[English] 日本語
Yorodumi
- PDB-4isq: Binding domain of Botulinum neurotoxin DC in complex with human s... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4isq
TitleBinding domain of Botulinum neurotoxin DC in complex with human synaptotagmin I
Components
  • Neurotoxin
  • Synaptotagmin-1
KeywordsTOXIN / Membrane binding / Synaptotagmin and Ganglioside binding
Function / homology
Function and homology information


clathrin-sculpted acetylcholine transport vesicle membrane / clathrin-sculpted glutamate transport vesicle membrane / Toxicity of botulinum toxin type G (botG) / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / clathrin-sculpted monoamine transport vesicle membrane / calcium-dependent activation of synaptic vesicle fusion / regulation of regulated secretory pathway ...clathrin-sculpted acetylcholine transport vesicle membrane / clathrin-sculpted glutamate transport vesicle membrane / Toxicity of botulinum toxin type G (botG) / synchronous neurotransmitter secretion / fast, calcium ion-dependent exocytosis of neurotransmitter / positive regulation of calcium ion-dependent exocytosis of neurotransmitter / syntaxin-3 binding / clathrin-sculpted monoamine transport vesicle membrane / calcium-dependent activation of synaptic vesicle fusion / regulation of regulated secretory pathway / Acetylcholine Neurotransmitter Release Cycle / Serotonin Neurotransmitter Release Cycle / calcium ion sensor activity / Toxicity of botulinum toxin type B (botB) / spontaneous neurotransmitter secretion / clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane / dense core granule / chromaffin granule membrane / GABA synthesis, release, reuptake and degradation / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / calcium ion-regulated exocytosis of neurotransmitter / vesicle docking / regulation of calcium ion-dependent exocytosis / exocytic vesicle / positive regulation of dopamine secretion / protein heterooligomerization / Glutamate Neurotransmitter Release Cycle / neurotransmitter secretion / regulation of exocytosis / positive regulation of dendrite extension / neuron projection terminus / calcium-dependent phospholipid binding / Neurexins and neuroligins / syntaxin-1 binding / low-density lipoprotein particle receptor binding / syntaxin binding / clathrin binding / phosphatidylserine binding / regulation of dopamine secretion / excitatory synapse / synaptic vesicle endocytosis / protein transmembrane transporter activity / detection of calcium ion / positive regulation of synaptic transmission / regulation of synaptic transmission, glutamatergic / phosphatidylinositol-4,5-bisphosphate binding / hippocampal mossy fiber to CA3 synapse / cellular response to calcium ion / SNARE binding / clathrin-coated endocytic vesicle membrane / metalloendopeptidase activity / synaptic vesicle membrane / calcium-dependent protein binding / synaptic vesicle / Cargo recognition for clathrin-mediated endocytosis / presynaptic membrane / Clathrin-mediated endocytosis / toxin activity / chemical synaptic transmission / cell differentiation / calmodulin binding / neuron projection / protein heterodimerization activity / axon / glutamatergic synapse / calcium ion binding / Golgi apparatus / proteolysis / zinc ion binding / extracellular region / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Synaptotagmin / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, N-terminal receptor binding ...Synaptotagmin / Clostridium neurotoxin, translocation / Clostridium neurotoxin, Translocation domain / Clostridium neurotoxin, translocation domain / Clostridial neurotoxin zinc protease / Botulinum/Tetanus toxin, catalytic chain / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / C2 domain superfamily / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Synaptotagmin-1 / Neurotoxin
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.65 Å
AuthorsBerntsson, R.P.-A. / Peng, L. / Svensson, L.M. / Dong, M. / Stenmark, P.
CitationJournal: Structure / Year: 2013
Title: Crystal Structures of Botulinum Neurotoxin DC in Complex with Its Protein Receptors Synaptotagmin I and II.
Authors: Berntsson, R.P. / Peng, L. / Svensson, L.M. / Dong, M. / Stenmark, P.
History
DepositionJan 17, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2013Group: Database references
Revision 1.2Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Neurotoxin
B: Neurotoxin
C: Neurotoxin
D: Synaptotagmin-1
E: Synaptotagmin-1
F: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,27034
Polymers157,6126
Non-polymers2,65828
Water4,738263
1
A: Neurotoxin
F: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,48212
Polymers52,5372
Non-polymers94510
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-79 kcal/mol
Surface area19490 Å2
MethodPISA
2
B: Neurotoxin
E: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,2069
Polymers52,5372
Non-polymers6687
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2440 Å2
ΔGint-78 kcal/mol
Surface area19270 Å2
MethodPISA
3
C: Neurotoxin
D: Synaptotagmin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,58213
Polymers52,5372
Non-polymers1,04511
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-111 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.227, 57.550, 165.274
Angle α, β, γ (deg.)90.000, 118.110, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Neurotoxin /


Mass: 50065.379 Da / Num. of mol.: 3 / Fragment: Hc domain (unp residues 864-1285)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LBR1
#2: Protein/peptide Synaptotagmin-1 / / Synaptotagmin I / SytI / p65


Mass: 2471.825 Da / Num. of mol.: 3 / Fragment: toxin binding site (unp residues 33-53) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P21579
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 4.37 Å3/Da / Density % sol: 71.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.0 M NaSO4, 0.1 M Na-cacodylate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→48.5 Å / Num. all: 80170 / Num. obs: 80166 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Rsym value: 0.125 / Net I/σ(I): 9.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.65-2.793.70.6581.142411115550.658100
2.79-2.963.60.4781.639195109800.47899.9
2.96-3.173.40.32.435437103490.399.9
3.17-3.423.70.1933.73569296530.193100
3.42-3.753.60.1235.73207788660.123100
3.75-4.193.40.0798.82760180910.079100
4.19-4.843.70.06111.52641271600.061100
4.84-5.933.50.06211.22091560440.062100
5.93-8.383.60.06511.11694547640.065100
8.38-48.5953.30.03419.1889227040.03499.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation9.47 Å48.59 Å
Translation9.47 Å48.59 Å

-
Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHASER2.5.1phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→48.65 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.1996 / WRfactor Rwork: 0.1816 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8645 / SU B: 16.041 / SU ML: 0.171 / SU R Cruickshank DPI: 0.3221 / SU Rfree: 0.2259 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.322 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2201 4003 5 %RANDOM
Rwork0.2036 ---
obs0.2045 80151 99.8 %-
all-80166 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 119.14 Å2 / Biso mean: 46.6984 Å2 / Biso min: 9.15 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20.47 Å2
2---4.26 Å2-0 Å2
3---2.37 Å2
Refinement stepCycle: LAST / Resolution: 2.65→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10534 0 148 263 10945
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0210960
X-RAY DIFFRACTIONr_bond_other_d0.0010.0210127
X-RAY DIFFRACTIONr_angle_refined_deg0.7861.9514818
X-RAY DIFFRACTIONr_angle_other_deg0.616323251
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.95951283
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.19525.099557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.568151917
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.0781542
X-RAY DIFFRACTIONr_chiral_restr0.0530.21601
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212366
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022678
LS refinement shellResolution: 2.65→2.719 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 285 -
Rwork0.317 5596 -
all-5881 -
obs--99.75 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.43880.9389-1.28434.08920.14463.8250.1356-0.0137-0.39920.19890.027-0.34530.33850.1741-0.16250.05390.033-0.03060.0448-0.00030.2557-76.8069-6.67218.5776
29.2933-5.6878-3.5196.2684-2.63599.57210.49881.03730.1519-0.4124-1.3297-0.64560.05540.82990.83090.35920.0355-0.22590.4067-0.04020.8331-63.62334.4723211.2519
32.45710.2980.48881.28320.54960.9686-0.0018-0.08380.24520.1124-0.0364-0.1318-0.08760.0450.03820.0734-0.01350.04140.14290.0130.2144-81.11511.972220.1461
44.48481.25480.35942.67260.19782.25120.0369-0.0250.10890.16640.0626-0.1236-0.33390.0482-0.09960.0720.02330.00160.0901-0.00170.2378-75.59496.8098219.2738
51.7488-0.1912-0.05341.10630.12320.3507-0.01020.06540.0106-0.0832-0.0015-0.0069-0.01570.01660.01170.1419-0.0110.05410.16980.01410.1082-112.1770.3345211.4043
64.445-0.43021.76394.7793-1.85993.73190.01310.122-0.6089-0.5560.20190.14450.95380.2112-0.21490.54160.0894-0.17470.0968-0.0620.2308-53.134513.2001183.8894
70.59451.6794-0.66354.9856-2.27221.4761-0.47010.43770.1702-0.92910.84170.48240.38220.1869-0.37170.7899-0.0379-0.31891.0852-0.06860.145-57.476720.9292172.6257
82.7840.24041.95612.6516-0.54923.6395-0.10560.55290.1597-0.42850.01280.0679-0.05440.40120.09280.11460.0111-0.04720.20260.04770.0582-49.171631.6436184.7301
92.9801-0.05491.63213.4106-0.19664.74190.14160.61230.2131-0.4761-0.05170.21640.20590.1862-0.08990.15080.0278-0.0760.16470.03380.0815-52.950428.3728181.9497
101.22140.44490.36621.10570.19281.28930.00410.03320.0418-0.0559-0.01230.1106-0.0317-0.04490.00820.10870.01190.00320.15090.00280.1702-43.528321.8855217.6332
118.79881.84655.10887.11324.34948.9239-0.4384-0.1778-0.21410.1420.07290.06520.39880.44360.36550.26680.06990.15320.10250.06970.0992-88.801-26.8502188.1095
122.1117-0.0172-1.07141.7938-0.08443.1503-0.0517-0.1038-0.19060.13870.02480.3646-0.0082-0.26230.02690.21190.02750.09580.1736-0.00520.1191-94.2773-17.5143182.3166
132.3117-0.47930.35522.77410.09964.2310.1007-0.32320.20530.2583-0.12620.2815-0.7584-0.1350.02550.3177-0.00280.12650.1043-0.0350.1049-89.4989-5.0776180.5276
140.5930.0882-0.94520.27380.24572.6833-0.0179-0.08410.05760.05720.01980.1197-0.0432-0.0288-0.00190.19320.00490.04990.1621-0.01850.1117-83.6727-18.7073165.8598
151.0516-0.1882-0.42141.637-0.16872.17390.0332-0.0455-0.01340.03750.0161-0.1746-0.01820.1406-0.04920.14240.00360.04250.1555-0.01410.0951-68.7197-19.8765149.6696
1618.60247.07433.65472.85850.691626.22020.7813-2.2923-1.03740.2445-1.1384-0.75020.21063.17210.35710.26650.0063-0.06351.25910.35571.0995-50.0052-21.1705149.6308
174.29311.9751.692715.72310.5360.6879-0.29660.1576-0.16330.42170.4078-1.1687-0.16050.0189-0.11120.3080.02520.01280.3280.04040.4336-55.8006-19.8223139.4023
1817.98985.754711.012811.2843-3.472111.93890.907-2.94861.14360.76190.02322.51880.2747-2.5082-0.93020.3592-0.00170.18070.78490.14010.7171-56.048420.9909237.0576
1911.4655-11.9401-4.138323.95255.13571.55850.28870.135-0.73350.4562-0.66042.0824-0.0709-0.05420.37160.2242-0.049-0.00080.3223-0.02140.3635-44.838322.0849239.2825
2024.38525.239-17.622110.6183.732518.7132-1.12593.2076-0.5953-2.09911.5908-1.2007-0.6746-1.6514-0.4650.6373-0.36060.13160.7211-0.1840.4722-122.5323-0.9733191.3088
210.21361.7624-0.762521.9128-13.52339.8439-0.242-0.0550.028-2.1452-0.3165-0.50130.98640.10490.55850.41340.03540.06480.3063-0.02010.2589-130.38690.5442200.1734
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A863 - 918
2X-RAY DIFFRACTION2A919 - 935
3X-RAY DIFFRACTION3A936 - 1029
4X-RAY DIFFRACTION4A1030 - 1079
5X-RAY DIFFRACTION5A1080 - 1284
6X-RAY DIFFRACTION6B863 - 913
7X-RAY DIFFRACTION7B914 - 931
8X-RAY DIFFRACTION8B932 - 1020
9X-RAY DIFFRACTION9B1021 - 1077
10X-RAY DIFFRACTION10B1078 - 1284
11X-RAY DIFFRACTION11C863 - 896
12X-RAY DIFFRACTION12C897 - 969
13X-RAY DIFFRACTION13C970 - 1036
14X-RAY DIFFRACTION14C1037 - 1151
15X-RAY DIFFRACTION15C1152 - 1284
16X-RAY DIFFRACTION16D43 - 47
17X-RAY DIFFRACTION17D48 - 57
18X-RAY DIFFRACTION18E43 - 47
19X-RAY DIFFRACTION19E48 - 57
20X-RAY DIFFRACTION20F43 - 47
21X-RAY DIFFRACTION21F48 - 57

+
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