8B8I: Nanobody
Nanobody (NbLumSyt1) bound to human Syt1. Determined by X-ray diffraction at 2.75 Å resolution. Released 17 Apr 2024.
- Method
- X-ray diffraction
- Resolution
- 2.75 Å
- Organisms
- Vicugna pacos, Homo sapiens
- Chains
- 16
- Atoms
- 7,778
- Mol. weight
- 152.48 kDa
- Released
- 17 Apr 2024
Explore 8B8I in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8B8I contains 26 α-helices and 89 β-strands across 16 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.
Chains A, E, F and G: 2 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-8 | 4 | 1 |
| β-strand | 11-14 | 4 | 2 |
| β-strand | 19-25 | 7 | 1 |
| α-helix | 29-31 | 3 | |
| β-strand | 34-40 | 7 | 2 |
| β-strand | 47-53 | 7 | 2 |
| β-strand | 58-60 | 3 | 2 |
| β-strand | 68-73 | 6 | 1 |
| β-strand | 78-83 | 6 | 1 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-99 | 8 | 2 |
| β-strand | 107 | 1 | 2 |
| β-strand | 112-117 | 6 | 2 |
Chains B, C and D: 2 helices, 11 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 5-8 | 4 | 3 |
| β-strand | 11-13 | 3 | 4 |
| β-strand | 19-25 | 7 | 3 |
| α-helix | 29-31 | 3 | |
| β-strand | 34-40 | 7 | 4 |
| β-strand | 47-53 | 7 | 4 |
| β-strand | 58-60 | 3 | 4 |
| β-strand | 68-73 | 6 | 3 |
| β-strand | 78-83 | 6 | 3 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-99 | 8 | 4 |
| β-strand | 107 | 1 | 4 |
| β-strand | 112-116 | 5 | 4 |
Chain H: 2 helices, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 7-8 | 2 | 12 |
| β-strand | 11-14 | 4 | 6 |
| β-strand | 19-24 | 6 | 12 |
| α-helix | 29-31 | 3 | |
| β-strand | 34-40 | 7 | 6 |
| β-strand | 47-53 | 7 | 6 |
| β-strand | 58-60 | 3 | 6 |
| β-strand | 68-73 | 6 | 12 |
| β-strand | 78-83 | 6 | 12 |
| α-helix | 88-90 | 3 | |
| β-strand | 92-95 | 4 | 6 |
| β-strand | 98-99 | 2 | 6 |
| β-strand | 107 | 1 | 6 |
| β-strand | 112-117 | 6 | 6 |
Chains I and J: 2 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 37-45 | 9 | |
| α-helix | 48-50 | 3 | |
Chain K: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 36-45 | 10 | |
Chains L, M, N and P: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 37-45 | 9 | |
Chain O: 1 helix, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-45 | 8 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Nanobody (NbLumSyt1) | A, B, C, D, E, F, G, H | protein | 118 | Vicugna pacos | |
| Synaptotagmin-1 | I, J, K, L, M, N, O, P | protein | 60 | Homo sapiens | P21579 (AlphaFold model) |
Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA
>8B8I_1 Nanobody (NbLumSyt1) (chains A, B, C, D, E, F, G, H)
MEVQLVESGGGLVQTGGSLRLSCTASGSIGSISVMGWYRQVPGTQYELVAGISRGGSTWY
EDSVKGRFTISRDNAKNTLYLQMNSLKPEDTGMYYCAGGDYSDRLGSWGQGTQVTVSS
Sequence of entity 2 (I, J, K, L, M, N, O, P), FASTA
>8B8I_2 Synaptotagmin-1 (chains I, J, K, L, M, N, O, P)
MVSESHHEALAAPPVTTVATVLPSNATEPASPGEGKEDAFSKLKEKFMNELHKIPLPPWA
Primary citation
A versatile nanobody platform for live and super-resolution imaging of synaptic vesicle dynamics and plasticity in rodent and human neurons. Goel, R., Jevdokimenko, K., Rehm, R. et al. J Nanobiotechnology (2026) 24. DOI 10.1186/s12951-026-04489-w · PubMed
Other PDB entries of the same protein (UniProt P21579 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6TZ3 1.17 Å, Crystal Structure of Human Synaptotagmin 1 C2B without Ca2+
- 6U4U 1.3 Å, 1.3 A structure of a pathogenic human Syt 1 C2B (I368T)
- 3F04 1.35 Å, Crystal Structure of Synaptotagmin I C2A domain
- 7TUA 1.35 Å, Human Synaptotagmin-1 C2B Y312F without Ca2+
- 3F00 1.36 Å, Crystal Structure of Synaptotagmin I C2A domain with Cu(II)
- 3F05 1.4 Å, Crystal Structure of Synaptotagmin I C2A domain with Mn(II)
- 6U4W 1.4 Å, 1.4 A structure of a pathogenic human Syt 1 C2B (D366E)
- 7U4Q 1.56 Å, Human Synaptotagmin-1 C2A Y181F Ca2+ bound
- 3F01 1.7 Å, Crystal Structure of Synaptotagmin I C2A domain with Cu(II)
- 6U41 1.7 Å, 1.7 angstrom structure of a pathogenic human Syt 1 C2B (D304G)
- 4V11 1.95 Å, Structure of Synaptotagmin-1 with SV2A peptide phosphorylated at Thr84
- 6G5K 2.0 Å, Crystal structure of the binding domain of Botulinum Neurotoxin type B in complex with…
Browse structure collections
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