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- PDB-2vua: Crystal Structure of the Botulinum Neurotoxin Serotype A binding ... -

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Basic information

Entry
Database: PDB / ID: 2vua
TitleCrystal Structure of the Botulinum Neurotoxin Serotype A binding domain
ComponentsBOTULINUM NEUROTOXIN A HEAVY CHAIN
KeywordsHYDROLASE / GANGLIOSIDE / RECEPTOR / TOXIN / MEMBRANE / SECRETED / METAL-BINDING / METALLOPROTEASE / NEUROTOXIN / PROTEASE
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
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 ...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 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Jelly Rolls - #200 / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Botulinum neurotoxin type A / Botulinum neurotoxin type A
Similarity search - Component
Biological speciesCLOSTRIDIUM BOTULINUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsStenmark, P. / Dupuy, J. / Stevens, R.C.
CitationJournal: Plos Pathog. / Year: 2008
Title: Crystal Structure of Botulinum Neurotoxin Type a in Complex with the Cell Surface Co-Receptor Gt1B- Insight Into the Toxin-Neuron Interaction.
Authors: Stenmark, P. / Dupuy, J. / Imamura, A. / Kiso, M. / Stevens, R.C.
History
DepositionMay 22, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BOTULINUM NEUROTOXIN A HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)51,7131
Polymers51,7131
Non-polymers00
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)73.000, 114.500, 105.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein BOTULINUM NEUROTOXIN A HEAVY CHAIN / BOTULINUM NEUROTOXIN SEROTYPE A BINDING DOMAIN / BONT/A / BONTOXILYSIN-A / BOTOX / BOTULINUM NEUROTOXIN TYPE A


Mass: 51713.398 Da / Num. of mol.: 1 / Fragment: BINDING DOMAIN, RESIDUES 876-1296
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM BOTULINUM (bacteria) / Strain: A1 / Plasmid: PET28A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P10845, UniProt: P0DPI1*PLUS, bontoxilysin
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.21 Å3/Da / Density % sol: 44 % / Description: NONE
Crystal growpH: 5.2 / Details: 18% PEG3350, 0.2 M MGCL2, 0.1 M BISTRIS PH 5.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 18, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 48513 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 7.8 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 27
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 4.2 / % possible all: 98.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NYY

2nyy


Resolution: 1.7→19.73 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.189 / SU ML: 0.07 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.205 2469 5.1 %RANDOM
Rwork0.168 ---
obs0.17 46044 99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å20 Å2
2--0.13 Å20 Å2
3----1.08 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3487 0 0 311 3798
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223591
X-RAY DIFFRACTIONr_bond_other_d0.0010.022448
X-RAY DIFFRACTIONr_angle_refined_deg1.4781.9344859
X-RAY DIFFRACTIONr_angle_other_deg0.8835955
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2815429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93124.844192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63815654
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.081521
X-RAY DIFFRACTIONr_chiral_restr0.0920.2519
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023997
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02743
X-RAY DIFFRACTIONr_nbd_refined0.2010.2617
X-RAY DIFFRACTIONr_nbd_other0.1980.22644
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21731
X-RAY DIFFRACTIONr_nbtor_other0.0860.21980
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2236
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2250.233
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2830.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.111.52748
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.37423436
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.28331777
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1854.51419
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
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.267 196
Rwork0.215 3300
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)
11.8523-0.78740.65142.68250.59272.26740.14730.2303-0.1292-0.3575-0.0308-0.6147-0.07640.4797-0.1165-0.1548-0.03740.07330.0774-0.00180.214932.77932.075-8.406
20.38960.21660.08361.8938-1.08543.43850.03630.06770.01480.1197-0.0883-0.3649-0.49860.27880.05190.0307-0.03790.01460.01980.00690.084525.4139.061-2.765
30.54010.1712-0.72541.3283-1.09134.18380.11150.07380.10220.26260.11780.0433-0.8309-0.3595-0.22930.13590.07670.03310.01960.02790.022214.85140.5770.921
41.0820.1873-0.26482.5007-1.55575.00590.06860.1398-0.0286-0.02580.0557-0.1444-0.3087-0.1522-0.1243-0.01930.010.0328-0.02260.00190.019418.78936.608-4.526
50.5958-0.0382-0.31452.4113-0.11611.8024-0.04120.01090.03310.02660.0820.165-0.0236-0.0646-0.04080.01540.0095-0.03620.04150.02080.080619.85812.75815.608
60.2450.4855-0.17591.2091-0.42641.8604-0.0334-0.0367-0.09140.18130.02280.0519-0.15990.0940.01060.0666-0.0022-0.02270.0572-0.00140.058819.66616.41519.215
71.61940.0749-0.3051.4182-0.06292.9412-0.1658-0.0323-0.12860.11010.0745-0.0060.42310.04630.09130.07790.02770.01520.0085-0.00530.049823.30.1116.43
81.2035-0.65760.04772.11050.4511.7596-0.05620.1730.0693-0.1173-0.03660.24490.1454-0.24320.09270.0192-0.0154-0.01620.111-0.00090.079913.4383.70911.222
98.5966-6.0070.152614.5541.532311.75380.26550.3649-0.1126-1.8630.03751.6204-0.394-1.2343-0.3030.0365-0.0103-0.18320.1805-0.01110.20565.9894.7344.571
100.9487-0.2827-1.03462.4763-0.98991.8328-0.0302-0.12780.070.1784-0.02820.0582-0.22480.12380.05840.0990.0091-0.03680.08960.02140.081420.10920.09717.814
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A873 - 910
2X-RAY DIFFRACTION2A911 - 954
3X-RAY DIFFRACTION3A955 - 1033
4X-RAY DIFFRACTION4A1034 - 1093
5X-RAY DIFFRACTION5A1094 - 1131
6X-RAY DIFFRACTION6A1132 - 1171
7X-RAY DIFFRACTION7A1172 - 1222
8X-RAY DIFFRACTION8A1223 - 1264
9X-RAY DIFFRACTION9A1265 - 1277
10X-RAY DIFFRACTION10A1278 - 1297

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