[English] 日本語
Yorodumi
- PDB-1e1h: Crystal Structure of recombinant Botulinum Neurotoxin Type A Ligh... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1e1h
TitleCrystal Structure of recombinant Botulinum Neurotoxin Type A Light Chain, self-inhibiting Zn endopeptidase.
Components(BOTULINUM NEUROTOXIN TYPE A LIGHT CHAIN) x 2
KeywordsHYDROLASE / NEUROTOXIN / ZN-ENDOPEPTIDASE / COMPLEX / SUBSTRATE BOUND / BOTULINUM / INHIBITOR BOUND
Function / homology
Function and homology information


bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / host cell plasma membrane / proteolysis / extracellular region ...bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / host cell plasma membrane / proteolysis / extracellular region / zinc ion binding / membrane
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #540 / Metalloproteases ("zincins"), catalytic domain fold / Clostridium neurotoxins / 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 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #540 / Metalloproteases ("zincins"), catalytic domain fold / Clostridium neurotoxins / 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 C-terminal / Clostridium neurotoxin, receptor binding N-terminal / Clostridium neurotoxin, C-terminal receptor binding / Clostridium neurotoxin, N-terminal receptor binding / Kunitz inhibitor STI-like superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Few Secondary Structures / Irregular / Concanavalin A-like lectin/glucanase domain superfamily / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Botulinum neurotoxin type A2
Similarity search - Component
Biological speciesCLOSTRIDIUM BOTULINUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKnapp, M. / Rupp, B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Crystal Structure of Clostridium Botulinum Neurotoxin Protease in a Product-Bound State: Evidence for Noncanonical Zinc Protease Activity
Authors: Segelke, B.W. / Knapp, M. / Kadhkodayan, S. / Balhorn, R. / Rupp, B.
History
DepositionMay 8, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 19, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 10, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant / _pdbx_database_status.recvd_author_approval
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.5Dec 6, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_conn.ptnr2_label_seq_id / _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 LIGHT CHAIN
B: BOTULINUM NEUROTOXIN TYPE A LIGHT CHAIN
C: BOTULINUM NEUROTOXIN TYPE A LIGHT CHAIN
D: BOTULINUM NEUROTOXIN TYPE A LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,5576
Polymers105,4264
Non-polymers1312
Water13,836768
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18930 Å2
ΔGint-197.3 kcal/mol
Surface area34360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.064, 94.263, 100.156
Angle α, β, γ (deg.)90.00, 103.52, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.8397, 0.5389, -0.0674), (0.5406, 0.8178, -0.1973), (-0.0512, -0.2021, -0.978)3.2947, 3.9508, 48.0381
2given(-0.8397, 0.5406, -0.0512), (0.5389, 0.8178, -0.2021), (-0.0674, -0.1973, -0.978)-3.2947, -3.9508, -48.0381

-
Components

#1: Protein BOTULINUM NEUROTOXIN TYPE A LIGHT CHAIN / BONT/A LC


Mass: 32153.004 Da / Num. of mol.: 2 / Fragment: RESIDUES 10-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM BOTULINUM (bacteria) / Strain: KYOTO-F / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): BLR DE-3 / References: UniProt: Q45894, bontoxilysin
#2: Protein BOTULINUM NEUROTOXIN TYPE A LIGHT CHAIN / BONT/A LC


Mass: 20560.143 Da / Num. of mol.: 2 / Fragment: RESIDUES 252-416 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: HOMODIMER, CONTAINING CLEAVED SUBSTRATE ANALOG (LOOP 245-255) IN ACTIVE SITE
Source: (gene. exp.) CLOSTRIDIUM BOTULINUM (bacteria) / Strain: KYOTO-F / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): BLR DE-3 / References: UniProt: Q45894, bontoxilysin
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 768 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTER TYR: PEPTIDE CHAIN CLEAVED AT AA 249 AND 250. HIS: PEPTIDE CHAIN CLEAVED AT AA 249 AND 250.
Sequence detailsEXPERIMENTAL PROTEIN HAS 6XHIS-TAG AND S-TAG AT N-TERMINUS FOLLOWED BY RESIDUES 9-415 OF NCBI: ...EXPERIMENTAL PROTEIN HAS 6XHIS-TAG AND S-TAG AT N-TERMINUS FOLLOWED BY RESIDUES 9-415 OF NCBI:CBNTOXA, THEN A C-TERM 6XHIS-TAG WITH A 2 RESIDUE LEADER (LE). SEQUENCE IN COORDINATE FILE IS NUMBERED AS IN NCBI:CBNTOXA RESIDUES 7&8 ARE FROM THE AFFINITY TAG.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 53 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 4.6
Details: HANGING DROP VAPOUR DIFFUSION, DROP: 4UL 5MG/ML PROTEIN & 2UL WELL. PROTEIN: 0.05M TRIS PH 8.0,10% GLYCEROL, 0.1% TRITON X-100,1.0MM 2-ME,4% XYLITOL. WELL: 0.2M (NH4)2SO4,0.1M NAOAC PH 4.6, 25% PEG4000.
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
20.1 %triton X-1001drop
325 mMTris1droppH8.0
410 %(v/v)glycerol1drop
51 mMMPD1drop
60.2 Mammonium sulfate1reservoir
70.1 Msodium acetate1reservoirpH4.6
825 %(w/v)PEG40001reservoir
93 %xylitol1reservoir

-
Data collection

DiffractionMean temperature: 125 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 15, 2000 / Details: DOUBLE FOCUSSING
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.8→19.34 Å / Num. obs: 93168 / % possible obs: 95.2 % / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 24.47 Å2 / Rsym value: 0.042 / Net I/σ(I): 7.9
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.383 / % possible all: 95.2
Reflection
*PLUS
Highest resolution: 1.8 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.042
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.9 Å / Redundancy: 1.9 % / Num. unique obs: 6918 / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 1.7

-
Processing

Software
NameClassification
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: LC COORDINATES OF PDB ENTRY 3BTA

3bta


Resolution: 1.8→19.34 Å / SU B: 2.746 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.129 / ESU R Free: 0.127
RfactorNum. reflection% reflectionSelection details
Rfree0.237 4649 5 %RANDOM
Rwork0.196 ---
obs-92076 95.2 %-
Displacement parametersBiso mean: 31.5 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6460 0 2 768 7230
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.0190.02
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0270.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.9042
X-RAY DIFFRACTIONp_mcangle_it2.6463
X-RAY DIFFRACTIONp_scbond_it3.4543
X-RAY DIFFRACTIONp_scangle_it5.0514
X-RAY DIFFRACTIONp_plane_restr0.0180.03
X-RAY DIFFRACTIONp_chiral_restr0.1910.15
X-RAY DIFFRACTIONp_singtor_nbd0.1820.3
X-RAY DIFFRACTIONp_multtor_nbd0.2760.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1430.3
X-RAY DIFFRACTIONp_planar_tor5.217
X-RAY DIFFRACTIONp_staggered_tor16.9515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor26.2120
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.8 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.02
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.85

+
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