Structure of synaptic vesicle protein 2A in complex with a nanobody. Determined by electron microscopy at 3.3 Å resolution. Released 22 May 2024.
Explore 8UO9 in 3D Show helices and sheets RCSB PDB PDBe
8UO9 contains 26 α-helices and 27 β-strands across 2 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.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 147-159 | 13 | |
| α-helix | 163-184 | 22 | |
| α-helix | 185-189 | 5 | |
| α-helix | 207-209 | 3 | |
| α-helix | 210-229 | 20 | |
| α-helix | 231-249 | 19 | |
| α-helix | 255-281 | 27 | |
| α-helix | 286-288 | 3 | |
| α-helix | 291-295 | 5 | |
| α-helix | 298-314 | 17 | |
| α-helix | 333-351 | 19 | |
| α-helix | 355-357 | 3 | |
| α-helix | 358-364 | 7 | |
| α-helix | 367-385 | 19 | |
| α-helix | 390-392 | 3 | |
| α-helix | 421-437 | 17 | |
| α-helix | 444-482 | 39 | |
| β-strand | 505 | 1 | 1 |
| β-strand | 509 | 1 | 1 |
| β-strand | 512 | 1 | 1 |
| β-strand | 515-516 | 2 | 1 |
| β-strand | 519 | 1 | 2 |
| β-strand | 522 | 1 | 3 |
| β-strand | 525-532 | 8 | 1 |
| β-strand | 535-536 | 2 | 1 |
| β-strand | 539 | 1 | 2 |
| β-strand | 542 | 1 | 3 |
| β-strand | 545-555 | 11 | 1 |
| β-strand | 558-559 | 2 | 4 |
| β-strand | 571-575 | 5 | 1 |
| β-strand | 578-579 | 2 | 4 |
| α-helix | 597-606 | 10 | |
| α-helix | 609-615 | 7 | |
| α-helix | 624-644 | 21 | |
| α-helix | 648-676 | 29 | |
| α-helix | 682-706 | 25 | |
| α-helix | 714-730 | 17 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| α-helix | 2 | 1 | |
| β-strand | 3-5 | 3 | 5 |
| β-strand | 10-12 | 3 | 6 |
| β-strand | 14 | 1 | 7 |
| β-strand | 16 | 1 | 7 |
| β-strand | 18-25 | 8 | 5 |
| β-strand | 32-39 | 8 | 6 |
| β-strand | 45-50 | 6 | 6 |
| β-strand | 58-59 | 2 | 6 |
| α-helix | 61-63 | 3 | |
| β-strand | 67-72 | 6 | 5 |
| α-helix | 73-75 | 3 | |
| β-strand | 77-82 | 6 | 5 |
| β-strand | 91-99 | 9 | 6 |
| β-strand | 106-109 | 4 | 6 |
| β-strand | 113-117 | 5 | 6 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Synaptic vesicle glycoprotein 2A | A | protein | 680 | Homo sapiens | Q7L0J3 (AlphaFold model) |
| Nanobody | B | protein | 142 | Lama glama |
>8UO9_1 Synaptic vesicle glycoprotein 2A (chains A) MGYYRGEGTQDEEEGGASSDATEGHDEDDEIYEGEYQGIPRAESGGKGERMADGAPLAGV RGGLSDGEGPPGGRGEAQRRKEREELAQQYEAILRECGHGRFQWTLYFVLGLALMADGVE VFVVGFVLPSAEKDMCLSDSNKGMLGLIVYLGMMVGAFLWGGLADRLGRRQCLLISLSVN SVFAFFSSFVQGYGTFLFCRLLSGVGIGGSIPIVFSYFSEFLAQEKRGEHLSWLCMFWMI GGVYAAAMAWAIIPHYGWSFQMGSAYQFHSWRVFVLVCAFPSVFAIGALTTQPESPRFFL ENGKHDEAWMVLKQVHDTNMRAKGHPERVFSVTHIKTIHQEDELIEIQSDTGTWYQRWGV RALSLGGQVWGNFLSCFGPEYRRITLMMMGVWFTMSFSYYGLTVWFPDMIRHLQAVDYAS RTKVFPGERVEHVTFNFTLENQIHRGGQYFNDKFIGLRLKSVSFEDSLFEECYFEDVTSS NTFFRNCTFINTVFYNTDLFEYKFVNSRLINSTFLHNKEGCPLDVTGTGEGAYMVYFVSF LGTLAVLPGNIVSALLMDKIGRLRMLAGSSVMSCVSCFFLSFGNSESAMIALLCLFGGVS IASWNALDVLTVELYPSDKRTTAFGFLNALCKLAAVLGISIFTSFVGITKAAPILFASAA LALGSSLALKLPETRGQVLQ
>8UO9_2 Nanobody (chains B) QVQLVESGGGLVQPGGSLRLSCAASGSIFNMRVMGWYRQAPGEQRESVASMASGDKTTYA DSVKGRFTISRDNAKNTVALQMNSLKPEDTAVYYCHAVDLTRNGPRVYWGQGTQVTVSSA AAENLYFQGGSGHHHHHHHHHH
| ID | Name | Formula | Copies |
|---|---|---|---|
| PS1 | 1,2-didecanoyl-sn-glycero-3-[phospho-L-serine] | C26 H49 N O10 P | 1 |
| Y01 | Cholesterol hemisuccinate | C31 H50 O4 | 1 |
| X49 | (4S)-1-{[(4S)-2-(methoxymethyl)-6-(trifluoromethyl)imidazo[2,1-b][1,3,4]thiadia… | C16 H18 F6 N4 O2 S | 1 |
Structures of synaptic vesicle protein 2A and 2B bound to anticonvulsants. Mittal, A., Martin, M.F., Levin, E.J. et al. Nat Struct Mol Biol (2024) 31:1964-1974. DOI 10.1038/s41594-024-01335-1 · PubMed
Other PDB entries of the same protein (UniProt Q7L0J3 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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