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- PDB-3v0a: 2.7 angstrom crystal structure of BoNT/Ai in complex with NTNHA -

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Basic information

Entry
Database: PDB / ID: 3v0a
Title2.7 angstrom crystal structure of BoNT/Ai in complex with NTNHA
Components
  • BoNT/A
  • Llama antibody F12
  • NTNH
KeywordsTOXIN / Botulinum neurotoxin / Neurotoxin associated protein / Progenitor toxin complex / VHH bound interlocked complex / NTNHA
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 / host cell plasma membrane / proteolysis / zinc ion binding ...bontoxilysin / host cell presynaptic membrane / host cell cytoplasmic vesicle / host cell cytosol / protein transmembrane transporter activity / metalloendopeptidase activity / toxin activity / host cell plasma membrane / proteolysis / zinc ion binding / extracellular region / membrane
Similarity search - Function
Nontoxic nonhaemagglutinin C-terminal / Nontoxic nonhaemagglutinin C-terminal / Botulinum neurotoxin, helical domain / 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 ...Nontoxic nonhaemagglutinin C-terminal / Nontoxic nonhaemagglutinin C-terminal / Botulinum neurotoxin, helical domain / 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 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 / Immunoglobulins / Alpha-Beta Complex / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Botulinum neurotoxin type A / Non-toxic nonhemagglutinin type A / BoNT/A
Similarity search - Component
Biological speciesClostridium botulinum (bacteria)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.703 Å
AuthorsGu, S. / Rumpel, S. / Zhou, J. / Strotmeier, J. / Bigalke, H. / Perry, K. / Shoemaker, C.B. / Rummel, A. / Jin, R.
CitationJournal: Science / Year: 2012
Title: Botulinum neurotoxin is shielded by NTNHA in an interlocked complex.
Authors: Gu, S. / Rumpel, S. / Zhou, J. / Strotmeier, J. / Bigalke, H. / Perry, K. / Shoemaker, C.B. / Rummel, A. / Jin, R.
History
DepositionDec 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BoNT/A
B: NTNH
C: Llama antibody F12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)306,87229
Polymers304,0643
Non-polymers2,80826
Water5,296294
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8690 Å2
ΔGint-27 kcal/mol
Surface area101760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.080, 156.080, 324.603
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein BoNT/A / Bont/A1 / Botulinum neurotoxin type A / Neurotoxin A / Neurotoxin BoNT


Mass: 149449.828 Da / Num. of mol.: 1 / Mutation: E224Q,R363A,Y366F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: bont/a, boNT/A, bonta / Production host: Escherichia coli (E. coli) / References: UniProt: Q7B8V4, UniProt: P0DPI1*PLUS
#2: Protein NTNH / Type A progenitor toxin nontoxic-nonHA


Mass: 138450.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum (bacteria) / Gene: ant, ntnh / Production host: Escherichia coli (E. coli) / References: UniProt: Q45914

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Antibody , 1 types, 1 molecules C

#3: Antibody Llama antibody F12


Mass: 16163.727 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 320 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.25 Å3/Da / Density % sol: 62.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 12% PEG MME2000, 16% pentaerythritol propoxylate(5/4 PO/OH), 0.1 M ammonium sulfate and 50mM MES, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.7→49.8 Å / Num. all: 109722 / Num. obs: 109570 / % possible obs: 99.9 % / Observed criterion σ(F): 13.6 / Observed criterion σ(I): 13.6 / Redundancy: 6.2 % / Rmerge(I) obs: 0.127
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.768 / Mean I/σ(I) obs: 2.7 / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.703→49.357 Å / SU ML: 0.79 / Isotropic thermal model: RANDOM / σ(F): 1.35 / Phase error: 23.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2239 5474 5 %RANDOM
Rwork0.1759 ---
all0.1783 109722 --
obs0.1783 109570 99.59 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.598 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-7.0759 Å20 Å2-0 Å2
2--7.0759 Å2-0 Å2
3----14.1518 Å2
Refinement stepCycle: LAST / Resolution: 2.703→49.357 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20719 0 150 294 21163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621300
X-RAY DIFFRACTIONf_angle_d1.01728873
X-RAY DIFFRACTIONf_dihedral_angle_d15.347867
X-RAY DIFFRACTIONf_chiral_restr0.0763150
X-RAY DIFFRACTIONf_plane_restr0.0043704
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7034-2.73420.31441510.28993264X-RAY DIFFRACTION95
2.7342-2.76630.34881820.28393424X-RAY DIFFRACTION100
2.7663-2.80010.35161720.27893441X-RAY DIFFRACTION99
2.8001-2.83550.32411930.26283430X-RAY DIFFRACTION100
2.8355-2.87280.33321800.2653378X-RAY DIFFRACTION100
2.8728-2.91220.30631880.25863426X-RAY DIFFRACTION100
2.9122-2.95380.31761910.25833421X-RAY DIFFRACTION100
2.9538-2.99780.3271990.24493427X-RAY DIFFRACTION100
2.9978-3.04470.29281760.22713419X-RAY DIFFRACTION100
3.0447-3.09460.26811850.23213435X-RAY DIFFRACTION100
3.0946-3.14790.29521830.22763429X-RAY DIFFRACTION100
3.1479-3.20520.26991790.22153448X-RAY DIFFRACTION100
3.2052-3.26680.2511990.21033442X-RAY DIFFRACTION100
3.2668-3.33350.30161860.20643440X-RAY DIFFRACTION100
3.3335-3.40590.25361870.20223445X-RAY DIFFRACTION100
3.4059-3.48510.24621880.19243445X-RAY DIFFRACTION100
3.4851-3.57230.24681890.18293452X-RAY DIFFRACTION100
3.5723-3.66880.22491660.17693482X-RAY DIFFRACTION100
3.6688-3.77680.20931930.16553465X-RAY DIFFRACTION100
3.7768-3.89860.19771750.15333469X-RAY DIFFRACTION100
3.8986-4.03790.1931810.14033468X-RAY DIFFRACTION100
4.0379-4.19950.18341770.12913498X-RAY DIFFRACTION100
4.1995-4.39050.17271800.1253503X-RAY DIFFRACTION100
4.3905-4.62180.14561860.1173508X-RAY DIFFRACTION100
4.6218-4.91110.15641790.11933525X-RAY DIFFRACTION100
4.9111-5.28990.18821830.1353509X-RAY DIFFRACTION100
5.2899-5.82150.19271570.16443584X-RAY DIFFRACTION100
5.8215-6.66220.23241780.18183552X-RAY DIFFRACTION100
6.6622-8.38690.19391880.15493628X-RAY DIFFRACTION100
8.3869-49.3650.19182030.17013739X-RAY DIFFRACTION98
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)
10.95121.49610.08492.8822-0.48171.3067-0.16290.30730.1921-0.4760.0125-0.2574-0.18450.54640.11720.3766-0.20220.04330.6640.02710.3043110.550785.6897.2829
20.99710.17420.25631.2053-0.20291.0782-0.02140.00160.20390.1393-0.0387-0.1403-0.2330.35610.04280.2611-0.16980.03560.5247-0.06120.2437109.006581.893324.7236
30.89240.52990.78180.71910.02582.10760.1999-0.1099-0.06450.0262-0.0779-0.2559-0.13320.33180.00030.2159-0.08560.00820.5681-0.06630.2499112.260259.529429.6051
40.48120.18630.37681.25310.0490.73360.07820.01220.02630.0086-0.0167-0.10870.05210.2242-0.06220.2119-0.00360.05690.4891-0.02580.2121100.575555.36718.8927
50.25140.37621.04960.76371.223.32820.02340.02940.01170.0750.0805-0.040.04640.3455-0.11540.1795-0.03130.0230.377-0.0280.190699.85354.767537.4286
60.32740.25750.38060.40540.13891.0604-0.04-0.03460.0801-0.00790.06350.1699-0.0676-0.2004-0.02150.16780.0130.04560.39530.05880.271160.486265.74131.2473
73.48191.03473.11082.8727-1.74236.37190.268-0.09520.10320.168-0.23110.30120.2982-0.3378-0.07610.33810.09560.14730.4563-0.0420.302549.648969.126754.3207
82.34990.1414-1.08860.7061-0.02151.9320.10.2154-0.00210.07120.04980.1485-0.0263-0.3379-0.13520.2677-0.05920.0210.16150.07050.161643.828329.977957.9552
90.75450.17750.36571.21120.09351.0005-0.00170.053-0.0422-0.01930.05070.08610.0678-0.0933-0.02790.07220.0040.09070.25570.040.071964.73242.089242.9586
101.4704-0.4382-0.23462.9572-1.34192.06550.1081-0.09770.44430.24310.0714-0.0894-0.5326-0.0615-0.1090.289-0.03850.03850.2733-0.08080.264381.745979.281952.0714
113.46140.83070.7212.5378-1.28231.05630.6705-0.0811.26-0.0963-0.3288-0.2365-1.66220.6041-0.35041.2109-0.58540.24160.99660.37471.3841123.1994114.3455-9.2465
123.7567-2.30580.0912.8063-1.84982.31290.3771.36820.387-0.6255-0.7225-0.01450.4782-0.00060.27341.0203-0.18950.29711.5943-0.09551.2732127.167698.1285-28.3743
132.6754-0.1009-0.12610.67631.59375.86490.34-0.03490.5817-0.4545-0.3403-0.6351-0.85330.9549-0.1661.057-0.62540.22441.13450.14130.8508127.9415106.5982-7.6077
144.6137-1.1719-2.36662.5944-0.47068.78690.33450.8795-0.019-0.7526-0.5530.0102-0.0778-0.73230.24581.188-0.2297-0.07231.35960.05510.6559116.4608100.2188-15.4438
156.13273.24483.34593.59021.04582.3699-0.52260.715-0.132-0.55080.06690.01350.4385-0.4560.40160.577-0.40530.181.61870.08270.619123.458495.9437-5.9815
162.7239-0.52781.5261.97180.04080.9155-0.03220.6951-0.3987-1.00170.0051-0.6335-0.37041.27580.05371.0678-0.21530.31031.3577-0.14561.1647124.270689.6305-14.4307
173.60721.7616-0.63763.0153-1.51030.78030.0330.1980.1342-0.1395-0.3504-0.8523-0.62640.80810.28010.8971-0.55240.23351.58220.11180.9018133.8699104.3682-6.824
183.2380.5857-0.01522.6812-1.74471.1784-0.09740.8103-0.0436-0.4883-0.0466-0.817-0.15140.9030.17531.0783-0.53810.47751.574-0.040.8843130.6044100.5018-14.2257
190.336-0.1829-0.8170.45050.51622.2460.05660.5848-0.2266-1.1709-0.3329-0.6871-0.5170.77090.18911.2369-0.30070.13961.69520.0960.6997120.096597.9899-15.8908
202.15240.5695-1.01713.18431.27745.73690.83810.538-0.0236-0.9281-0.31970.1916-0.65190.4757-0.54931.3102-0.2632-0.16771.38890.21030.5978116.3865105.4665-13.7236
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:99)
2X-RAY DIFFRACTION2chain 'A' and (resseq 100:412)
3X-RAY DIFFRACTION3chain 'A' and (resseq 413:495)
4X-RAY DIFFRACTION4chain 'A' and (resseq 496:628)
5X-RAY DIFFRACTION5chain 'A' and (resseq 629:825)
6X-RAY DIFFRACTION6chain 'A' and (resseq 826:1194)
7X-RAY DIFFRACTION7chain 'A' and (resseq 1195:1295)
8X-RAY DIFFRACTION8chain 'B' and (resseq 1:536)
9X-RAY DIFFRACTION9chain 'B' and (resseq 537:910)
10X-RAY DIFFRACTION10chain 'B' and (resseq 911:1194)
11X-RAY DIFFRACTION11chain 'C' and (resseq 0:7)
12X-RAY DIFFRACTION12chain 'C' and (resseq 8:16)
13X-RAY DIFFRACTION13chain 'C' and (resseq 17:33)
14X-RAY DIFFRACTION14chain 'C' and (resseq 34:44)
15X-RAY DIFFRACTION15chain 'C' and (resseq 45:59)
16X-RAY DIFFRACTION16chain 'C' and (resseq 60:67)
17X-RAY DIFFRACTION17chain 'C' and (resseq 68:76)
18X-RAY DIFFRACTION18chain 'C' and (resseq 77:83)
19X-RAY DIFFRACTION19chain 'C' and (resseq 84:101)
20X-RAY DIFFRACTION20chain 'C' and (resseq 102:118)

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