[English] 日本語
Yorodumi
- PDB-5v8u: Small Molecule Inhibitor ABS-143 Bound to the Botulinum Neurotoxi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5v8u
TitleSmall Molecule Inhibitor ABS-143 Bound to the Botulinum Neurotoxin Serotype A Light Chain
ComponentsBotulinum neurotoxin type A
KeywordsHYDROLASE/HYDROLASE INHIBITOR / metalloprotease / drug design / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


host cell junction / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / membrane => GO:0016020 ...host cell junction / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / membrane => GO:0016020 / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / membrane
Similarity search - Function
Zincin-like / Metalloproteases ("zincins"), catalytic domain like / 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 ...Zincin-like / Metalloproteases ("zincins"), catalytic domain like / 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 / Alpha Beta
Similarity search - Domain/homology
Chem-90M / Botulinum neurotoxin type A / Botulinum neurotoxin type A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsAllen, K.N. / Silvaggi, N.R.
CitationJournal: Toxicon / Year: 2017
Title: Small molecule metalloprotease inhibitor with in vitro, ex vivo and in vivo efficacy against botulinum neurotoxin serotype A.
Authors: Jacobson, A.R. / Adler, M. / Silvaggi, N.R. / Allen, K.N. / Smith, G.M. / Fredenburg, R.A. / Stein, R.L. / Park, J.B. / Feng, X. / Shoemaker, C.B. / Deshpande, S.S. / Goodnough, M.C. / ...Authors: Jacobson, A.R. / Adler, M. / Silvaggi, N.R. / Allen, K.N. / Smith, G.M. / Fredenburg, R.A. / Stein, R.L. / Park, J.B. / Feng, X. / Shoemaker, C.B. / Deshpande, S.S. / Goodnough, M.C. / Malizio, C.J. / Johnson, E.A. / Pellett, S. / Tepp, W.H. / Tzipori, S.
History
DepositionMar 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Botulinum neurotoxin type A
B: Botulinum neurotoxin type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,2966
Polymers101,6352
Non-polymers6614
Water7,350408
1
A: Botulinum neurotoxin type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1483
Polymers50,8171
Non-polymers3312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Botulinum neurotoxin type A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1483
Polymers50,8171
Non-polymers3312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.095, 67.653, 98.087
Angle α, β, γ (deg.)90.00, 105.22, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Botulinum neurotoxin type A / BoNT/A / Bontoxilysin-A / BOTOX


Mass: 50817.273 Da / Num. of mol.: 2 / Fragment: residues 1-424 / Mutation: P2Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botA, atx, bna / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P10845, UniProt: P0DPI1*PLUS, bontoxilysin
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-90M / N-[3-(4-fluorophenyl)-4-methyl-1H-pyrazol-5-yl]-2-sulfanylacetamide


Mass: 265.307 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H12FN3OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 408 / 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: 2.3 Å3/Da / Density % sol: 46.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Mix equal volumes of 10-12 mg/ml enzyme (50 mM Na2HPO4, 2 mM EDTA, pH 6.5) and crystallization buffer (10-15% polyethylene glycol [PEG] 2,000 monomethyl ester, 0.2-0.3 M K2HPO4, 0.1 M D,L-malic acid pH 7.0)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.0809 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 28, 2008
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0809 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 55823 / % possible obs: 95.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 11.3
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.339 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4395 / % possible all: 76.1

-
Processing

Software
NameVersionClassification
PHENIX(1.11_2567)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BON

3bon


Resolution: 2.05→37.563 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2601 2000 3.58 %
Rwork0.2292 --
obs0.2303 55806 95.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→37.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6276 0 38 417 6731
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026451
X-RAY DIFFRACTIONf_angle_d0.5658707
X-RAY DIFFRACTIONf_dihedral_angle_d13.7443816
X-RAY DIFFRACTIONf_chiral_restr0.043945
X-RAY DIFFRACTIONf_plane_restr0.0021116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10130.36941080.29532906X-RAY DIFFRACTION74
2.1013-2.15810.30991260.28343384X-RAY DIFFRACTION85
2.1581-2.22160.28921370.2613680X-RAY DIFFRACTION92
2.2216-2.29330.32021420.24893834X-RAY DIFFRACTION96
2.2933-2.37520.27621450.25373908X-RAY DIFFRACTION99
2.3752-2.47030.26961480.25233972X-RAY DIFFRACTION100
2.4703-2.58270.28351470.24613960X-RAY DIFFRACTION100
2.5827-2.71880.27051490.25063998X-RAY DIFFRACTION100
2.7188-2.88910.30791480.24263985X-RAY DIFFRACTION100
2.8891-3.11210.27511490.23954010X-RAY DIFFRACTION100
3.1121-3.42510.2451490.22714013X-RAY DIFFRACTION100
3.4251-3.92020.2451500.21284020X-RAY DIFFRACTION100
3.9202-4.93730.21490.18494025X-RAY DIFFRACTION100
4.9373-37.56910.26091530.22544111X-RAY DIFFRACTION100
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)
10.2864-0.25330.03630.227-0.0390.14610.0834-0.0785-0.14130.21430.0119-0.0650.07950.096700.23220.0036-0.03520.18540.0510.1727-10.626-6.1521-15.3199
20.4148-0.04730.10390.5029-0.00240.35310.0375-0.0278-0.09640.1013-0.03370.04520.0444-0.04170.00030.1289-0.0070.00980.120.02060.0943-21.920.9102-20.0824
30.0577-0.0693-0.01850.2033-0.05360.1069-0.03960.0019-0.03460.39640.22270.4646-0.1669-0.25850.3961-0.02420.14510.28980.36560.00240.3834-35.678317.6417-18.4746
40.36710.14740.34620.6366-0.36880.60160.08220.0914-0.1088-0.1099-0.03830.0953-0.006-0.0706-0.00090.13330.0038-0.00150.1454-0.00070.1575-19.01024.1651-29.4869
50.2046-0.22030.00150.2656-0.09540.1109-0.0199-0.04580.06120.0112-0.047-0.0263-0.07330.073200.1702-0.0093-0.01260.1369-0.02510.1183-2.959930.959-20.9875
60.2705-0.26380.02340.5269-0.27980.0206-0.00590.0112-0.0210.0378-0.0293-0.1616-0.05350.010400.1511-0.0193-0.01550.16390.02060.18377.463822.712-22.5793
70.03240.007-0.0250.0121-0.03940.020.05260.3110.0615-0.01810.1104-0.27020.00070.117700.2223-0.04620.0730.39750.00910.362517.962120.9277-37.6039
80.19630.0439-0.10670.14140.06770.06050.063-0.1372-0.42710.1505-0.1123-0.19490.14010.24380.01680.22830.0193-0.0260.27880.01340.340315.8595.6395-21.0551
90.58210.4225-0.02830.478-0.01970.05670.08440.1049-0.0183-0.2706-0.0957-0.09720.0491-0.0170.00740.16540.01860.0150.1589-0.02360.17763.468816.987-35.3665
100.0960.0832-0.19410.0906-0.17880.3582-0.04240.24990.1977-0.3260.07260.2890.223-0.44890.00260.31180.0151-0.02840.25460.0270.2107-9.17434.9246-46.1979
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -9 through 80 )
2X-RAY DIFFRACTION2chain 'A' and (resid 81 through 275 )
3X-RAY DIFFRACTION3chain 'A' and (resid 276 through 299 )
4X-RAY DIFFRACTION4chain 'A' and (resid 300 through 416 )
5X-RAY DIFFRACTION5chain 'B' and (resid -9 through 100 )
6X-RAY DIFFRACTION6chain 'B' and (resid 101 through 232 )
7X-RAY DIFFRACTION7chain 'B' and (resid 233 through 275 )
8X-RAY DIFFRACTION8chain 'B' and (resid 276 through 321 )
9X-RAY DIFFRACTION9chain 'B' and (resid 322 through 390 )
10X-RAY DIFFRACTION10chain 'B' and (resid 391 through 416 )

+
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://pdbjlvh1.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