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- PDB-4aea: Dimeric alpha-cobratoxin X-ray structure: Localization of intermo... -

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Basic information

Entry
Database: PDB / ID: 4aea
TitleDimeric alpha-cobratoxin X-ray structure: Localization of intermolecular disulfides and possible mode of binding to nicotinic acetylcholine receptors
ComponentsLONG NEUROTOXIN 1
KeywordsTOXIN / THREE-FINGER TOXIN / NICOTINIC ACETYLCHOLINE RECEPTOR
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake toxin, conserved site / Snake toxins signature. / Snake three-finger toxin / : / Snake toxin cobra-type / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
GLYCINE / Alpha-cobratoxin
Similarity search - Component
Biological speciesNAJA KAOUTHIA (monocled cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsRucktooa, P. / Osipov, A.V. / Kasheverov, I.E. / Filkin, S.Y. / Starkov, V.G. / Andreeva, T.V. / Bertrand, D. / Utkin, Y.N. / Tsetlin, V.I. / Sixma, T.K.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Dimeric Alpha-Cobratoxin X-Ray Structure: Localization of Intermolecular Disulfides and Possible Mode of Binding to Nicotinic Acetylcholine Receptors.
Authors: Osipov, A.V. / Rucktooa, P. / Kasheverov, I.E. / Filkin, S.Y. / Starkov, V.G. / Andreeva, T.V. / Sixma, T.K. / Bertrand, D. / Utkin, Y.N. / Tsetlin, V.I.
History
DepositionJan 9, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 15, 2012Group: Database references
Revision 1.2Dec 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LONG NEUROTOXIN 1
B: LONG NEUROTOXIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8774
Polymers15,6842
Non-polymers1932
Water1,24369
1
A: LONG NEUROTOXIN 1
hetero molecules

A: LONG NEUROTOXIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0716
Polymers15,6842
Non-polymers3864
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area3430 Å2
ΔGint-38.1 kcal/mol
Surface area8910 Å2
MethodPISA
2
B: LONG NEUROTOXIN 1

B: LONG NEUROTOXIN 1


Theoretical massNumber of molelcules
Total (without water)15,6842
Polymers15,6842
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area2870 Å2
ΔGint-18.3 kcal/mol
Surface area8780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.000, 86.000, 37.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein LONG NEUROTOXIN 1 / ALPHA-COBRATOXIN / ALPHA-CBT / CBTX / NEUROTOXIN 3 / DIMERIC ALPHA-COBRATOXIN


Mass: 7842.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: ISOLATED FROM N. KAOUTHIA VENOM / Source: (natural) NAJA KAOUTHIA (monocled cobra) / References: UniProt: P01391
#2: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
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: 2.48 Å3/Da / Density % sol: 50.44 % / Description: NONE
Crystal growpH: 2
Details: 60% (V/V) 2-METHYL-2,4- PENTANEDIOL, 0.1 M GLYCINE-HCL PH 2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.94→37.24 Å / Num. obs: 11890 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 7.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.9
Reflection shellResolution: 1.94→2.05 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.88 / Mean I/σ(I) obs: 2.1 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.5.0099refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CTX

2ctx


Resolution: 1.94→37.24 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.91 / SU B: 8.758 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.171 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25142 594 5 %RANDOM
Rwork0.21874 ---
obs0.22037 11282 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.338 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å2-0.27 Å20 Å2
2---0.55 Å20 Å2
3---0.82 Å2
Refinement stepCycle: LAST / Resolution: 1.94→37.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1004 0 13 69 1086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221047
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0541.9541428
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0255132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.18223.68438
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.75115160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.027156
X-RAY DIFFRACTIONr_chiral_restr0.0660.2165
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022772
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_it0.4341.5674
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.79921106
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.7463373
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.2264.5322
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: 1.942→1.993 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 42 -
Rwork0.297 800 -
obs--100 %
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)
10.49030.25170.74030.53631.09082.3674-0.05850.07940.0893-0.12830.01540.004-0.23310.06050.0430.1621-0.06150.02720.14310.02660.1594-20.27649.08912.284
20.32060.2271-0.80081.7607-1.75813.0202-0.09620.0978-0.0686-0.25440.02890.06620.4447-0.08880.06740.2008-0.0697-0.03580.1761-0.04270.1907-21.57820.93110.774
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 67
2X-RAY DIFFRACTION2B1 - 67

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