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- PDB-5lr0: Binding domain of Botulinum Neurotoxin DC in complex with SialylT -

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Basic information

Entry
Database: PDB / ID: 5lr0
TitleBinding domain of Botulinum Neurotoxin DC in complex with SialylT
ComponentsBotulinum neurotoxin D/C protein
KeywordsHYDROLASE / botulnimun neurotoxin / carbohydrate binding
Function / homology
Function and homology information


bontoxilysin / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / proteolysis / zinc ion binding / extracellular region
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 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
N-acetyl-alpha-neuraminic acid / Neurotoxin
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.59 Å
AuthorsBerntsson, R.P.-A. / Stenmark, P.
CitationJournal: Nat Commun / Year: 2017
Title: Structural basis for the unique ganglioside and cell membrane recognition mechanism of botulinum neurotoxin DC.
Authors: Zhang, S. / Berntsson, R.P. / Tepp, W.H. / Tao, L. / Johnson, E.A. / Stenmark, P. / Dong, M.
History
DepositionAug 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 30, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / 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 / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Botulinum neurotoxin D/C protein
B: Botulinum neurotoxin D/C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4985
Polymers100,1312
Non-polymers1,3673
Water2,576143
1
A: Botulinum neurotoxin D/C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7402
Polymers50,0651
Non-polymers6751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Botulinum neurotoxin D/C protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7583
Polymers50,0651
Non-polymers6932
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.699, 109.699, 210.461
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: 864 - 1284 / Label seq-ID: 11 - 431

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Botulinum neurotoxin D/C protein / D/C mosaic neurotoxin / Neurotoxin / Neurotoxin type DC


Mass: 50065.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: bont, boNT D, C, DC, NT / Production host: Escherichia coli (E. coli) / References: UniProt: A5JGM8, bontoxilysin
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose


Type: oligosaccharide / Mass: 674.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGalpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a3-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][b-D-GalpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGalpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GalpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE
#4: Sugar ChemComp-SIA / N-acetyl-alpha-neuraminic acid / N-acetylneuraminic acid / sialic acid / alpha-sialic acid / O-SIALIC ACID / Sialic acid


Type: D-saccharide, alpha linking / Mass: 309.270 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C11H19NO9
IdentifierTypeProgram
DNeup5AcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-neuraminic acidCOMMON NAMEGMML 1.0
a-D-Neup5AcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Neu5AcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 3.16 Å3/Da / Density % sol: 61.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M Ammonium Nitrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.98405 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98405 Å / Relative weight: 1
ReflectionResolution: 2.59→48.64 Å / Num. obs: 40710 / % possible obs: 99.2 % / Redundancy: 14.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.239 / Net I/σ(I): 13.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.59-2.6913.11.4370.789192.6
9.32-48.6413.50.0530.998199.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
PHASERphasing
REFMAC5.8.0073refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ISQ

4isq


Resolution: 2.59→48.64 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.919 / SU B: 9.842 / SU ML: 0.202 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.438 / ESU R Free: 0.258
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2309 2032 5 %RANDOM
Rwork0.2074 ---
obs0.2086 38598 99.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 137.56 Å2 / Biso mean: 40.977 Å2 / Biso min: 15.11 Å2
Baniso -1Baniso -2Baniso -3
1--2.03 Å20 Å20 Å2
2---2.03 Å20 Å2
3---4.06 Å2
Refinement stepCycle: final / Resolution: 2.59→48.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6709 0 92 143 6944
Biso mean--65.76 33.04 -
Num. residues----819
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.026956
X-RAY DIFFRACTIONr_bond_other_d0.0030.026470
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.9479413
X-RAY DIFFRACTIONr_angle_other_deg0.921314845
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3135813
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.69424.929351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.811151206
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9221528
X-RAY DIFFRACTIONr_chiral_restr0.1010.21029
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027860
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021716
X-RAY DIFFRACTIONr_mcbond_it1.6224.0183270
X-RAY DIFFRACTIONr_mcbond_other1.6224.0183269
X-RAY DIFFRACTIONr_mcangle_it2.8676.0114077
Refine LS restraints NCS

Ens-ID: 1 / Number: 22871 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.586→2.653 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 128 -
Rwork0.324 2484 -
all-2612 -
obs--88.93 %

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