6VN7: Activated VIP1 receptor-G protein complex
Cryo-EM structure of an activated VIP1 receptor-G protein complex. Determined by electron microscopy at 3.2 Å resolution. Released 2 Sept 2020.
- Method
- Electron microscopy
- Resolution
- 3.2 Å
- Organisms
- Homo sapiens, synthetic construct
- Chains
- 6
- Atoms
- 8,620
- Mol. weight
- 182.1 kDa
- Ligands
- PLM, CLR
- Released
- 2 Sept 2020
Explore 6VN7 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
6VN7 contains 32 α-helices and 45 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: 10 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 10-39 | 30 | |
| β-strand | 41-47 | 7 | 1 |
| α-helix | 53-61 | 9 | |
| β-strand | 207-214 | 8 | 1 |
| β-strand | 217-224 | 8 | 1 |
| α-helix | 234-237 | 4 | |
| β-strand | 243-249 | 7 | 1 |
| α-helix | 265-278 | 14 | |
| β-strand | 287-292 | 6 | 1 |
| α-helix | 294-299 | 6 | |
| α-helix | 301-303 | 3 | |
| α-helix | 307-311 | 5 | |
| α-helix | 325-327 | 3 | |
| α-helix | 332-352 | 21 | |
| β-strand | 359-363 | 5 | 1 |
| α-helix | 371-390 | 20 | |
Chain B: 1 helix, 28 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 5-24 | 20 | |
| β-strand | 45-51 | 7 | 2 |
| β-strand | 58-63 | 6 | 3 |
| β-strand | 69-74 | 6 | 3 |
| β-strand | 78-83 | 6 | 3 |
| β-strand | 89-94 | 6 | 3 |
| β-strand | 102-105 | 4 | 4 |
| β-strand | 111-115 | 5 | 4 |
| β-strand | 120-125 | 6 | 4 |
| β-strand | 134-140 | 7 | 4 |
| β-strand | 146-151 | 6 | 5 |
| β-strand | 156-161 | 6 | 5 |
| β-strand | 166-170 | 5 | 5 |
| β-strand | 176-180 | 5 | 5 |
| β-strand | 187-192 | 6 | 6 |
| β-strand | 198-203 | 6 | 6 |
| β-strand | 208-212 | 5 | 6 |
| β-strand | 218-222 | 5 | 6 |
| β-strand | 229-234 | 6 | 7 |
| β-strand | 240-245 | 6 | 7 |
| β-strand | 250-254 | 5 | 7 |
| β-strand | 260-264 | 5 | 7 |
| β-strand | 273-278 | 6 | 8 |
| β-strand | 284-289 | 6 | 8 |
| β-strand | 294-298 | 5 | 8 |
| β-strand | 303-308 | 6 | 8 |
| β-strand | 315-320 | 6 | 2 |
| β-strand | 327-331 | 5 | 2 |
| β-strand | 336-341 | 6 | 2 |
Chain G: 3 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 9-23 | 15 | |
| α-helix | 30-43 | 14 | |
| α-helix | 53-55 | 3 | |
Chain L: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 2-26 | 25 | |
Chain N: 3 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-7 | 5 | 9 |
| β-strand | 10-12 | 3 | 10 |
| β-strand | 17-25 | 9 | 9 |
| α-helix | 29-31 | 3 | |
| β-strand | 34-39 | 6 | 10 |
| β-strand | 45-51 | 7 | 10 |
| β-strand | 58-60 | 3 | 10 |
| α-helix | 62-64 | 3 | |
| β-strand | 68-73 | 6 | 9 |
| β-strand | 78-84 | 7 | 9 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-98 | 7 | 10 |
| β-strand | 118 | 1 | 10 |
| β-strand | 122-126 | 5 | 10 |
Chain R: 14 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 130-166 | 37 | |
| α-helix | 173-200 | 28 | |
| α-helix | 213-245 | 33 | |
| α-helix | 251-259 | 9 | |
| α-helix | 260-264 | 5 | |
| α-helix | 265-280 | 16 | |
| α-helix | 291-294 | 4 | |
| α-helix | 299-323 | 25 | |
| α-helix | 336-344 | 9 | |
| α-helix | 347-350 | 4 | |
| α-helix | 352-356 | 5 | |
| α-helix | 366-385 | 20 | |
| α-helix | 386-390 | 5 | |
| α-helix | 393-408 | 16 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Vasoactive intestinal polypeptide receptor 1 | R | protein | 582 | Homo sapiens | P32241 (AlphaFold model) |
| Pituitary adenylate cyclase-activating polypeptide | L | protein | 27 | Homo sapiens | P18509 (AlphaFold model) |
| Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | A | protein | 394 | Homo sapiens | P63092 (AlphaFold model) |
| Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | B | protein | 377 | Homo sapiens | P62873 (AlphaFold model) |
| Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | G | protein | 71 | Homo sapiens | P59768 |
| Nanobody 35 | N | protein | 134 | synthetic construct | |
Sequence of entity 1 (R), FASTA
>6VN7_1 Vasoactive intestinal polypeptide receptor 1 (chains R)
DYKDDDDVDHHHHHHHHARLQEECDYVQMIEVQHKQCLEEAQLENETIGCSKMWDNLTCW
PATPRGQVVVLACPLIFKLFSSIQGRNVSRSCTDEGWTHLEPGPYPIACGLDDKAASLDE
QQTMFYGSVKTGYTIGYGLSLATLLVATAILSLFRKLHCTRNYIHMHLFISFILRAAAVF
IKDLALFDSGESDQCSEGSVGCKAAMVFFQYCVMANFFWLLVEGLYLYTLLAVSFFSERK
YFWGYILIGWGVPSTFTMVWTIARIHFEDYGCWDTINSSLWWIIKGPILTSILVNFILFI
CIIRILLQKLRPPDIRKSDSSPYSRLARSTLLLIPLFGVHYIMFAFFPDNFKPEVKMVFE
LVVGSFQGFVVAILYCFLNGEVQAELRRKWRRWHLQGVLGWNPKYRHPSGGSNGATCSTQ
VSMLVFTLEDFVGDWEQTAAYNLDQVLEQGGVSSLLQNLAVSVTPIQRIVRSGENALKID
IHVIIPYEGLSADQMAQIEEVFKVVYPVDDHHFKVILPYGTLVIDGVTPNMLNYFGRPYE
GIAVFDGKKITVTGTLWNGNKIIDERLITPDGSMLFRVTINS
Sequence of entity 2 (L), FASTA
>6VN7_2 Pituitary adenylate cyclase-activating polypeptide (chains L)
HSDGIFTDSYSRYRKQMAVKKYLAAVL
Sequence of entity 3 (A), FASTA
>6VN7_3 Guanine nucleotide-binding protein G(s) subunit alpha isoforms short (chains A)
MGCLGNSKTEDQRNEEKAQREANKKIEKQLQKDKQVYRATHRLLLLGAGESGKNTIVKQM
RILHVNGFNGEGGEEDPQAARSNSDGEKATKVQDIKNNLKEAIETIVAAMSNLVPPVELA
NPENQFRVDYILSVMNVPDFDFPPEFYEHAKALWEDEGVRACYERSNEYQLIDCAQYFLD
KIDVIKQDDYVPSDQDLLRCRVLTSGIFETKFQVDKVNFHMFDVGAQRDERRKWIQCFND
VTAIIFVVASSSYNMVIREDNQTNRLQAALKLFDSIWNNKWLRDTSVILFLNKQDLLAEK
VLAGKSKIEDYFPEFARYTTPEDATPEPGEDPRVTRAKYFIRDEFLRISTASGDGRHYCY
PHFTCAVDTENIRRVFNDCRDIIQRMHLRQYELL
Sequence of entity 4 (B), FASTA
>6VN7_4 Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 (chains B)
MHHHHHHGSLLQSELDQLRQEAEQLKNQIRDARKACADATLSQITNNIDPVGRIQMRTRR
TLRGHLAKIYAMHWGTDSRLLVSASQDGKLIIWDSYTTNKVHAIPLRSSWVMTCAYAPSG
NYVACGGLDNICSIYNLKTREGNVRVSRELAGHTGYLSCCRFLDDNQIVTSSGDTTCALW
DIETGQQTTTFTGHTGDVMSLSLAPDTRLFVSGACDASAKLWDVREGMCRQTFTGHESDI
NAICFFPNGNAFATGSDDATCRLFDLRADQELMTYSHDNIICGITSVSFSKSGRLLLAGY
DDFNCNVWDALKADRAGVLAGHDNRVSCLGVTDDGMAVATGSWDSFLKIWNGSSGGGGSG
GGGSSGVSGWRLFKKIS
Sequence of entity 5 (G), FASTA
>6VN7_5 Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 (chains G)
MASNNTASIAQARKLVEQLKMEANIDRIKVSKAAADLMAYCEAHAKEDPLLTPVPASENP
FREKKFFCAIL
Sequence of entity 6 (N), FASTA
>6VN7_6 Nanobody 35 (chains N)
QVQLQESGGGLVQPGGSLRLSCAASGFTFSNYKMNWVRQAPGKGLEWVSDISQSGASISY
TGSVKGRFTISRDNAKNTLYLQMNSLKPEDTAVYYCARCPAPFTRDCFDVTSTTYAYRGQ
GTQVTVSSHHHHHH
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| PLM | Palmitic acid | C16 H32 O2 | 4 |
| CLR | Cholesterol | C27 H46 O | 6 |
Primary citation
Cryo-EM structure of an activated VIP1 receptor-G protein complex revealed by a NanoBiT tethering strategy. Duan, J., Shen, D.D., Zhou, X.E. et al. Nat Commun (2020) 11:4121-4121. DOI 10.1038/s41467-020-17933-8 · PubMed
Other PDB entries of the same protein (UniProt P32241 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5IB2 1.44 Å, Crystal structure of HLA-B*27:05 complexed with the self-peptide pVIPR
- 1OGT 1.47 Å, Crystal structure of HLA-B*2705 complexed with the vasoactive intestinal peptide type 1…
- 5DEF 1.6 Å, Crystal structure of B*27:04 complex bound to the pVIPR peptide
- 3B6S 1.8 Å, Crystal Structure of hla-b*2705 Complexed with the Citrullinated Vasoactive Intestinal…
- 7ALO 1.8 Å, Structure of B*27:09/photoRL9
- 5DEG 1.83 Å, Crystal structure of B*27:06 bound to the pVIPR peptide
- 3B3I 1.86 Å, Citrullination-dependent differential presentation of a self-peptide by HLA-B27 subtypes
- 5IB1 1.91 Å, Crystal structure of HLA-B*27:05 complexed with the self-peptide pVIPR measured at 295 K
- 5IB3 1.91 Å, Crystal structure of HLA-B*27:05 complexed with the self-peptide pVIPR and Copper
- 3HCV 1.95 Å, Crystal structure of HLA-B*2709 complexed with the double citrullinated vasoactive…
- 5IB4 1.95 Å, Crystal structure of HLA-B*27:05 complexed with the self-peptide pVIPR and Nickel
- 3DTX 2.1 Å, Crystal structure of HLA-B*2705 complexed with the double citrullinated vasoactive…
Browse structure collections
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