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- PDB-3rsj: Structure of HCRF in complex with Ganglioside GD1a -

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Basic information

Entry
Database: PDB / ID: 3rsj
TitleStructure of HCRF in complex with Ganglioside GD1a
ComponentsBoNT/F
KeywordsTOXIN / clostridium botulinum type F / ganglioside binding site / GD1a
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 / lipid binding / host cell plasma membrane / proteolysis ...bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / lipid binding / 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 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 ...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 / 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 F / Neurotoxin type F
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFu, Z. / Benson, M.A. / Barbieri, J.T. / Kim, J.-J.P. / Baldwin, M.R.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Unique ganglioside recognition strategies for clostridial neurotoxins.
Authors: Benson, M.A. / Fu, Z. / Kim, J.J. / Baldwin, M.R.
History
DepositionMay 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Database references
Revision 1.2Oct 12, 2011Group: Database references
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _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 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BoNT/F
B: BoNT/F
C: BoNT/F
D: BoNT/F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,9648
Polymers191,6504
Non-polymers3,3144
Water7,638424
1
A: BoNT/F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5872
Polymers47,9121
Non-polymers6751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BoNT/F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0402
Polymers47,9121
Non-polymers1,1281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: BoNT/F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7492
Polymers47,9121
Non-polymers8371
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: BoNT/F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5872
Polymers47,9121
Non-polymers6751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)65.468, 84.266, 117.600
Angle α, β, γ (deg.)72.55, 87.01, 67.13
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
BoNT/F / Botulinum neurotoxin type F / Neurotoxin type F


Mass: 47912.449 Da / Num. of mol.: 4 / Fragment: Receptor Binding Domain (UNP Residues 866-1276)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: bont/f, Botulinum Neurotoxin / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q57236, UniProt: A7GBG3*PLUS
#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.: 2
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 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


Type: oligosaccharide / Mass: 1127.999 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGalpNAcb1-4[DNeup5Aca2-3]DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a2112h-1b_1-5_2*NCC/3=O]/1-2-3-1-2/a3-b2_a4-c1_c3-d1_d3-e2WURCSPDB2Glycan 1.1.0
[][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
#4: 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)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 836.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-3DGalpNAcb1-4DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2112h-1b_1-5][a2112h-1b_1-5_2*NCC/3=O][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-1-3/a4-b1_b3-c1_c3-d2WURCSPDB2Glycan 1.1.0
[][b-D-Galp]{[(4+1)][b-D-GalpNAc]{[(3+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}LINUCSPDB-CARE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 424 / 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: 2.97 Å3/Da / Density % sol: 58.55 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7
Details: 0.1 M Hepes pH 7.0, 24% PEG3350, 200 mM Mg(NO3)2, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 26, 2009 / Details: graphite
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→29.86 Å / Num. all: 346226 / Num. obs: 138215 / % possible obs: 93.2 % / Observed criterion σ(I): -3 / Redundancy: 2.5 % / Biso Wilson estimate: 30.6 Å2 / Rsym value: 0.059 / Net I/σ(I): 16.2
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.1 / % possible all: 65.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.3refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FUQ

3fuq


Resolution: 2→29.86 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 161374.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.263 12918 10 %RANDOM
Rwork0.232 ---
obs0.232 129599 87 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.453 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 41.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.87 Å2-3.48 Å2-13.75 Å2
2---12.9 Å24.83 Å2
3---11.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13272 0 226 424 13922
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.41.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it1.852
X-RAY DIFFRACTIONc_scangle_it2.692.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.345 873 9.8 %
Rwork0.34 7993 -
obs--59.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5GD1a.parGD1a.top

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