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- PDB-1kmd: SOLUTION STRUCTURE OF THE VAM7P PX DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1kmd
TitleSOLUTION STRUCTURE OF THE VAM7P PX DOMAIN
ComponentsVacuolar morphogenesis protein VAM7
KeywordsENDOCYTOSIS/EXOCYTOSIS / PX domain / Vam7p / phosphoinositide binding / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


vacuole fusion, non-autophagic / cytoplasm to vacuole targeting by the Cvt pathway / autophagosome-lysosome fusion / vesicle fusion / vesicle docking / SNARE complex / SNAP receptor activity / piecemeal microautophagy of the nucleus / phosphatidylinositol-3-phosphate binding / fungal-type vacuole membrane ...vacuole fusion, non-autophagic / cytoplasm to vacuole targeting by the Cvt pathway / autophagosome-lysosome fusion / vesicle fusion / vesicle docking / SNARE complex / SNAP receptor activity / piecemeal microautophagy of the nucleus / phosphatidylinositol-3-phosphate binding / fungal-type vacuole membrane / phagophore assembly site / endomembrane system / SNARE binding / macroautophagy / intracellular protein transport / membrane => GO:0016020
Similarity search - Function
Phox-like domain / PX Domain / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily ...Phox-like domain / PX Domain / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / PhoX homologous domain, present in p47phox and p40phox. / PX domain profile. / PX domain / Phox homology / PX domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Vacuolar morphogenesis protein 7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsLu, J. / Garcia, J. / Dulubova, I. / Sudhof, T.C. / Rizo, J.
CitationJournal: Biochemistry / Year: 2002
Title: Solution structure of the Vam7p PX domain.
Authors: Lu, J. / Garcia, J. / Dulubova, I. / Sudhof, T.C. / Rizo, J.
History
DepositionDec 14, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vacuolar morphogenesis protein VAM7


Theoretical massNumber of molelcules
Total (without water)14,4181
Polymers14,4181
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 500STRUCTURES WITH THE MINIMAL NOE ENERGY
RepresentativeModel #1

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Components

#1: Protein Vacuolar morphogenesis protein VAM7 / Vam7p


Mass: 14418.483 Da / Num. of mol.: 1 / Fragment: PX domain, Residues 8-124
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: pGEX-KG / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P32912

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM Vam7p PX domain U-15N,20mM Mes buffer90% H2O/10% D2O
20.5mM Vam7p PX domain U-15N, 13C, 20mM Mes buffer90% H2O/10% D2O
30.5mM Vam7p PX domain U-15N, 20mM Mes Buffer100% D2O
40.5mM Vam7p PX domain 10%-13C, 20mM Mes buffer90% H2O/10% D2O
Sample conditionsIonic strength: 20mM Mes / pH: 6.2 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA5001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe1.8DeLaglio, F. et al.processing
VNMR6.1Variancollection
NMRView4.1.2Johnson, B. and Blevins R.data analysis
CNS1Brunger, A.T. et al.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: the structures are based on a total of 1443 restraints, 1193 are NOE-derived distance constraints, 152 dihedral angle restraints, 98 distance restraints from hydrogen bonds.
NMR ensembleConformer selection criteria: STRUCTURES WITH THE MINIMAL NOE ENERGY
Conformers calculated total number: 500 / Conformers submitted total number: 20

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