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- PDB-4kbb: Structure of Botulinum neurotoxin B binding domain in complex wit... -

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Basic information

Entry
Database: PDB / ID: 4kbb
TitleStructure of Botulinum neurotoxin B binding domain in complex with both synaptotagmin II and GD1a
Components
  • Botulinum neurotoxin type B
  • Synaptotagmin-2
KeywordsSignaling Protein/Toxin / Toxin binding domain / Synaptotagmin and ganglioside / Signaling Protein-Toxin complex
Function / homology
Function and homology information


calcium-dependent activation of synaptic vesicle fusion / Toxicity of botulinum toxin type B (botB) / dense core granule / chromaffin granule membrane / inositol 1,3,4,5 tetrakisphosphate binding / calcium ion-regulated exocytosis of neurotransmitter / regulation of calcium ion-dependent exocytosis / exocytic vesicle / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis ...calcium-dependent activation of synaptic vesicle fusion / Toxicity of botulinum toxin type B (botB) / dense core granule / chromaffin granule membrane / inositol 1,3,4,5 tetrakisphosphate binding / calcium ion-regulated exocytosis of neurotransmitter / regulation of calcium ion-dependent exocytosis / exocytic vesicle / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / bontoxilysin / host cell presynaptic membrane / calcium-dependent phospholipid binding / host cell cytoplasmic vesicle / syntaxin binding / host cell cytosol / clathrin binding / regulation of dopamine secretion / phosphatidylserine binding / synaptic vesicle endocytosis / protein transmembrane transporter activity / cellular response to calcium ion / neuromuscular junction / metalloendopeptidase activity / synaptic vesicle membrane / toxin activity / cell differentiation / axon / lipid binding / calcium ion binding / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / membrane / plasma membrane
Similarity search - Function
Synaptotagmin / 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 ...Synaptotagmin / 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 / C2 domain / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain profile. / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Jelly Rolls - #200 / C2 domain superfamily / 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 B / Synaptotagmin-2
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBerntsson, R.P.A. / Peng, L. / Dong, M. / Stenmark, P.
CitationJournal: Nat Commun / Year: 2013
Title: Structure of dual receptor binding to botulinum neurotoxin B.
Authors: Berntsson, R.P. / Peng, L. / Dong, M. / Stenmark, P.
History
DepositionApr 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_label_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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Botulinum neurotoxin type B
B: Botulinum neurotoxin type B
C: Synaptotagmin-2
D: Synaptotagmin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,6199
Polymers124,9444
Non-polymers2,6755
Water4,756264
1
A: Botulinum neurotoxin type B
C: Synaptotagmin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7984
Polymers62,4722
Non-polymers1,3262
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-10 kcal/mol
Surface area20000 Å2
MethodPISA
2
B: Botulinum neurotoxin type B
D: Synaptotagmin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8225
Polymers62,4722
Non-polymers1,3503
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-3 kcal/mol
Surface area20250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.163, 158.237, 75.244
Angle α, β, γ (deg.)90.00, 108.44, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Botulinum neurotoxin type B / BoNT/B / Bontoxilysin-B / Botulinum neurotoxin B light chain / Botulinum neurotoxin B heavy chain


Mass: 54915.766 Da / Num. of mol.: 2 / Fragment: UNP residues 857-1291
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botB / Production host: Escherichia coli (E. coli) / References: UniProt: P10844, bontoxilysin
#2: Protein Synaptotagmin-2 / Synaptotagmin II / SytII


Mass: 7556.237 Da / Num. of mol.: 2 / Fragment: UNP residues 8-61
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Syt2 / Production host: Escherichia coli (E. coli) / References: UniProt: P46097

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Sugars , 1 types, 2 molecules

#3: 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-(1-4)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1290.140 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGalpNAcb1-4[DNeup5Aca2-3]DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O]/1-2-3-4-2-3/a4-b1_b3-c2_b4-d1_d3-e1_e3-f2WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][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

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Non-polymers , 3 types, 267 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 0.2 M MgCl2, 0.1 M Hepes pH 7.0 -7.2 and 20-24% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: h,-k,-h-l / Fraction: 0.38
ReflectionResolution: 2.3→79.119 Å / Num. all: 46386 / Num. obs: 46386 / % possible obs: 100 % / Redundancy: 4.3 % / Rsym value: 0.129 / Net I/σ(I): 8.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.424.30.6951.12923867700.695100
2.42-2.574.30.5081.52758163690.508100
2.57-2.754.30.37822612860160.378100
2.75-2.974.30.2453.12429856030.245100
2.97-3.254.30.1644.52235951480.164100
3.25-3.644.30.1066.82032346740.106100
3.64-4.24.30.0749.51789541260.074100
4.2-5.144.30.05811.51506634640.058100
5.14-7.274.30.05811.91168327130.058100
7.27-44.8244.10.04710.3623615030.04799.7

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Processing

Software
NameVersionClassificationNB
SCALA3.3.20data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→44.824 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7284 / σ(F): 0.37 / Phase error: 33.84 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.1893 4653 5.08 %
Rwork0.1562 --
obs0.1588 91567 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.41 Å2 / Biso mean: 24.715 Å2 / Biso min: 8.22 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.824 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7414 0 179 264 7857
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017799
X-RAY DIFFRACTIONf_angle_d1.32610532
X-RAY DIFFRACTIONf_chiral_restr0.0781053
X-RAY DIFFRACTIONf_plane_restr0.0051313
X-RAY DIFFRACTIONf_dihedral_angle_d23.8343166
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.33970.29252390.24854384462394
2.3397-2.38220.28322240.24594252447694
2.3822-2.4280.28232240.2394419464395
2.428-2.47760.29322270.22974322454995
2.4776-2.53140.26772160.22194291450795
2.5314-2.59030.25262230.21744413463695
2.5903-2.65510.23162050.20824353455895
2.6551-2.72680.23031990.20514361456096
2.7268-2.8070.21882470.18974340458794
2.807-2.89760.20612220.18144358458095
2.8976-3.00120.19892430.16824360460395
3.0012-3.12130.21122080.16484426463495
3.1213-3.26330.22492200.1594270449095
3.2633-3.43520.20712200.14844408462895
3.4352-3.65030.16562330.13874339457295
3.6503-3.93190.15912580.1314351460994
3.9319-4.32710.13682690.11434269453894
4.3271-4.95220.14332310.10694360459195
4.9522-6.23510.14652760.12514331460794
6.2351-39.00530.17872540.13984313456794

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