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- PDB-2czp: Structural analysis of membrane-bound mastoparan-X by solid-state NMR -

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Basic information

Entry
Database: PDB / ID: 2czp
TitleStructural analysis of membrane-bound mastoparan-X by solid-state NMR
ComponentsMastoparan X
KeywordsTOXIN / MASTOPARAN X / MP-X / membrane bound / Mast cell degranulation / Venom / Amidation
Function / homology
Function and homology information


other organism cell membrane / defense response to fungus / toxin activity / killing of cells of another organism / defense response to bacterium / innate immune response / extracellular region / membrane
Similarity search - Function
Mastoparan / Mastoparan protein
Similarity search - Domain/homology
Biological speciesVespa simillima xanthoptera (Japanese yellow hornet)
MethodSOLID-STATE NMR / simulated annealing
AuthorsTodokoro, Y. / Fujiwara, T. / Yumen, I. / Fukushima, K. / Kang, S.-W. / Park, J.-S. / Kohno, T. / Wakamatsu, K. / Akutsu, H.
CitationJournal: Biophys.J. / Year: 2006
Title: Structure of tightly membrane-bound mastoparan-x, a g-protein-activating Peptide, determined by solid-state NMR.
Authors: Todokoro, Y. / Yumen, I. / Fukushima, K. / Kang, S.-W. / Park, J.-S. / Kohno, T. / Wakamatsu, K. / Akutsu, H. / Fujiwara, T.
History
DepositionJul 14, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mastoparan X


Theoretical massNumber of molelcules
Total (without water)1,5581
Polymers1,5581
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)10 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Mastoparan X / MP-X


Mass: 1557.987 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vespa simillima xanthoptera (Japanese yellow hornet)
Species: Vespa simillima / Strain: xanthoptera / Plasmid: pUBK19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: P01515
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D N-CA-CO
1213D Ni-COi+1-CAi+1
1312D RFDR
1412D SPCz5
2512D (CACB)i+1-(COCA)i
2612D Ni-(COCA)i+1
2712D N-CA
1812D Ni-(COCACB)i+1
292RR
1103REDOR
NMR detailsText: The structure was determined using triple-resonance 1H/13C/15N and double-resonance 1H/13C probes with 4mm and 3.2mm spinner modules.

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Sample preparation

Details
Solution-IDContentsSolvent system
12mg or 5mg uniformly 13C, 15N labeled MP-X bound to membrane: Molar ratio MP-X:membrane=1:20membrane DPPC:DPPG=4:1 relative humidity 32%
22mg selectively 13C labeled MP-X bound to membrane: Molar ratio MP-X:membrane=1:20membrane DPPC:DPPG=4:1 relative humidity 32%
32mg selectively 13C, 15N labeled MP-X bound to membrane: Molar ratio MP-X:membrane=1:20membrane DPPC:DPPG=4:1 relative humidity 32%
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
17.4ambient 253 K
27.4ambient 283 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian CMXVarianCMX5001
Varian CMXVarianCMX6002

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Processing

NMR software
NameVersionDeveloperClassification
Felix2000Accelrys Inc.processing
CYANA1.0.6Guentertstructure solution
TALOS2003.027.13.05Delagliodata analysis
CYANA1.0.6Guentertrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 31 restraints, 5 distance restraints derived by RR and REDOR experiments and 26 dihedral angle restraints predicted by TALOS.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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