[English] 日本語
Yorodumi
- PDB-6zvn: Botulinum neurotoxin B2 binding domain in complex with human syna... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6zvn
TitleBotulinum neurotoxin B2 binding domain in complex with human synaptotagmin I
Components
  • Neurotoxin
  • Synaptotagmin-1
KeywordsTOXIN / botulinum neurotoxin / ganglioside / gt1b / bont / b2
Function / homology
Function and homology information


Toxicity of botulinum toxin type G (botG) / clathrin-sculpted acetylcholine transport vesicle membrane / clathrin-sculpted glutamate transport vesicle membrane / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / spontaneous neurotransmitter secretion / regulation of regulated secretory pathway / Toxicity of botulinum toxin type B (botB) / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane ...Toxicity of botulinum toxin type G (botG) / clathrin-sculpted acetylcholine transport vesicle membrane / clathrin-sculpted glutamate transport vesicle membrane / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / spontaneous neurotransmitter secretion / regulation of regulated secretory pathway / Toxicity of botulinum toxin type B (botB) / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / calcium-dependent activation of synaptic vesicle fusion / chromaffin granule membrane / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / GABA synthesis, release, reuptake and degradation / Acetylcholine Neurotransmitter Release Cycle / clathrin-sculpted monoamine transport vesicle membrane / regulation of calcium ion-dependent exocytosis / Serotonin Neurotransmitter Release Cycle / calcium ion sensor activity / exocytic vesicle / Norepinephrine Neurotransmitter Release Cycle / Dopamine Neurotransmitter Release Cycle / vesicle organization / protein heterooligomerization / positive regulation of dendrite extension / vesicle docking / regulation of exocytosis / Glutamate Neurotransmitter Release Cycle / positive regulation of dopamine secretion / vesicle fusion / dense core granule / calcium-dependent phospholipid binding / neuron projection terminus / membraneless organelle assembly / host cell presynaptic membrane / neurotransmitter secretion / host cell cytoplasmic vesicle / presynaptic active zone / Neurexins and neuroligins / syntaxin-1 binding / low-density lipoprotein particle receptor binding / clathrin binding / host cell cytosol / phosphatidylserine binding / regulation of synaptic vesicle exocytosis / excitatory synapse / protein transmembrane transporter activity / detection of calcium ion / positive regulation of synaptic transmission / postsynaptic cytosol / regulation of synaptic transmission, glutamatergic / presynaptic cytosol / vesicle-mediated transport / phosphatidylinositol-4,5-bisphosphate binding / cellular response to calcium ion / hippocampal mossy fiber to CA3 synapse / SNARE binding / molecular condensate scaffold activity / clathrin-coated endocytic vesicle membrane / metalloendopeptidase activity / calcium-dependent protein binding / synaptic vesicle / synaptic vesicle membrane / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / toxin activity / presynaptic membrane / chemical synaptic transmission / postsynaptic membrane / cell differentiation / calmodulin binding / neuron projection / postsynaptic density / protein heterodimerization activity / axon / calcium ion binding / lipid binding / host cell plasma membrane / glutamatergic synapse / Golgi apparatus / proteolysis / extracellular region / zinc ion binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Synaptotagmin / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, N-terminal receptor binding ...Synaptotagmin / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / C2 domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Synaptotagmin-1 / Neurotoxin
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDavies, J.R. / Masuyer, G. / Stenmark, P.
CitationJournal: Toxins / Year: 2020
Title: Structural and Biochemical Characterization of Botulinum Neurotoxin Subtype B2 Binding to Its Receptors.
Authors: Davies, J.R. / Masuyer, G. / Stenmark, P.
History
DepositionJul 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 2.0Sep 7, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Structure summary
Category: atom_site / atom_type ...atom_site / atom_type / database_2 / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_ref_seq
Item: _atom_site.auth_seq_id / _atom_type.pdbx_N_electrons ..._atom_site.auth_seq_id / _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_seq_id / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end
Revision 2.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Neurotoxin
BBB: Synaptotagmin-1


Theoretical massNumber of molelcules
Total (without water)54,9372
Polymers54,9372
Non-polymers00
Water70339
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-9 kcal/mol
Surface area19670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.677, 82.528, 106.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Neurotoxin / Neurotoxin B


Mass: 52464.891 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: bontb / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8GR96
#2: Protein/peptide Synaptotagmin-1 / Synaptotagmin I / SytI / p65


Mass: 2471.825 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P21579
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 46.78 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M imidazole pH 8.0, 10% (w/v) PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.5→106.7 Å / Num. obs: 18223 / % possible obs: 99.7 % / Redundancy: 11.1 % / Biso Wilson estimate: 46.89 Å2 / CC1/2: 0.949 / Rmerge(I) obs: 0.252 / Rpim(I) all: 0.082 / Rrim(I) all: 0.267 / Χ2: 0.97 / Net I/σ(I): 5.7
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 11 % / Rmerge(I) obs: 2.563 / Num. unique obs: 2009 / CC1/2: 0.447 / Rpim(I) all: 0.799 / Rrim(I) all: 2.687 / Χ2: 0.92 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4kbb

4kbb


Resolution: 2.5→50.79 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.28 / WRfactor Rwork: 0.246 / Average fsc free: 0.8278 / Average fsc work: 0.8471 / Cross valid method: FREE R-VALUE / ESU R: 0.779 / ESU R Free: 0.333
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2834 1103 6.086 %
Rwork0.2592 17021 -
all0.261 --
obs-18124 99.451 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 53.889 Å2
Baniso -1Baniso -2Baniso -3
1-0.157 Å20 Å20 Å2
2--0.595 Å20 Å2
3----0.751 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3564 0 0 39 3603
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0133646
X-RAY DIFFRACTIONr_bond_other_d0.0350.0183286
X-RAY DIFFRACTIONr_angle_refined_deg1.1681.6424909
X-RAY DIFFRACTIONr_angle_other_deg2.2871.5857640
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7595412
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.94523.514222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.97615672
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.131518
X-RAY DIFFRACTIONr_chiral_restr0.0370.2465
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024027
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02823
X-RAY DIFFRACTIONr_nbd_refined0.1610.2529
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.22992
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21670
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0630.21510
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1020.292
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.020.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1350.24
X-RAY DIFFRACTIONr_nbd_other0.2090.223
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1630.23
X-RAY DIFFRACTIONr_mcbond_it1.255.8211666
X-RAY DIFFRACTIONr_mcbond_other1.2515.821665
X-RAY DIFFRACTIONr_mcangle_it2.2498.722072
X-RAY DIFFRACTIONr_mcangle_other2.2488.7212073
X-RAY DIFFRACTIONr_scbond_it0.8645.8741980
X-RAY DIFFRACTIONr_scbond_other0.8645.8751981
X-RAY DIFFRACTIONr_scangle_it1.6028.7742837
X-RAY DIFFRACTIONr_scangle_other1.6028.7752838
X-RAY DIFFRACTIONr_lrange_it3.37961.5663906
X-RAY DIFFRACTIONr_lrange_other3.37961.563906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.5650.393800.3641224X-RAY DIFFRACTION99.8469
2.565-2.6350.37930.3741191X-RAY DIFFRACTION100
2.635-2.7110.42750.3851112X-RAY DIFFRACTION94.2064
2.711-2.7950.382710.3311138X-RAY DIFFRACTION99.9174
2.795-2.8860.368600.3161145X-RAY DIFFRACTION100
2.886-2.9870.337750.3031057X-RAY DIFFRACTION100
2.987-3.10.277600.281038X-RAY DIFFRACTION100
3.1-3.2260.266660.2891027X-RAY DIFFRACTION99.9086
3.226-3.3690.292680.273956X-RAY DIFFRACTION100
3.369-3.5330.373550.288903X-RAY DIFFRACTION98.6612
3.533-3.7230.294570.269888X-RAY DIFFRACTION99.7888
3.723-3.9490.322570.274838X-RAY DIFFRACTION99.777
3.949-4.220.221530.199787X-RAY DIFFRACTION100
4.22-4.5570.307460.183740X-RAY DIFFRACTION100
4.557-4.9890.2390.17683X-RAY DIFFRACTION100
4.989-5.5740.234350.193636X-RAY DIFFRACTION100
5.574-6.4280.277420.2559X-RAY DIFFRACTION99.8339
6.428-7.8540.215290.212477X-RAY DIFFRACTION100
7.854-11.0280.232310.248383X-RAY DIFFRACTION100
11.028-50.790.223110.356239X-RAY DIFFRACTION98.4252

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more