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- PDB-2mj4: Neurotoxin II from snake venom Naja Oxiana in solution -

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Basic information

Entry
Database: PDB / ID: 2mj4
TitleNeurotoxin II from snake venom Naja Oxiana in solution
ComponentsShort neurotoxin 1
KeywordsTOXIN / 13C relaxation / side chain dynamics / molecular dynamics / molecular mechanics force fields / optimization
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
Biological speciesNaja oxiana (Central Asian cobra)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model1
AuthorsLesovoy, D.M. / Nolde, S.B. / Bocharov, E.V. / Lyukmanova, E.N. / Arseniev, A.S.
CitationJournal: To be Published
Title: An NMR-based approach for validation of protein side-chains dynamics in silico
Authors: Lesovoy, D.M. / Nolde, S.B. / Bocharov, E.V. / Lyukmanova, E.N. / Arseniev, A.S.
History
DepositionDec 26, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 28, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 30, 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_nmr_spectrometer / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Short neurotoxin 1


Theoretical massNumber of molelcules
Total (without water)6,8961
Polymers6,8961
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200target function
RepresentativeModel #1fewest violations

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Components

#1: Protein Short neurotoxin 1 / Neurotoxin II / NTX II / Neurotoxin alpha


Mass: 6895.784 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naja oxiana (Central Asian cobra) / Production host: Escherichia coli (E. coli) / References: UniProt: P01427
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Side chains dynamics from 13CH, 13CH2, 13CH3, 15NH, and 15NH2 NMR relaxation: R1, R2, NOE, dipole-dipole cross-correlation contribution to R1 and R2. Simulated NMR parameters from molecular dynamics trajectory.
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1122D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1412D 13C-15N HSQC carbon
1512D 13C->13C carbon
1612D 1H->(13C)->13C carbon
1713D HNCO
1813D HNCA
1913D HN(CO)CA
11013D HN(CA)CO
11113D (H)CCH-TOCSY
11223D HNHA
11323D HNHB
11442D DQF-COSY
11523D 1H-15N NOESY
11613D 1H-13C NOESY aliphatic
11713D 1H-13C NOESY aromatic
11822D 1H-15N CLEANEX
11913D HNCO
12022D 1H-15N HSQC H/D
12122D 1H-15N 15N R1
12222D 1H-15N NH-NH/15N R1
12322D 1H-15N 15N R2
12422D 1H-15N 15N-1H NOE
12512D 1H-13C 13C R1
12612D 1H-13C 13C-1H NOE
12712D 1H-13C CH-CH/13C R1
12812D 1H-13C CH-CH/13C R2
12932D 1H-15N 15N R1
13032D 1H-15N 15N R2
13132D 1H-15N 15N-1H NOE

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-99% 13C; U-99% 15N] Neurotoxin II-1, 0.3 mM sodium azide-2, 10 mM citric acid-3, 20 mM Na2HPO4-4, 95% H2O/5% D2O95% H2O/5% D2O
21 mM [U-99% 15N] Neurotoxin II-5, 0.3 mM sodium azide-6, 10 mM citric acid-7, 20 mM Na2HPO4-8, 100% D2O100% D2O
31 mM [U-99% 15N] Neurotoxin II-9, 0.3 mM sodium azide-10, 10 mM citric acid-11, 20 mM Na2HPO4-12, 50% H2O/50% D2O50% H2O/50% D2O
42 mM Neurotoxin II-13, 0.3 mM sodium azide-14, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMNeurotoxin II-1[U-99% 13C; U-99% 15N]1
0.3 mMsodium azide-21
10 mMcitric acid-31
20 mMNa2HPO4-41
1 mMNeurotoxin II-5[U-99% 15N]2
0.3 mMsodium azide-62
10 mMcitric acid-72
20 mMNa2HPO4-82
1 mMNeurotoxin II-9[U-99% 15N]3
0.3 mMsodium azide-103
10 mMcitric acid-113
20 mMNa2HPO4-123
2 mMNeurotoxin II-134
0.3 mMsodium azide-144
Sample conditionsIonic strength: 50 / pH: 5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3Guntert, Mumenthaler and Wuthrichstructure solution
CARA1.8.4Rochus Kellerchemical shift assignment
MathematicaWolfram Researchdata analysis
NMRPipe(ACME)Delaglio, Zhengrong and Baxprocessing
NMRPipe(ACME)Delaglio, Zhengrong and Baxdata analysis
CYANArefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The 1H-1H NOE amplitudes should be treated only according to the flexibility of the corresponding backbone or side chain groups: derived from the heteronuclear NOE, R1, R2, 1chch(dipolar ...Details: The 1H-1H NOE amplitudes should be treated only according to the flexibility of the corresponding backbone or side chain groups: derived from the heteronuclear NOE, R1, R2, 1chch(dipolar cross-correlation contribution to R1), 2chch(dipolar cross-correlation contribution to R2), and 3J scalar coupling constant values.
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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