[English] 日本語
Yorodumi
- PDB-7z5s: Crystal Structure of botulinum neurotoxin A2 cell binding domain ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7z5s
TitleCrystal Structure of botulinum neurotoxin A2 cell binding domain in complex with GD1a
ComponentsBotulinum neurotoxin
KeywordsTOXIN / ganglioside / neurotoxin / botulinum / receptor / GD1a
Function / homology
Function and homology information


host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / proteolysis / extracellular region / zinc ion binding
Similarity search - Function
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 / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGregory, K.S. / Acharya, K.R. / Liu, S.M. / Mahadeva, T.B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Toxins / Year: 2022
Title: Structural Features of Clostridium botulinum Neurotoxin Subtype A2 Cell Binding Domain.
Authors: Gregory, K.S. / Mahadeva, T.B. / Liu, S.M. / Acharya, K.R.
History
DepositionMar 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Botulinum neurotoxin
BBB: Botulinum neurotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,5876
Polymers100,8332
Non-polymers1,7554
Water5,242291
1
AAA: Botulinum neurotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7613
Polymers50,4161
Non-polymers3442
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: Botulinum neurotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8273
Polymers50,4161
Non-polymers1,4102
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.068, 105.068, 132.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein Botulinum neurotoxin


Mass: 50416.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: A, bont / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: K4GGE0
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[N-acetyl-alpha-neuraminic acid-(2-3)]beta-D-galactopyranose


Type: oligosaccharide / Mass: 1127.999 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGalpNAcb1-4[DNeup5Aca2-3]DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O]/1-2-3-1-2/a3-b2_a4-c1_c3-d1_d3-e2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}[(4+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.63 Å3/Da / Density % sol: 66.1 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Lithium citrate tribasic tetrahydrate 20 % w/v PEG 3350

-
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: Oct 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.1→105.07 Å / Num. obs: 83782 / % possible obs: 100 % / Redundancy: 27.3 % / CC1/2: 0.99 / Net I/σ(I): 11.1
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 21.9 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 4633 / CC1/2: 0.4 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5MOY

5moy


Resolution: 2.1→105.068 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.194 / WRfactor Rwork: 0.159 / Average fsc free: 0.8683 / Average fsc work: 0.8793 / Cross valid method: FREE R-VALUE / ESU R: 0.151 / ESU R Free: 0.145
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2264 4166 4.976 %
Rwork0.1883 79553 -
all0.19 --
obs-83719 99.981 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 46.052 Å2
Baniso -1Baniso -2Baniso -3
1-0.747 Å2-0 Å2-0 Å2
2--0.747 Å2-0 Å2
3----1.493 Å2
Refinement stepCycle: LAST / Resolution: 2.1→105.068 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6733 0 119 291 7143
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0136991
X-RAY DIFFRACTIONr_bond_other_d0.0340.0166677
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.6429423
X-RAY DIFFRACTIONr_angle_other_deg2.2721.59415327
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9085816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.86423.74377
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.987151258
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg16.632152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7851531
X-RAY DIFFRACTIONr_chiral_restr0.0710.2921
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.027834
X-RAY DIFFRACTIONr_gen_planes_other0.010.021689
X-RAY DIFFRACTIONr_nbd_refined0.1960.21096
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2170.26335
X-RAY DIFFRACTIONr_nbtor_refined0.1730.23365
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.23474
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2378
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1590.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1430.223
X-RAY DIFFRACTIONr_nbd_other0.3160.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1460.215
X-RAY DIFFRACTIONr_mcbond_it3.9054.4853282
X-RAY DIFFRACTIONr_mcbond_other3.8974.4853281
X-RAY DIFFRACTIONr_mcangle_it5.5646.7124092
X-RAY DIFFRACTIONr_mcangle_other5.5646.7134093
X-RAY DIFFRACTIONr_scbond_it4.8785.0823709
X-RAY DIFFRACTIONr_scbond_other4.8775.0833710
X-RAY DIFFRACTIONr_scangle_it7.2517.3795331
X-RAY DIFFRACTIONr_scangle_other7.257.3815332
X-RAY DIFFRACTIONr_lrange_it8.93851.0837634
X-RAY DIFFRACTIONr_lrange_other8.92750.997595
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.1-2.1550.3482970.32158830.32361800.6840.6941000.321
2.155-2.2140.3062820.29457350.29460170.7820.7761000.289
2.214-2.2780.2972850.27855590.27958480.8070.80799.93160.269
2.278-2.3480.2942740.26754430.26957180.8270.83199.98250.253
2.348-2.4250.3312950.25751510.26154470.8150.84599.98160.238
2.425-2.510.2862760.24350800.24653580.8620.87499.96270.221
2.51-2.6040.2922840.24548810.24851660.8620.87399.98060.22
2.604-2.7110.2722530.2346710.23249250.8820.89799.97970.202
2.711-2.8310.3012090.22545470.22847590.8760.90799.9370.197
2.831-2.9690.2782370.20943170.21345550.890.92199.97810.183
2.969-3.130.2352130.19641070.19843210.9270.93399.97690.176
3.13-3.3190.2312300.18838810.1941120.930.94399.97570.17
3.319-3.5480.2171960.17836420.1838380.9350.9481000.164
3.548-3.8320.1951670.15734070.15835740.9460.9641000.146
3.832-4.1980.1651450.13631740.13833190.9670.971000.127
4.198-4.6920.1711670.11827980.12129650.9680.9781000.11
4.692-5.4160.1471340.12725200.12826540.9730.9751000.119
5.416-6.6290.212890.15921570.16222460.9540.9611000.152
6.629-9.3560.207790.17916690.1817480.9440.9521000.171
9.356-105.0680.17540.1989310.1979850.9650.9571000.19

+
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