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- PDB-3v0b: 3.9 angstrom crystal structure of BoNT/Ai in complex with NTNHA -

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Basic information

Entry
Database: PDB / ID: 3v0b
Title3.9 angstrom crystal structure of BoNT/Ai in complex with NTNHA
Components
  • BoNT/A
  • NTNH
KeywordsTOXIN / VHH free inlocked complex / Botulinum neurotoxin
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 / Alpha-Beta Complex / Up-down Bundle / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.9 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 1.1Sep 25, 2013Group: Derived calculations

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BoNT/A
B: NTNH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)288,0064
Polymers287,9002
Non-polymers1052
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7600 Å2
ΔGint-68 kcal/mol
Surface area96810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)282.232, 282.232, 374.818
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

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


Mass: 149449.828 Da / Num. of mol.: 1 / Fragment: Inactive full length BoNT/A1 / 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 / Fragment: Full length NTNHA1
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
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 40.078 Da / Num. of mol.: 1 / 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: 7.48 Å3/Da / Density % sol: 83.57 %
Crystal growTemperature: 293 K / pH: 5.8
Details: 1.5M sodium malonate, 100mM MgSO4, 0.5% w/v n-dodecyl-N,N-dimethylamine-N-oxide, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97945
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 26, 2010
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 3.9→50 Å / Num. obs: 73988 / % possible obs: 92.2 % / Observed criterion σ(I): 11.9
Reflection shellResolution: 3.9→4 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.673 / Mean I/σ(I) obs: 2.6 / % possible all: 93.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.9→48.47 Å / SU ML: 1.19 / σ(F): 1.35 / Phase error: 28.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.28 3736 5.05 %
Rwork0.252 --
obs0.253 73988 92.1 %
all-74110 -
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 114.43 Å2 / ksol: 0.31 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.0128 Å20 Å20 Å2
2---4.0128 Å20 Å2
3---8.0257 Å2
Refinement stepCycle: LAST / Resolution: 3.9→48.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19828 0 2 0 19830
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00620254
X-RAY DIFFRACTIONf_angle_d0.97827433
X-RAY DIFFRACTIONf_dihedral_angle_d14.8447509
X-RAY DIFFRACTIONf_chiral_restr0.0773020
X-RAY DIFFRACTIONf_plane_restr0.0043540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9001-3.94940.36731720.33962570X-RAY DIFFRACTION93
3.9494-4.00130.36431320.32182577X-RAY DIFFRACTION93
4.0013-4.05610.37931500.31112590X-RAY DIFFRACTION93
4.0561-4.11410.32411200.30942610X-RAY DIFFRACTION93
4.1141-4.17540.3181360.30522610X-RAY DIFFRACTION94
4.1754-4.24060.32921310.29662621X-RAY DIFFRACTION94
4.2406-4.31010.33671440.29622603X-RAY DIFFRACTION93
4.3101-4.38440.32671400.28542622X-RAY DIFFRACTION94
4.3844-4.46410.29281420.27572618X-RAY DIFFRACTION93
4.4641-4.54990.34891410.26592603X-RAY DIFFRACTION94
4.5499-4.64270.28511430.25442628X-RAY DIFFRACTION94
4.6427-4.74350.26431350.24932615X-RAY DIFFRACTION94
4.7435-4.85380.2641330.24422636X-RAY DIFFRACTION94
4.8538-4.9750.30731370.24712613X-RAY DIFFRACTION93
4.975-5.10940.27111310.25022621X-RAY DIFFRACTION93
5.1094-5.25960.30411390.25212624X-RAY DIFFRACTION93
5.2596-5.42910.26261280.24562616X-RAY DIFFRACTION93
5.4291-5.62290.26571450.24742608X-RAY DIFFRACTION93
5.6229-5.84770.27891380.24352616X-RAY DIFFRACTION93
5.8477-6.11330.30431390.25862607X-RAY DIFFRACTION92
6.1133-6.43490.29051470.25662591X-RAY DIFFRACTION91
6.4349-6.83710.26271180.26212615X-RAY DIFFRACTION92
6.8371-7.36330.29411380.2422578X-RAY DIFFRACTION91
7.3633-8.10120.24781480.23792561X-RAY DIFFRACTION89
8.1012-9.26640.21921390.2132562X-RAY DIFFRACTION89
9.2664-11.64780.23841430.19932548X-RAY DIFFRACTION87
11.6478-48.47720.27311270.25852589X-RAY DIFFRACTION83
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)
10.02650.1672-0.07881.0148-0.80740.62770.08270.19280.2663-0.2670.34490.6980.0961-0.41790.00111.03590.1843-0.39311.25970.1381.839685.3493-27.277273.8038
20.60370.36750.50580.5301-0.16670.96-0.15230.2070.1367-0.63890.33710.14780.2592-0.20190.04241.16730.0149-0.38660.7776-0.21131.0916111.161-30.249168.3713
30.61730.0159-0.13210.9837-0.61250.37180.1237-0.0549-0.04520.1294-0.0520.3455-0.0258-0.005100.80870.01550.01490.6435-0.16690.6815116.5254-49.2586104.6788
40.3771-0.2307-0.13770.16060.04530.11940.0793-0.11530.0364-0.0967-0.145-0.08330.2114-0.3024-01.2329-0.12930.02740.9205-0.09740.8246135.7991-37.3949116.8882
50.7735-0.4842-0.25810.4242-0.0371.0385-0.0276-0.3820.1557-0.04390.0743-0.35470.08940.373-0.00090.64430.1408-0.10540.6908-0.24680.3975162.0808-59.018295.9867
60.15790.0181-0.5250.18960.0050.9689-0.0590.1195-0.0236-0.08260.050.0979-0.0058-0.18080.00320.77390.1869-0.09710.5956-0.10650.456135.7576-57.199685.6247
70.4392-0.0043-0.28950.59-0.01190.37450.0214-0.10920.1999-0.0591-0.13430.3074-0.04670.1476-0.05570.44030.34330.28660.1665-0.29460.627119.4866-17.512198.5997
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:628)
2X-RAY DIFFRACTION2chain 'A' and (resseq 629:825)
3X-RAY DIFFRACTION3chain 'A' and (resseq 826:1194)
4X-RAY DIFFRACTION4chain 'A' and (resseq 1195:1295)
5X-RAY DIFFRACTION5chain 'B' and (resseq 1:536)
6X-RAY DIFFRACTION6chain 'B' and (resseq 537:853)
7X-RAY DIFFRACTION7chain 'B' and (resseq 854:1194)

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