[English] 日本語
Yorodumi
- PDB-3zur: Crystal structure of an engineered botulinum neurotoxin type A- S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zur
TitleCrystal structure of an engineered botulinum neurotoxin type A- SNARE23 derivative, LC0-A-SNAP25-Hn-A
ComponentsBOTULINUM NEUROTOXIN TYPE A, SYNAPTOSOMAL-ASSOCIATED PROTEIN
KeywordsHYDROLASE/SIGNALING PROTEIN / HYDROLASE-SIGNALING PROTEIN COMPLEX / HYDROLASE / SNARE / PROTEIN ENGINEERING
Function / homology
Function and homology information


Toxicity of botulinum toxin type C (botC) / neurotransmitter uptake / Toxicity of botulinum toxin type E (botE) / host cell junction / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Toxicity of botulinum toxin type A (botA) / Acetylcholine Neurotransmitter Release Cycle / extrinsic component of presynaptic membrane / synaptic vesicle fusion to presynaptic active zone membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex ...Toxicity of botulinum toxin type C (botC) / neurotransmitter uptake / Toxicity of botulinum toxin type E (botE) / host cell junction / exocytic insertion of neurotransmitter receptor to postsynaptic membrane / Toxicity of botulinum toxin type A (botA) / Acetylcholine Neurotransmitter Release Cycle / extrinsic component of presynaptic membrane / synaptic vesicle fusion to presynaptic active zone membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex / synaptobrevin 2-SNAP-25-syntaxin-1a complex / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / Serotonin Neurotransmitter Release Cycle / GABA synthesis, release, reuptake and degradation / presynaptic dense core vesicle exocytosis / ribbon synapse / synaptic vesicle docking / Dopamine Neurotransmitter Release Cycle / Norepinephrine Neurotransmitter Release Cycle / SNARE complex / negative regulation of neurotransmitter secretion / SNAP receptor activity / Glutamate Neurotransmitter Release Cycle / bontoxilysin / host cell presynaptic membrane / neurotransmitter receptor internalization / host cell cytoplasmic vesicle / Sensory processing of sound by inner hair cells of the cochlea / syntaxin-1 binding / SNARE complex assembly / synaptic vesicle priming / host cell cytosol / regulation of synapse assembly / endosomal transport / Other interleukin signaling / myosin binding / regulation of neuron projection development / exocytosis / synaptic vesicle exocytosis / voltage-gated potassium channel activity / tertiary granule membrane / associative learning / regulation of insulin secretion / protein transmembrane transporter activity / long-term memory / specific granule membrane / voltage-gated potassium channel complex / axonal growth cone / presynaptic active zone membrane / photoreceptor inner segment / axonogenesis / locomotory behavior / filopodium / long-term synaptic potentiation / Regulation of insulin secretion / trans-Golgi network / positive regulation of insulin secretion / metalloendopeptidase activity / calcium-dependent protein binding / synaptic vesicle / actin cytoskeleton / presynaptic membrane / lamellipodium / cell cortex / growth cone / toxin activity / chemical synaptic transmission / postsynapse / transmembrane transporter binding / membrane => GO:0016020 / cytoskeleton / endosome / neuron projection / protein domain specific binding / neuronal cell body / glutamatergic synapse / lipid binding / Neutrophil degranulation / host cell plasma membrane / perinuclear region of cytoplasm / proteolysis / zinc ion binding / extracellular region / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Clostridium botulinum neurotoxin B, "coiled-coil" domain / Clostridium botulinum neurotoxin b, "coiled-coil" domain / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Zincin-like / Metalloproteases ("zincins"), catalytic domain like / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain ...Clostridium botulinum neurotoxin B, "coiled-coil" domain / Clostridium botulinum neurotoxin b, "coiled-coil" domain / Synaptosomal-associated protein 25 / SNAP-25 domain / SNAP-25 family / Zincin-like / Metalloproteases ("zincins"), catalytic domain like / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / 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 / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Botulinum neurotoxin type A / Botulinum neurotoxin type A / Synaptosomal-associated protein 25
Similarity search - Component
Biological speciesCLOSTRIDIUM BOTULINUM (bacteria)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsMasuyer, G. / Stancombe, P. / Chaddock, J.A. / Acharya, K.R.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structures of Engineered Clostridium Botulinum Neurotoxin Derivatives
Authors: Masuyer, G. / Stancombe, P. / Chaddock, J.A. / Acharya, K.R.
History
DepositionJul 19, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Other
Revision 1.2Mar 15, 2017Group: Source and taxonomy
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: BOTULINUM NEUROTOXIN TYPE A, SYNAPTOSOMAL-ASSOCIATED PROTEIN
B: BOTULINUM NEUROTOXIN TYPE A, SYNAPTOSOMAL-ASSOCIATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,6207
Polymers217,1402
Non-polymers4805
Water2,684149
1
A: BOTULINUM NEUROTOXIN TYPE A, SYNAPTOSOMAL-ASSOCIATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,9545
Polymers108,5701
Non-polymers3844
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BOTULINUM NEUROTOXIN TYPE A, SYNAPTOSOMAL-ASSOCIATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,6662
Polymers108,5701
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)78.957, 157.495, 209.357
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 430
2114B1 - 430
1125A450 - 865
2125B450 - 865

NCS ensembles :
ID
1
2

-
Components

#1: Protein BOTULINUM NEUROTOXIN TYPE A, SYNAPTOSOMAL-ASSOCIATED PROTEIN / LC-A0-SNAP25-HN-A / BONT/A / BONTOXILYSIN-A / BOTOX / BOTULINUM NEUROTOXIN A LIGHT CHAIN / ...LC-A0-SNAP25-HN-A / BONT/A / BONTOXILYSIN-A / BOTOX / BOTULINUM NEUROTOXIN A LIGHT CHAIN / BOTULINUM NEUROTOXIN A HEAVY CHAIN / SNAP-25 / SUPER PROTEIN / SUP / SYNAPTOSOMAL-ASSOCIATED 25 KDA PROTEIN


Mass: 108569.992 Da / Num. of mol.: 2
Fragment: CATALYTIC DOMAIN, RESIDUES 3-431, SNAP25, RESIDUES 145-206, TRANSLOCATION DOMAIN RESIDUES, 454-865
Mutation: YES
Source method: isolated from a genetically manipulated source
Details: INACTIVE CATALYTIC DOMAIN OF BONT TYPE A, SNAP25, TRANSLOCATION DOMAIN OF BONT TYPE A
Source: (gene. exp.) CLOSTRIDIUM BOTULINUM (bacteria), (gene. exp.) HOMO SAPIENS (human)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P10845, UniProt: P60880, UniProt: P0DPI1*PLUS, bontoxilysin
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 224 TO GLN ENGINEERED RESIDUE IN CHAIN A, HIS 227 TO TYR ...ENGINEERED RESIDUE IN CHAIN A, GLU 224 TO GLN ENGINEERED RESIDUE IN CHAIN A, HIS 227 TO TYR ENGINEERED RESIDUE IN CHAIN B, GLU 224 TO GLN ENGINEERED RESIDUE IN CHAIN B, HIS 227 TO TYR
Sequence detailsHUMAN SNAP25 PEPTIDE ENGINEERED BETWEEN LC AND HN OF BOTULINUM NEUROTOXIN A

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1 M TRIS PH 7.5, 0.2 M LISO4, 15% PEG 3350.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.7→29.6 Å / Num. obs: 69459 / % possible obs: 96.6 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.5
Reflection shellResolution: 2.7→2.9 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.9 / % possible all: 79.7

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W2D

2w2d


Resolution: 2.71→125.86 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.884 / SU B: 27.885 / SU ML: 0.259 / Cross valid method: THROUGHOUT / ESU R: 0.678 / ESU R Free: 0.341 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SNAP25 PEPTIDE RESIDUES 434-527 ARE UNOBSERVED.
RfactorNum. reflection% reflectionSelection details
Rfree0.2664 3500 5.1 %RANDOM
Rwork0.21213 ---
obs0.21484 65805 96.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.874 Å2
Baniso -1Baniso -2Baniso -3
1--1.16 Å20 Å20 Å2
2--1.71 Å20 Å2
3----0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.71→125.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13649 0 25 149 13823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02213954
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0941.95818908
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.69851683
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.81425.546696
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.539152452
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5551544
X-RAY DIFFRACTIONr_chiral_restr0.0780.22107
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02110572
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.491.58419
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.934213676
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.07435535
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9134.55232
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0 Å

Ens-IDDom-IDAuth asym-IDNumberTypeWeight position
11A3486medium positional0.5
12B3486medium positional0.5
21A1656medium positional0.5
22B1656medium positional0.5
21A1686loose positional5
22B1686loose positional5
11A3486medium thermal2
12B3486medium thermal2
21A1656medium thermal2
22B1656medium thermal2
21A1686loose thermal10
22B1686loose thermal10
LS refinement shellResolution: 2.709→2.779 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 177 -
Rwork0.29 3380 -
obs--68.61 %
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)
10.8184-0.0159-0.24560.23890.05580.2338-0.0809-0.00620.0248-0.00150.04520.02840.03610.01920.03570.0696-0.0066-0.02460.06530.0070.0382.9129-9.4944-26.239
20.16280.04160.02230.31480.03840.1458-0.0160.05030.0866-0.00910.0503-0.045-0.0127-0.0056-0.03430.04750.0194-0.02870.05710.00570.085527.91583.7195-29.2618
30.577-0.1044-0.17810.51010.16020.50110.0383-0.052-0.0143-0.0074-0.0395-0.01160.0648-0.04740.00120.1163-0.0064-0.01510.0541-0.01220.007926.3812-19.49110.14
40.35580.1172-0.07460.2022-0.05240.49130.0311-0.05990.13310.0406-0.0223-0.0115-0.1305-0.1178-0.00880.09770.0336-0.0020.0677-0.04120.079519.09427.989812.7553
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 433
2X-RAY DIFFRACTION2A528 - 944
3X-RAY DIFFRACTION3B1 - 433
4X-RAY DIFFRACTION4B528 - 944

+
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