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- PDB-1vcs: Solution Structure of RSGI RUH-009, an N-Terminal Domain of Vti1a... -

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Entry
Database: PDB / ID: 1vcs
TitleSolution Structure of RSGI RUH-009, an N-Terminal Domain of Vti1a [Mus musculus]
ComponentsVesicle transport through interaction with t-SNAREs homolog 1A
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / SNARE / Habc domain / Vti1 / up and down three helix bundle / left-handed twist / vesicle transport / membrane fusion / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


synaptic vesicle to endosome fusion / Retrograde transport at the Trans-Golgi-Network / Intra-Golgi traffic / vesicle fusion with Golgi apparatus / Golgi ribbon formation / Golgi to vacuole transport / voluntary musculoskeletal movement / SNARE complex / SNAP receptor activity / intra-Golgi vesicle-mediated transport ...synaptic vesicle to endosome fusion / Retrograde transport at the Trans-Golgi-Network / Intra-Golgi traffic / vesicle fusion with Golgi apparatus / Golgi ribbon formation / Golgi to vacuole transport / voluntary musculoskeletal movement / SNARE complex / SNAP receptor activity / intra-Golgi vesicle-mediated transport / protein targeting to vacuole / neuron projection terminus / retrograde transport, endosome to Golgi / clathrin-coated vesicle / autophagosome / endoplasmic reticulum to Golgi vesicle-mediated transport / SNARE binding / ER to Golgi transport vesicle membrane / autophagy / synaptic vesicle / late endosome membrane / membrane => GO:0016020 / endosome / Golgi membrane / intracellular membrane-bounded organelle / neuronal cell body / endoplasmic reticulum membrane / perinuclear region of cytoplasm / Golgi apparatus / cytosol
Similarity search - Function
t-snare proteins / GOSR2/Membrin/Bos1 / Vesicle transport v-SNARE, N-terminal / Vesicle transport v-SNARE, N-terminal domain superfamily / Vesicle transport v-SNARE protein N-terminus / SNARE / Helical region found in SNAREs / Target SNARE coiled-coil homology domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Vesicle transport through interaction with t-SNAREs homolog 1A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, torsion angle dyanamics
AuthorsAbe, T. / Hirota, H. / Tomizawa, T. / Koshiba, S. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution Structure of RSGI RUH-009, an N-Terminal Domain of Vti1a [Mus musculus]
Authors: Abe, T. / Hirota, H. / Tomizawa, T. / Koshiba, S. / Kigawa, T. / Yokoyama, S.
History
DepositionMar 10, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Remark 650HELIX determination method: author determined

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Assembly

Deposited unit
A: Vesicle transport through interaction with t-SNAREs homolog 1A


Theoretical massNumber of molelcules
Total (without water)11,4671
Polymers11,4671
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 / 100structures with the least restraint violations, structures with the lowest energy, target function
RepresentativeModel #1lowest energy and target function

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Components

#1: Protein Vesicle transport through interaction with t-SNAREs homolog 1A / Vesicle transport v-SNARE protein Vti1-like 2 / Vti1-rp2


Mass: 11466.877 Da / Num. of mol.: 1 / Fragment: N-terminal domain (Residues 6-94)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: Cell-free protein synthesis system
Gene: Mus musculus adult male lung cDNA, RIKEN full-length enriched library, clone:1200014A22 product: Vti1a (amino acid 6-94)
Plasmid: P030825-55 / References: UniProt: O89116

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1.0mM RSGI RUH-009 U-15N, 13C; 20mM d-Tris-HCl buffer; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 100mM / pH: 7.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.893Kobayashi, N.data analysis
CYANA1.0.7Guntert, P.refinement
RefinementMethod: simulated annealing, torsion angle dyanamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy and target function
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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