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- PDB-2nz9: Crystal structure of botulinum neurotoxin type A complexed with m... -

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Basic information

Entry
Database: PDB / ID: 2nz9
TitleCrystal structure of botulinum neurotoxin type A complexed with monoclonal antibody AR2
Components
  • (AR2 monoclonal antibody) x 2
  • Botulinum neurotoxin type A
KeywordsTOXIN/IMMUNE SYSTEM / BOTULINUM / NEUROTOXIN / FAB / PROTEIN ANTIBODY COMPLEX / TOXIN-IMMUNE SYSTEM COMPLEX
Function / homology
Function and homology information


host cell junction / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / membrane => GO:0016020 ...host cell junction / negative regulation of neurotransmitter secretion / bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / membrane => GO:0016020 / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / membrane
Similarity search - Function
Clostridium botulinum neurotoxin B, "coiled-coil" domain / Clostridium botulinum neurotoxin b, "coiled-coil" domain / Zincin-like / Metalloproteases ("zincins"), catalytic domain like / 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 botulinum neurotoxin B, "coiled-coil" domain / Clostridium botulinum neurotoxin b, "coiled-coil" domain / Zincin-like / Metalloproteases ("zincins"), catalytic domain like / 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 / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Immunoglobulins / Alpha-Beta Complex / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Botulinum neurotoxin type A / Botulinum neurotoxin type A
Similarity search - Component
Biological speciesHomo sapiens (human)
Clostridium botulinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.79 Å
AuthorsStevens, R.C. / Arndt, J.W.
CitationJournal: Nat.Biotechnol. / Year: 2007
Title: Molecular evolution of antibody cross-reactivity for two subtypes of type A botulinum neurotoxin.
Authors: Garcia-Rodriguez, C. / Levy, R. / Arndt, J.W. / Forsyth, C.M. / Razai, A. / Lou, J. / Geren, I. / Stevens, R.C. / Marks, J.D.
History
DepositionNov 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 2, 2013Group: Source and taxonomy
Revision 1.4Feb 17, 2016Group: Derived calculations
Revision 1.5Aug 30, 2023Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE There is no aminoacid sequence database reference available for the CR1 monoclonal ...SEQUENCE There is no aminoacid sequence database reference available for the CR1 monoclonal antibody light and heavy chains

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Botulinum neurotoxin type A
B: Botulinum neurotoxin type A
C: AR2 monoclonal antibody
D: AR2 monoclonal antibody
E: AR2 monoclonal antibody
F: AR2 monoclonal antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)395,13910
Polymers394,9286
Non-polymers2114
Water0
1
A: Botulinum neurotoxin type A
C: AR2 monoclonal antibody
D: AR2 monoclonal antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,5695
Polymers197,4643
Non-polymers1052
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-67 kcal/mol
Surface area70520 Å2
MethodPISA
2
B: Botulinum neurotoxin type A
E: AR2 monoclonal antibody
F: AR2 monoclonal antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,5695
Polymers197,4643
Non-polymers1052
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-68 kcal/mol
Surface area70520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.965, 197.596, 146.105
Angle α, β, γ (deg.)90.00, 91.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Botulinum neurotoxin type A


Mass: 149479.812 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Clostridium botulinum (bacteria) / Strain: Type A1 (Hall strain)
References: UniProt: P10845, UniProt: P0DPI1*PLUS, bontoxilysin
#2: Antibody AR2 monoclonal antibody


Mass: 23896.471 Da / Num. of mol.: 2 / Fragment: light chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO DG44 CELLS / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody AR2 monoclonal antibody


Mass: 24087.695 Da / Num. of mol.: 2 / Fragment: heavy chain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): CHO DG44 CELLS / Production host: Cricetulus griseus (Chinese hamster)
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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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: 3.58 Å3/Da / Density % sol: 65.63 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 8% PEG 20000, 8% PEG 550 MME, 200 mM calcium acetate, 100 mM sodium acetate, pH 5.60, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 1, 2006 / Details: MIRRORS
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→40 Å / Num. obs: 214725 / % possible obs: 86.5 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8.9
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.45 / % possible all: 59

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BTA

3bta


Resolution: 3.79→40 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.829 / SU B: 94.958 / SU ML: 0.63 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.802 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2686 5.1 %RANDOM
Rwork0.224 ---
obs0.227 49884 95.5 %-
all-49884 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å2-0.1 Å2
2--0.88 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 3.79→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26981 0 4 0 26985
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02227604
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5691.9537422
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.76753388
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.71924.9621322
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.868154690
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.42515114
X-RAY DIFFRACTIONr_chiral_restr0.1040.24108
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221046
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2450.212786
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3230.218672
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2924
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.2960.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.2102
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.491.517294
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.866227308
X-RAY DIFFRACTIONr_scbond_it0.975311893
X-RAY DIFFRACTIONr_scangle_it1.6074.510114
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.79→3.89 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 180 -
Rwork0.252 3416 -
obs--90.37 %
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)
14.7069-0.48111.41512.72650.92292.62650.04490.104-0.1849-0.07310.1942-0.0596-0.00830.0839-0.239-0.46880.03220.0734-0.3915-0.0072-0.386550.8612-17.676710.3281
223.018118.707823.196415.72319.66127.2390.56660.2927-0.1033-0.23650.2921-0.94450.07630.0035-0.8587-0.47720.25750.0701-0.18180.0551-0.46827.4704-4.76018.2607
34.1078-1.2857-1.48342.71051.31533.72560.1314-1.28660.45120.0470.0648-0.4127-0.3594-0.0029-0.1962-0.2639-0.0943-0.06270.6956-0.1017-0.191640.6452-4.946830.293
48.07732.24297.25973.02093.450912.00240.4689-1.2309-0.29880.2503-0.31110.07760.6789-0.3881-0.1578-0.53990.07380.10390.00540.0098-0.506319.3816-10.714720.3912
57.46850.7639-1.97293.86940.96024.28140.08120.7428-0.4332-0.38840.1325-0.2549-0.21730.2008-0.2136-0.59180.0701-0.0039-0.3548-0.1329-0.4871-10.0677-4.896824.8086
68.7706-1.50883.21254.3111-3.06388.73960.1072-0.2093-0.51440.7423-0.0954-0.357-0.0560.1291-0.0118-0.26390.0524-0.0613-0.5691-0.0158-0.3205-13.7535-12.717557.8989
73.9586-0.3619-0.86742.963-1.44753.27680.0623-0.1087-0.2362-0.16730.16280.24260.14170.0668-0.2251-0.5411-0.0328-0.055-0.64360.0468-0.2945-1.286845.986982.6825
818.372216.4855-22.738816.1267-21.077229.04870.50420.3088-0.1124-0.4040.27950.8159-0.0167-0.0215-0.7838-0.45420.0817-0.2244-0.17380.1795-0.031822.244432.993580.5497
93.7085-1.24432.23973.6882-2.69554.42920.0647-1.3187-0.73920.2920.02150.20540.2542-0.0575-0.0862-0.3076-0.06430.21560.60140.2275-0.05449.043833.3591102.5012
105.74851.425-5.27363.1426-3.155611.25210.3943-1.19320.27070.1249-0.2655-0.0899-0.52510.43-0.1287-0.57520.041-0.0435-0.21560.1705-0.200930.368138.986692.6388
117.22870.28352.06654.7107-1.61644.50010.14470.42190.5088-0.10440.14790.1120.0405-0.3045-0.2926-0.62360.00240.0812-0.57960.2302-0.12159.738733.250497.2806
126.9235-0.6527-2.94854.52993.435412.84130.152-0.98570.76970.99980.05410.4297-1.0665-0.2986-0.20610.28090.11910.018-0.30260.00530.115263.74140.7874130.581
138.3992-6.5107-3.13696.17281.73954.63270.018-0.6132-0.16530.98910.71740.5809-2.0689-0.9945-0.73540.99960.64780.2536-0.00410.3499-0.4481-36.990723.446844.4781
146.7792-0.81340.76725.9082-6.425824.97740.23280.2941-0.0191-0.75150.2051.03060.7619-0.9432-0.43780.07030.02320.1032-0.13220.24320.1143-61.203449.381935.9956
156.4343-6.932.01489.266-2.79450.8473-0.5311-0.71470.32221.06390.9323-0.05270.64130.509-0.40120.39350.3364-0.1487-0.0201-0.1106-0.462186.13534.7275117.3314
165.5312-3.997-5.47787.82218.795727.38870.05990.1688-0.2919-0.51270.089-0.5528-0.58961.0219-0.1489-0.17910.1177-0.2072-0.1642-0.0876-0.3129108.4955-22.5335110.0845
173.6958-3.52011.13599.0602-3.878514.15020.18010.3049-0.0595-0.23590.17910.1902-2.5132-0.074-0.35920.41490.26460.1877-0.29860.0215-0.6104-28.211624.407823.8547
185.8516-1.1251-0.744114.03720.9939.22880.20820.10860.40360.0678-0.4997-0.31120.13741.45990.29150.18120.37110.04790.10470.5628-0.2331-45.942952.115229.3406
198.5232-4.4767-4.94038.59222.29239.8480.15510.3637-0.0797-0.17210.2710.20921.29880.2491-0.426-0.17830.134-0.2432-0.440.1638-0.498677.63033.66596.577
207.43980.9773-0.895211.4729-3.548113.17730.31190.1627-0.7215-0.4222-0.3053-0.06611.2951-0.3976-0.0066-0.01370.2634-0.1624-0.1488-0.4277-0.425593.3426-24.3898102.9857
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 4311 - 430
2X-RAY DIFFRACTION2AA453 - 488452 - 487
3X-RAY DIFFRACTION3AA493 - 621492 - 620
4X-RAY DIFFRACTION4AA627 - 872626 - 871
5X-RAY DIFFRACTION5AA873 - 1091872 - 1090
6X-RAY DIFFRACTION6AA1092 - 12941091 - 1293
7X-RAY DIFFRACTION7BB2 - 4311 - 430
8X-RAY DIFFRACTION8BB453 - 488452 - 487
9X-RAY DIFFRACTION9BB493 - 621492 - 620
10X-RAY DIFFRACTION10BB627 - 872626 - 871
11X-RAY DIFFRACTION11BB873 - 1091872 - 1090
12X-RAY DIFFRACTION12BB1092 - 12941091 - 1293
13X-RAY DIFFRACTION13CC1 - 1201 - 120
14X-RAY DIFFRACTION14CC121 - 216121 - 216
15X-RAY DIFFRACTION15EE1 - 1201 - 120
16X-RAY DIFFRACTION16EE121 - 216121 - 216
17X-RAY DIFFRACTION17DD2 - 1092 - 109
18X-RAY DIFFRACTION18DD110 - 218110 - 218
19X-RAY DIFFRACTION19FF2 - 1092 - 109
20X-RAY DIFFRACTION20FF110 - 218110 - 218

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