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- PDB-1hs7: VAM3P N-TERMINAL DOMAIN SOLUTION STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1hs7
TitleVAM3P N-TERMINAL DOMAIN SOLUTION STRUCTURE
ComponentsSYNTAXIN VAM3
KeywordsENDOCYTOSIS/EXOCYTOSIS / up-and-down three-helix bundle insertion preceding proline in an alpha-helix / ENDOCYTOSIS-EXOCYTOSIS COMPLEX
Function / homology
Function and homology information


vacuolar calcium ion homeostasis / amphisome-lysosome fusion / vacuole fusion, non-autophagic / vesicle fusion with vacuole / COPII-mediated vesicle transport / vesicle fusion / vesicle docking / SNARE complex / SNAP receptor activity / piecemeal microautophagy of the nucleus ...vacuolar calcium ion homeostasis / amphisome-lysosome fusion / vacuole fusion, non-autophagic / vesicle fusion with vacuole / COPII-mediated vesicle transport / vesicle fusion / vesicle docking / SNARE complex / SNAP receptor activity / piecemeal microautophagy of the nucleus / fungal-type vacuole membrane / vacuolar membrane / autophagosome membrane / autophagosome maturation / endomembrane system / SNARE binding / intracellular protein transport
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #70 / SNARE domain / Syntaxin/epimorphin, conserved site / Syntaxin / Syntaxin / epimorphin family signature. / SNARE / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #70 / SNARE domain / Syntaxin/epimorphin, conserved site / Syntaxin / Syntaxin / epimorphin family signature. / SNARE / Helical region found in SNAREs / t-SNARE coiled-coil homology domain profile. / Target SNARE coiled-coil homology domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsDulubova, I. / Yamaguchi, T. / Wang, Y. / Sudhof, T.C. / Rizo, J.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: Vam3p structure reveals conserved and divergent properties of syntaxins.
Authors: Dulubova, I. / Yamaguchi, T. / Wang, Y. / Sudhof, T.C. / Rizo, J.
History
DepositionDec 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2001Provider: 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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SYNTAXIN VAM3


Theoretical massNumber of molelcules
Total (without water)11,3551
Polymers11,3551
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 / 400structures with the lowest NOE energy
RepresentativeModel #1lowest noe and total energy

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Components

#1: Protein SYNTAXIN VAM3


Mass: 11354.979 Da / Num. of mol.: 1 / Fragment: RESIDUES 23-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Plasmid: PGEX-KT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q12241

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1212D NOESY
131HNHA
2423D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance spectroscopy

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Sample preparation

Details
Solution-IDContentsSolvent system
10.9 mM 15N-labeled Vam3p N-terminal domain; 20 mM phosphate pH 6.0, 30 C95% H2O, 5% D2O AND 100% D2O
20.8 mM 15N,13C-labeled Vam3p N-terminal domain; 20 mM phosphate pH 6.0, 30 C95% H2O/5% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
120 mM phosphate 6ambient 303 K
220 mM phosphate 6ambient 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA5002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1BVariancollection
NMRPipe1.7Delaglioprocessing
NMRView4.1Johnsondata analysis
CNS0.9Brungerstructure solution
CNS0.9Brungerrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: 1771 total experimental restraints, 1565 NOE distance restraints, 130 hydrogen bond restraints, 76 dihedral angle restraints
NMR representativeSelection criteria: lowest noe and total energy
NMR ensembleConformer selection criteria: structures with the lowest NOE energy
Conformers calculated total number: 400 / Conformers submitted total number: 20

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