8C5H: NbSyt1 anti-(rat Synaptotagmin-1) nanobody

NbSyt1 anti-(rat Synaptotagmin-1) nanobody bound to target cytosolic domain of Synaptotagmin-1. Determined by X-ray diffraction at 1.68 Å resolution. Released 2 Aug 2023.

Method: X-ray diffraction
Resolution: 1.68 Å
Organisms: Rattus norvegicus, Vicugna pacos
Chains: 2
Atoms: 2,034
Mol. weight: 29.5 kDa
Ligands: CA
Released: 2 Aug 2023

Explore 8C5H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8C5H contains 6 α-helices and 22 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.

Chain N: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	10-14	5	4
β-strand	17-19	3	5
β-strand	25-32	8	4
α-helix	36-38	3
β-strand	41-46	6	5
β-strand	52-58	7	5
β-strand	65-67	3	5
α-helix	69-71	3
β-strand	75-80	6	4
β-strand	85-90	6	4
α-helix	95-97	3
β-strand	99-105	7	5
β-strand	114	1	5
β-strand	118-122	5	5

Chain S: 3 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	144-152	9	1
β-strand	157-166	10	1
α-helix	168-170	3
β-strand	172	1	2
β-strand	176	1	2
β-strand	179-186	8	3
β-strand	192-194	3	3
α-helix	195-197	3
β-strand	205-213	9	1
α-helix	216-219	4
β-strand	223-230	8	3
β-strand	238-246	9	3
β-strand	257-261	5	1
β-strand	263	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Synaptotagmin-1	S	protein	132	Rattus norvegicus	P21707 (AlphaFold model)
NbSyt1 nanobody	N	protein	125	Vicugna pacos

Sequence of entity 1 (S), FASTA

>8C5H_1 Synaptotagmin-1 (chains S)
MHHHHHHHLGKLQYSLDYDFQNNQLLVGIIQAAELPALDMGGTSDPYVKVFLLPDKKKKF
ETKVHRKTLNPVFNEQFTFKVPYSELGGKTLVMAVYDFDRFSKHDIIGEFKVPMNTVDFG
HVTEEWRDLQSA

Sequence of entity 2 (N), FASTA

>8C5H_2 NbSyt1 nanobody (chains N)
SGDASDSEVQLEESGGGLVRPGGSLRLSCAASGFPFSKYFMSWVRQAPGKGLEWVSTISA
SGNYETYTESVKGRFTIARDNAKNTLYLQMNSLKPEDTAVYYCAKGSWARDMTRGQGTQV
TVSSE

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1

Water and common crystallization additives (GOL) are not listed.

Primary citation

A Versatile Synaptotagmin-1 Nanobody Provides Perturbation-Free Live Synaptic Imaging And Low Linkage-Error in Super-Resolution Microscopy. Queiroz Zetune Villa Real, K., Mougios, N., Rehm, R. et al. Small Methods (2023) 7:e2300218-e2300218. DOI 10.1002/smtd.202300218 · PubMed

Other PDB entries of the same protein (UniProt P21707 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4WEE 0.89 Å, High-resolution structure of Synaptotagmin 1 C2A
1TJX 1.04 Å, Crystallographic Identification of Ca2+ Coordination Sites in Synaptotagmin I C2B Domain
1UOW 1.04 Å, Calcium binding domain C2B
1TJM 1.18 Å, Crystallographic Identification of Sr2+ Coordination Site in Synaptotagmin I C2B Domain
2YOA 1.5 Å, Synaptotagmin-1 C2B domain with phosphoserine
1UOV 1.65 Å, Calcium binding domain C2B
5CCJ 1.65 Å, Crystal structure of the quintuple mutant of the synaptotagmin-1 C2B domain
6CXW 1.83 Å, Synaptotagmin 1 C2A beta4 chimera with enhanced PIP2 binding function
5W5C 1.85 Å, Crystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C2AB complex
1RSY 1.9 Å, Structure of the first C2-domain of synaptotagmin I: a novel CA2+(SLASH)PHOSPHOLIPID…
5W5D 2.5 Å, Crystal structure of the primed SNARE-Complexin-Synaptotagmin-1 C2B complex
5CCG 3.5 Å, Structure of the Ca2+-bound synaptotagmin-1 SNARE complex (long unit cell form)

Browse structure collections

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