[English] 日本語
Yorodumi
- PDB-5v38: Crystal Structure of The Receptor-binding Domain of Botulinum Neu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5v38
TitleCrystal Structure of The Receptor-binding Domain of Botulinum Neurotoxin Type HA
ComponentsHcHA
KeywordsTOXIN / botulinum neurotoxin (BoNT) / BoNT/HA / BoNT/H / BoNT/FA / receptor-binding domain / host receptor / neutralizing antibody
Function / homology
Function and homology information


negative regulation of neurotransmitter secretion
Similarity search - Function
Clostridium neurotoxin, receptor-binding C-terminal / Clostridium neurotoxin, C-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Jelly Rolls - #200 / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETIC ACID / Neurotoxin heavy chain 18 kDa fragment
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYao, G. / Lam, K.-H. / Jin, R.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI091823 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI125704 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI123920 United States
CitationJournal: Toxins (Basel) / Year: 2017
Title: Crystal Structure of the Receptor-Binding Domain of Botulinum Neurotoxin Type HA, Also Known as Type FA or H.
Authors: Yao, G. / Lam, K.H. / Perry, K. / Weisemann, J. / Rummel, A. / Jin, R.
History
DepositionMar 6, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 22, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.classification
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HcHA
B: HcHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,3809
Polymers100,9602
Non-polymers4207
Water16,682926
1
A: HcHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7205
Polymers50,4801
Non-polymers2404
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HcHA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,6604
Polymers50,4801
Non-polymers1803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.940, 80.121, 78.380
Angle α, β, γ (deg.)90.00, 105.94, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein HcHA


Mass: 50480.051 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9R540*PLUS
#2: Chemical
ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 926 / 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: 2.37 Å3/Da / Density % sol: 48.12 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 100 mM sodium acetate, pH 4.2; 20% Polyethylene glyco (PEG) 3,350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.8→49.23 Å / Num. obs: 83495 / % possible obs: 97.5 % / Redundancy: 3.3 % / Net I/σ(I): 8.1
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.2 / % possible all: 97

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
iMOSFLMdata reduction
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JLV

5jlv


Resolution: 1.8→49.23 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.79
RfactorNum. reflection% reflection
Rfree0.217 1986 2.38 %
Rwork0.179 --
obs0.18 83495 97.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→49.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6837 0 28 926 7791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077003
X-RAY DIFFRACTIONf_angle_d1.0019453
X-RAY DIFFRACTIONf_dihedral_angle_d12.4192595
X-RAY DIFFRACTIONf_chiral_restr0.0441006
X-RAY DIFFRACTIONf_plane_restr0.0041221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8450.28561380.26875800X-RAY DIFFRACTION97
1.845-1.89490.26581400.25445757X-RAY DIFFRACTION97
1.8949-1.95070.28291450.23925746X-RAY DIFFRACTION96
1.9507-2.01360.23441360.21465738X-RAY DIFFRACTION97
2.0136-2.08560.2811400.1995769X-RAY DIFFRACTION97
2.0856-2.16910.23071430.18735770X-RAY DIFFRACTION96
2.1691-2.26780.25371450.18295718X-RAY DIFFRACTION96
2.2678-2.38740.18691350.18155812X-RAY DIFFRACTION97
2.3874-2.5370.2471410.17795800X-RAY DIFFRACTION97
2.537-2.73280.22891450.17645852X-RAY DIFFRACTION98
2.7328-3.00780.21571460.175907X-RAY DIFFRACTION98
3.0078-3.4430.15351390.15495906X-RAY DIFFRACTION98
3.443-4.33740.16051440.13835957X-RAY DIFFRACTION98
4.3374-49.24690.21461490.1615977X-RAY DIFFRACTION98
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)
14.1911-0.32381.84652.0221-0.06413.473-0.1662-0.18990.33390.13040.0682-0.0314-0.3451-0.05860.04570.13250.0152-0.01140.04230.00210.126172.460643.23319.0378
24.2340.28831.29920.7190.06321.25910.00440.2715-0.0762-0.07440.0328-0.12670.00330.2-0.05260.07940.01220.01140.05530.00380.0769178.706128.779313.9517
32.30530.33450.7230.61080.2450.87060.01610.1367-0.168-0.04530.0039-0.11650.04120.1448-0.0220.08430.0160.00430.0749-0.00830.0783177.397923.890615.5656
41.8106-0.0635-0.06170.39610.0520.3495-0.0012-0.0969-0.03190.0181-0.04270.05520.0265-0.11390.03370.09550.00030.01820.08110.00070.0664153.094624.912418.8457
54.28980.2431-0.24191.4218-0.34512.3270.0212-0.12210.1199-0.0023-0.03260.1084-0.012-0.30460.02290.09080.00520.01270.11940.0050.0745135.772830.254423.8875
62.8048-0.1813-1.38290.60880.02413.0758-0.1076-0.296-0.28020.06070.01620.05540.3210.02250.04520.1202-0.00130.00530.11470.02240.1136142.233822.107625.5777
72.9291-0.04530.76212.20650.20043.9403-0.0509-0.12050.54280.04850.0878-0.0514-0.41840.09260.00460.1788-0.01910.00690.0673-0.00990.2612175.70482.887119.1677
86.17090.72621.96970.81680.17382.09950.01930.2247-0.0357-0.07550.1185-0.1622-0.00580.3215-0.13920.10140.01320.01290.0732-0.0120.1422181.857-11.61413.979
92.34990.45630.44640.79360.40991.3706-0.0131-0.00240.01150.00080.0881-0.18620.06540.2597-0.0620.08540.0249-0.0030.1077-0.00750.114180.5104-16.399515.5215
101.4181-0.1692-0.1930.51630.19790.676-0.0221-0.1010.0430.0447-0.03870.07710.0179-0.1010.04620.1020.00020.00710.09890.02420.0741156.1761-15.280518.7192
113.8934-0.1839-0.54571.6321-0.12783.7794-0.07570.01710.16980.00180.08220.1185-0.0861-0.4270.00570.11320.03950.00670.15310.00140.0757138.8727-10.043723.7063
122.8013-0.1499-1.56610.5944-0.01923.0767-0.2297-0.1755-0.19260.07580.05390.03220.3925-0.13170.11150.15920.00880.01180.11480.00230.1205145.5906-17.683525.1693
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 863 THROUGH 922 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 923 THROUGH 959 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 960 THROUGH 1057 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 1058 THROUGH 1158 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 1159 THROUGH 1205 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 1206 THROUGH 1288 )
7X-RAY DIFFRACTION7CHAIN 'B' AND (RESID 863 THROUGH 922 )
8X-RAY DIFFRACTION8CHAIN 'B' AND (RESID 923 THROUGH 959 )
9X-RAY DIFFRACTION9CHAIN 'B' AND (RESID 960 THROUGH 1057 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 1058 THROUGH 1158 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 1159 THROUGH 1205 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 1206 THROUGH 1288 )

+
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