYSKAGNISKNCTSDGWSETFPDFVDACGYSDPEDESKITFYILV
KAIYTLGYSVSLMSLATGSIILCLFRKLHCTRNYIHLNLFLSFILRAISVLVKDDVLYSS
SGTLHCPDQPSSWVGCKLSLVFLQYCIMANFFWLLVEGLYLHTLLVAMLPPRRCFLAYLL
IGWGLPTVCIGAWTAARLYLEDTGCWDTNDHSVPWWVIRIPILISIIVNFVLFISIIRIL
LQKLTSPDVGGNDQSQYKRLAKSTLLLIPLFGVHYMVFAVFPISISSKYQILFELCLGSF
QGLVVAVLYCFLNSEVQCELKRKWRSRCPTPSASRDYRVCGSSFSRNGSEGALQFHRGSR
AQSFLQTETSVI

Sequence of entity 2 (L), FASTA

>7WBJ_2 Pituitary adenylate cyclase-activating polypeptide 27 (chains L)
HSDGIFTDSYSRYRKQMAVKKYLAAVL

Sequence of entity 3 (A), FASTA

>7WBJ_3 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (chains A)
MGCLGNSKTEDQRNEEKAQREANKKIEKQLQKDKQVYRATHRLLLLGAGESGKNTIVKQM
RILHVNGFNGEGGEEDPQAARSNSDGEKATKVQDIKNNLKEAIETIVAAMSNLVPPVELA
NPENQFRVDYILSVMNVPDFDFPPEFYEHAKALWEDEGVRACYERSNEYQLIDCAQYFLD
KIDVIKQDDYVPSDQDLLRCRVLTSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFND
VTAIIFVVASSSYNMVIREDNQTNRLQAALKLFDSIWNNKWLRDTSVILFLNKQDLLAEK
VLAGKSKIEDYFPEFARYTTPEDATPEPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCY
PHFTCSVDTENIRRVFNDCRDIIQRMHLRQYELL

Sequence of entity 4 (B), FASTA

>7WBJ_4 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHSSGLVPRGSHMASHHHHHHHHHHGSLLQSELDQLRQEAEQLKNQIRDARKACA
DATLSQITNNIDPVGRIQMRTRRTLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYT
TNKVHAIPLRSSWVMTCAYAPSGNYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYL
SCCRFLDDNQIVTSSGDTTCALWDIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDA
SAKLWDVREGMCRQTFTGHESDINAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSH
DNIICGITSVSFSKSGRLLLAGYDDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMA
VATGSWDSFLKIWNGSSGGGGSGGGGSSGVSGWRLFKKIS

Sequence of entity 5 (G), FASTA

>7WBJ_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL

Sequence of entity 6 (N), FASTA

>7WBJ_6 Nanobody-35 (chains N)
MAQVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASI
SYTGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYR
GQGTQVTVSSHHHHHHEPEA

Primary citation

A distinctive ligand recognition mechanism by the human vasoactive intestinal polypeptide receptor 2. Xu, Y., Feng, W., Zhou, Q. et al. Nat Commun (2022) 13:2272-2272. DOI 10.1038/s41467-022-30041-z · PubMed

Other PDB entries of the same protein (UniProt P41587 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2X57 2.1 Å, Crystal structure of the extracellular domain of human Vasoactive intestinal polypeptide…
7VQX 2.74 Å, Cryo-EM structure of human vasoactive intestinal polypeptide receptor 2 (VIP2R) in…

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