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- PDB-1y7x: Solution structure of a two-repeat fragment of major vault protein -

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Basic information

Entry
Database: PDB / ID: 1y7x
TitleSolution structure of a two-repeat fragment of major vault protein
ComponentsMajor vault protein
KeywordsSTRUCTURAL PROTEIN / PROTEIN BINDING / structural repeats / beta-sheet modules
Function / homology
Function and homology information


negative regulation of protein tyrosine kinase activity / neutrophil degranulation / negative regulation of protein autophosphorylation / ERBB signaling pathway / negative regulation of epidermal growth factor receptor signaling pathway / mRNA transport / nuclear pore / protein transport / protein phosphatase binding / secretory granule lumen ...negative regulation of protein tyrosine kinase activity / neutrophil degranulation / negative regulation of protein autophosphorylation / ERBB signaling pathway / negative regulation of epidermal growth factor receptor signaling pathway / mRNA transport / nuclear pore / protein transport / protein phosphatase binding / secretory granule lumen / ficolin-1-rich granule lumen / cytoskeleton / Neutrophil degranulation / protein kinase binding / perinuclear region of cytoplasm / extracellular exosome / extracellular region / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Major Vault Protein repeat / Major vault protein, N-terminal / Major vault protein, shoulder domain / Major vault protein / Major vault protein repeat domain 3 / Major vault protein repeat domain 2 / Major vault protein repeat domain 4 / Major vault protein repeat domain / Major vault protein repeat domain superfamily / Major vault protein repeat domain 2 superfamily ...Major Vault Protein repeat / Major vault protein, N-terminal / Major vault protein, shoulder domain / Major vault protein / Major vault protein repeat domain 3 / Major vault protein repeat domain 2 / Major vault protein repeat domain 4 / Major vault protein repeat domain / Major vault protein repeat domain superfamily / Major vault protein repeat domain 2 superfamily / Major Vault Protein repeat domain / Shoulder domain / Major Vault Protein repeat domain / Major Vault Protein Repeat domain / Major Vault Protein repeat domain / MVP (vault) repeat profile. / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsKozlov, G. / Vavelyuk, O. / Minailiuc, O. / Banville, D. / Gehring, K. / Ekiel, I.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Solution structure of a two-repeat fragment of major vault protein.
Authors: Kozlov, G. / Vavelyuk, O. / Minailiuc, O. / Banville, D. / Gehring, K. / Ekiel, I.
History
DepositionDec 10, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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_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 / _struct_ref_seq_dif.details
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: Major vault protein


Theoretical massNumber of molelcules
Total (without water)12,7731
Polymers12,7731
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 lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Major vault protein / / MVP / Lung resistance-related protein


Mass: 12772.561 Da / Num. of mol.: 1 / Fragment: domains 3-4 of MVP repeats (residues 113-221)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MVP / Plasmid: pGEX-4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q14764

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
121HNHA
1322D NOESY
NMR detailsText: This structure was determined using standard triple-resonance and homonuclear techniques.

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Sample preparation

Details
Solution-IDContentsSolvent system
11mM MVP U-15N, 20mM bis-Tris, 150mM NaCl, 2mM CaCl2, 15mM DTT, 90% H2O, 10% D2O90% H2O/10% D2O
21mM MVP, 20mM bis-Tris, 150mM NaCl, 2mM CaCl2, 15mM DTT, 90% H2O, 10% D2O90% H2O/10% D2O
Sample conditionsIonic strength: 150mM NaCl / pH: 6.8 / Pressure: ambient / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 500 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.1Bruker Biospincollection
XwinNMR2.1Bruker Biospinprocessing
XEASY1.3.13Wuthrichdata analysis
CYANA1.0.6Guentertstructure solution
Xplor-NIH2.9.2Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The structures are based on a total of 1083 restraints, 930 are NOE-derived distance constraints, 124 dihedral angle restraints, 29 distance restraints from hydrogen bonds.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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