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- PDB-3zus: Crystal structure of an engineered botulinum neurotoxin type A- S... -

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Basic information

Entry
Database: PDB / ID: 3zus
TitleCrystal structure of an engineered botulinum neurotoxin type A- SNARE23 derivative, LC-A-SNAP23-Hn-A
ComponentsBOTULINUM NEUROTOXIN TYPE A, SYNAPTOSOMAL-ASSOCIATED PROTEIN 23
KeywordsHYDROLASE/SIGNALING PROTEIN / HYDROLASE-SIGNALING PROTEIN COMPLEX / BOTULINUM NEUROTOXIN / SNARE / PROTEIN ENGINEERING
Function / homology
Function and homology information


vesicle targeting / trans-Golgi Network Vesicle Budding / host cell junction / synaptic vesicle fusion to presynaptic active zone membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / post-Golgi vesicle-mediated transport / negative regulation of neurotransmitter secretion / SNARE complex / SNAP receptor activity / bontoxilysin ...vesicle targeting / trans-Golgi Network Vesicle Budding / host cell junction / synaptic vesicle fusion to presynaptic active zone membrane / synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex / post-Golgi vesicle-mediated transport / negative regulation of neurotransmitter secretion / SNARE complex / SNAP receptor activity / bontoxilysin / specific granule / histamine secretion by mast cell / host cell presynaptic membrane / host cell cytoplasmic vesicle / RHOF GTPase cycle / syntaxin binding / syntaxin-1 binding / azurophil granule / host cell cytosol / synaptic vesicle priming / RHOB GTPase cycle / RHOJ GTPase cycle / RHOQ GTPase cycle / exocytosis / tertiary granule membrane / CDC42 GTPase cycle / protein transmembrane transporter activity / RHOA GTPase cycle / RAC3 GTPase cycle / specific granule membrane / membrane => GO:0016020 / RAC1 GTPase cycle / Translocation of SLC2A4 (GLUT4) to the plasma membrane / adherens junction / metalloendopeptidase activity / phagocytic vesicle membrane / protein transport / presynapse / ER-Phagosome pathway / toxin activity / membrane fusion / neuron projection / focal adhesion / Neutrophil degranulation / host cell plasma membrane / mitochondrion / proteolysis / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / membrane / plasma membrane / cytoplasm
Similarity search - Function
Clostridium botulinum neurotoxin B, "coiled-coil" domain / Clostridium botulinum neurotoxin b, "coiled-coil" domain / SNAP-25 domain / SNAP-25 family / Zincin-like / Metalloproteases ("zincins"), catalytic domain like / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Clostridium neurotoxin, translocation ...Clostridium botulinum neurotoxin B, "coiled-coil" domain / Clostridium botulinum neurotoxin b, "coiled-coil" domain / SNAP-25 domain / SNAP-25 family / Zincin-like / Metalloproteases ("zincins"), catalytic domain like / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / 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 / 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
Synaptosomal-associated protein 23 / Botulinum neurotoxin type A / Botulinum neurotoxin type A
Similarity search - Component
Biological speciesCLOSTRIDIUM BOTULINUM (bacteria)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsMasuyer, G. / Stancombe, P. / Chaddock, J.A. / Acharya, K.R.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structures of Engineered Clostridium Botulinum Neurotoxin Derivatives
Authors: Masuyer, G. / Stancombe, P. / Chaddock, J.A. / Acharya, K.R.
History
DepositionJul 19, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Other
Revision 1.2Mar 15, 2017Group: Source and taxonomy
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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 / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_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 TYPE A, SYNAPTOSOMAL-ASSOCIATED PROTEIN 23
B: BOTULINUM NEUROTOXIN TYPE A, SYNAPTOSOMAL-ASSOCIATED PROTEIN 23
C: BOTULINUM NEUROTOXIN TYPE A, SYNAPTOSOMAL-ASSOCIATED PROTEIN 23
D: BOTULINUM NEUROTOXIN TYPE A, SYNAPTOSOMAL-ASSOCIATED PROTEIN 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)425,4618
Polymers425,1994
Non-polymers2624
Water1,26170
1
A: BOTULINUM NEUROTOXIN TYPE A, SYNAPTOSOMAL-ASSOCIATED PROTEIN 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3652
Polymers106,3001
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BOTULINUM NEUROTOXIN TYPE A, SYNAPTOSOMAL-ASSOCIATED PROTEIN 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3652
Polymers106,3001
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: BOTULINUM NEUROTOXIN TYPE A, SYNAPTOSOMAL-ASSOCIATED PROTEIN 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3652
Polymers106,3001
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: BOTULINUM NEUROTOXIN TYPE A, SYNAPTOSOMAL-ASSOCIATED PROTEIN 23
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3652
Polymers106,3001
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.179, 204.969, 130.883
Angle α, β, γ (deg.)90.00, 91.91, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
BOTULINUM NEUROTOXIN TYPE A, SYNAPTOSOMAL-ASSOCIATED PROTEIN 23 / BONT/A / BONTOXILYSIN-A / BOTOX / BOTULINUM NEUROTOXIN A LIGHT CHAIN / BOTULINUM NEUROTOXIN A HEAVY ...BONT/A / BONTOXILYSIN-A / BOTOX / BOTULINUM NEUROTOXIN A LIGHT CHAIN / BOTULINUM NEUROTOXIN A HEAVY CHAIN / SNAP-23 / VESICLE-MEMBRANE FUSION PROTEIN SNAP-23 PROTEIN


Mass: 106299.859 Da / Num. of mol.: 4
Fragment: LC-A-SNAP23-HN-A, LC-A, RESIDUES 3-431,SNAP23,RESIDUES 150-211,8-RESIDUE LINKER, HN-A, RESIDUES 454-865
Source method: isolated from a genetically manipulated source
Details: CHIMERA, DERIVATIVE OF BOTULINUM NEUROTOXIN TYPE A WITH ADDED SNAP23 DOMAIN BETWEEN LC AND HN, CONFLICT AT ASN 7 B CHAIN
Source: (gene. exp.) CLOSTRIDIUM BOTULINUM (bacteria), (gene. exp.) HOMO SAPIENS (human)
Description: ENGINEERED HUMAN SNAP23 PEPTIDE INSERTED WITHIN LC AND HN OF BOTULINUM NEUROTOXIN
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P10845, UniProt: O00161, UniProt: P0DPI1*PLUS, bontoxilysin
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsHUMAN SNAP23 ENGINEERED BETWEEN LC AND HN OF BOTULINUM NEUROTOXIN A. PRO-ARG VARIANT IN O00161 NOT ...HUMAN SNAP23 ENGINEERED BETWEEN LC AND HN OF BOTULINUM NEUROTOXIN A. PRO-ARG VARIANT IN O00161 NOT DESCRIBED IN UNIPROT

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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: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 6 / Details: 0.1 M IMIDAZOLE MALATE PH 6.0, 15% PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.979
DetectorType: ADSC CCD / Detector: CCD / Date: Jan 15, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.95→50.4 Å / Num. obs: 97807 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 10.4
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W2D

2w2d


Resolution: 2.95→130.81 Å / Cor.coef. Fo:Fc: 0.885 / Cor.coef. Fo:Fc free: 0.834 / SU B: 49.172 / SU ML: 0.413 / Cross valid method: THROUGHOUT / ESU R Free: 0.481 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. UNOBSERVED SNAP23 PEPTIDE - RESIDUES 435-498.
RfactorNum. reflection% reflectionSelection details
Rfree0.2926 4884 5 %RANDOM
Rwork0.24765 ---
obs0.2499 92854 99.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.509 Å2
Baniso -1Baniso -2Baniso -3
1-2 Å20 Å2-1.74 Å2
2---2.15 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.95→130.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27578 0 4 70 27652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02228166
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8211.95738154
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.38153401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.19125.5181410
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.446154997
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5461592
X-RAY DIFFRACTIONr_chiral_restr0.0550.24257
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02121348
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.3321.516989
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.598227614
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.312311177
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.5724.510540
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: 2.952→3.029 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 352 -
Rwork0.323 6630 -
obs--96.2 %
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)
11.12320.45410.23870.83030.32580.95610.0537-0.0592-0.2045-0.0464-0.0242-0.16940.01730.0132-0.02950.0279-0.02830.01630.0447-0.01160.066516.1091-25.638965.4293
20.64350.03730.17150.45060.34580.82850.0808-0.00130.0178-0.069-0.06390.06040.0628-0.0799-0.01690.0833-0.00770.00320.07610.01820.0405-11.9768-26.047861.2363
30.5548-0.0276-0.14010.8993-0.5431.70950.02720.11310.01070.2343-0.06060.1017-0.04430.00830.03340.15480.00610.06860.03770.00790.036436.0151-7.888916.4406
40.61510.19470.3170.8546-0.18630.8078-0.04570.0409-0.1703-0.016-0.0164-0.17110.04760.06590.06210.0650.0263-0.00630.12880.00950.123844.1583-6.9109-10.7923
51.4829-0.61810.19882.3398-0.06161.25360.10940.2776-0.0443-0.0969-0.13710.7517-0.2003-0.08340.02780.13680.1073-0.02250.1225-0.0110.388824.159-48.4741-1.493
61.0702-0.21310.24681.2257-0.22351.52910.06170.21120.19660.0237-0.066-0.1566-0.2430.23110.00440.1983-0.05770.01960.1441-0.02030.102751.8508-47.77542.5256
70.669-0.3958-0.2731.3810.4661.44210.1330.0822-0.0303-0.5737-0.1051-0.0366-0.018-0.1642-0.02780.3988-0.0103-0.00060.0533-0.020.12044.248514.843746.4893
80.62480.1897-0.16461.2852-0.040.3688-0.09430.0061-0.0969-0.04030.01070.0009-0.0642-0.0480.08360.04870.0134-0.03660.09340.02660.1666-2.954814.74574.3886
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 434
2X-RAY DIFFRACTION2A499 - 915
3X-RAY DIFFRACTION3B1 - 434
4X-RAY DIFFRACTION4B499 - 915
5X-RAY DIFFRACTION5C1 - 435
6X-RAY DIFFRACTION6C499 - 915
7X-RAY DIFFRACTION7D0 - 434
8X-RAY DIFFRACTION8D499 - 916

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