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- PDB-5bqm: Crystal structure of SXN101959, a Clostridium botulinum neurotoxi... -

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Basic information

Entry
Database: PDB / ID: 5bqm
TitleCrystal structure of SXN101959, a Clostridium botulinum neurotoxin type D derivative and targeted secretion inhibitor
Components
  • Botulinum neurotoxin type D
  • Somatoliberin,Botulinum neurotoxin type D
KeywordsHYDROLASE / botulinum neurotoxin / targeted secretion inhibitors / endopeptidase / type D / protein engineering
Function / homology
Function and homology information


growth hormone-releasing hormone receptor binding / positive regulation of circadian sleep/wake cycle, REM sleep / growth hormone-releasing hormone activity / Toxicity of botulinum toxin type D (botD) / growth hormone secretion / adenohypophysis development / ganglioside GT1b binding / positive regulation of growth hormone secretion / bontoxilysin / neuropeptide hormone activity ...growth hormone-releasing hormone receptor binding / positive regulation of circadian sleep/wake cycle, REM sleep / growth hormone-releasing hormone activity / Toxicity of botulinum toxin type D (botD) / growth hormone secretion / adenohypophysis development / ganglioside GT1b binding / positive regulation of growth hormone secretion / bontoxilysin / neuropeptide hormone activity / positive regulation of multicellular organism growth / positive regulation of insulin-like growth factor receptor signaling pathway / response to food / peptide hormone receptor binding / protein transmembrane transporter activity / multicellular organism growth / adenylate cyclase-activating G protein-coupled receptor signaling pathway / terminal bouton / metalloendopeptidase activity / Glucagon-type ligand receptors / cell-cell signaling / toxin activity / perikaryon / G alpha (s) signalling events / positive regulation of cell population proliferation / proteolysis / extracellular space / zinc ion binding / extracellular region
Similarity search - Function
: / Clostridium botulinum neurotoxin B, "coiled-coil" domain / Clostridium botulinum neurotoxin b, "coiled-coil" domain / Zincin-like / Metalloproteases ("zincins"), catalytic domain like / Glucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones / Clostridium neurotoxin, translocation ...: / Clostridium botulinum neurotoxin B, "coiled-coil" domain / Clostridium botulinum neurotoxin b, "coiled-coil" domain / Zincin-like / Metalloproteases ("zincins"), catalytic domain like / Glucagon/GIP/secretin/VIP / Peptide hormone / Glucagon / GIP / secretin / VIP family signature. / Glucagon like hormones / 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 / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Alpha-Beta Complex / Up-down Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Somatoliberin / Botulinum neurotoxin type D
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMasuyer, G. / Davies, J.R. / Moore, K. / Chaddock, J.A. / Acharya, K.R.
CitationJournal: Sci Rep / Year: 2015
Title: Structural analysis of Clostridium botulinum neurotoxin type D as a platform for the development of targeted secretion inhibitors.
Authors: Masuyer, G. / Davies, J.R. / Moore, K. / Chaddock, J.A. / Ravi Acharya, K.
History
DepositionMay 29, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Botulinum neurotoxin type D
B: Somatoliberin,Botulinum neurotoxin type D
C: Botulinum neurotoxin type D
D: Somatoliberin,Botulinum neurotoxin type D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,9226
Polymers210,7914
Non-polymers1312
Water1267
1
A: Botulinum neurotoxin type D
B: Somatoliberin,Botulinum neurotoxin type D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,4613
Polymers105,3962
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9750 Å2
ΔGint-89 kcal/mol
Surface area36100 Å2
MethodPISA
2
C: Botulinum neurotoxin type D
D: Somatoliberin,Botulinum neurotoxin type D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,4613
Polymers105,3962
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9610 Å2
ΔGint-93 kcal/mol
Surface area36060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.201, 143.916, 172.762
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Botulinum neurotoxin type D / BoNT/D / Bontoxilysin-D


Mass: 51677.230 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Correspond to the catalytic domain of LHn/D. The whole molecule is expressed as a single polypeptide cleaved into an active di-chain using an engineered protease recognition site
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: botD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P19321, bontoxilysin
#2: Protein Somatoliberin,Botulinum neurotoxin type D / Growth hormone-releasing factor / GRF / Growth hormone-releasing hormone / GHRH / Somatocrinin / ...Growth hormone-releasing factor / GRF / Growth hormone-releasing hormone / GHRH / Somatocrinin / Somatorelin / BoNT/D / Bontoxilysin-D


Mass: 53718.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Correspond to the catalytic domain of LHn/D. The whole molecule is expressed as a single polypeptide cleaved into an active di-chain using an engineered protease recognition site
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Clostridium botulinum (bacteria)
Gene: GHRH, GHRF, botD / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01286, UniProt: P19321, 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 / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 289.1 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M sodium actetate pH 5.5, 0.8 M sodium formate, 10 % w /v polyethylene glycol 8000, 10 % w /v polyethylene glycol 1000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 3.1→110 Å / Num. all: 35774 / Num. obs: 35774 / % possible obs: 89 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.127 / Net I/σ(I): 6
Reflection shellResolution: 3.1→3.25 Å / Redundancy: 2.6 % / Rmerge(I) obs: 1.02 / Mean I/σ(I) obs: 1 / % possible all: 81.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
Aimlessdata scaling
PHASERphasing
DIALSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FPQ

2fpq


Resolution: 3.1→110 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.891 / SU B: 85.872 / SU ML: 0.612 / Cross valid method: THROUGHOUT / ESU R Free: 0.607 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29532 1739 4.9 %RANDOM
Rwork0.24969 ---
obs0.25194 34012 87.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 100.488 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å2-0 Å20 Å2
2--5.38 Å20 Å2
3----4.82 Å2
Refinement stepCycle: 1 / Resolution: 3.1→110 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13249 0 2 7 13258
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0213547
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212753
X-RAY DIFFRACTIONr_angle_refined_deg0.9681.95718407
X-RAY DIFFRACTIONr_angle_other_deg0.829329399
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.50751656
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.10525.531640
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.972152335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.9341542
X-RAY DIFFRACTIONr_chiral_restr0.0550.22090
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02115365
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023077
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0269.3236636
X-RAY DIFFRACTIONr_mcbond_other1.0269.3236635
X-RAY DIFFRACTIONr_mcangle_it1.93513.9848285
X-RAY DIFFRACTIONr_mcangle_other1.93513.9838286
X-RAY DIFFRACTIONr_scbond_it0.4689.2156911
X-RAY DIFFRACTIONr_scbond_other0.4689.2156912
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.02313.82610122
X-RAY DIFFRACTIONr_long_range_B_refined3.35772.06314851
X-RAY DIFFRACTIONr_long_range_B_other3.35772.06314852
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.42 115 -
Rwork0.406 2191 -
obs--76.99 %
Refinement TLS params.Method: refined / Origin x: -16.7454 Å / Origin y: -5.9356 Å / Origin z: 46.3708 Å
111213212223313233
T0.1089 Å2-0.0041 Å2-0.0015 Å2-0.0316 Å2-0.0275 Å2--0.0367 Å2
L0.0573 °2-0.043 °2-0.1425 °2-0.0927 °20.1889 °2--0.5808 °2
S0.0139 Å °0.0039 Å °0.0073 Å °0.0212 Å °0.0145 Å °-0.0427 Å °0.056 Å °-0.0432 Å °-0.0283 Å °

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