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- PDB-2rpw: Structure of a peptide derived from H+-V-ATPase subunit a -

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Basic information

Entry
Database: PDB / ID: 2rpw
TitleStructure of a peptide derived from H+-V-ATPase subunit a
Components25 meric peptide from V-type proton ATPase subunit a, vacuolar isoform
KeywordsTRANSPORT PROTEIN / V-ATPase subunit a / Acetylation / Coiled coil / Glycoprotein / Hydrogen ion transport / Ion transport / Membrane / Phosphoprotein / Transmembrane / Transport / Vacuole
Function / homology
Function and homology information


cellular response to alkaline pH / polyphosphate metabolic process / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase complex / fungal-type vacuole / vacuolar acidification ...cellular response to alkaline pH / polyphosphate metabolic process / Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase complex / fungal-type vacuole / vacuolar acidification / cellular hyperosmotic response / fungal-type vacuole membrane / phosphatidylinositol-3,5-bisphosphate binding / Neutrophil degranulation / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / ATPase binding / protein-containing complex assembly
Similarity search - Function
ATPase, V0 complex, subunit 116kDa, eukaryotic / V-type ATPase, V0 complex, 116kDa subunit family / V-type ATPase 116kDa subunit family
Similarity search - Domain/homology
V-type proton ATPase subunit a, vacuolar isoform
Similarity search - Component
MethodSOLUTION NMR / molecular dynamics
AuthorsVermeer, L.S. / Reat, V. / Hemminga, M.A. / Milon, A.
CitationJournal: Biochim.Biophys.Acta / Year: 2009
Title: Structural properties of a peptide derived from H(+)-V-ATPase subunit a
Authors: Vermeer, L.S. / Reat, V. / Hemminga, M.A. / Milon, A.
History
DepositionNov 8, 2008Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: 25 meric peptide from V-type proton ATPase subunit a, vacuolar isoform


Theoretical massNumber of molelcules
Total (without water)2,8321
Polymers2,8321
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 #1closest to the average

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Components

#1: Protein/peptide 25 meric peptide from V-type proton ATPase subunit a, vacuolar isoform / KMTM7 / V-ATPase a 1 subunit / Vacuolar proton translocating ATPase subunit a 1 / Vacuolar proton ...KMTM7 / V-ATPase a 1 subunit / Vacuolar proton translocating ATPase subunit a 1 / Vacuolar proton pump a subunit / V-ATPase 95 kDa subunit / Vacuolar pH protein 1


Mass: 2832.328 Da / Num. of mol.: 1 / Fragment: TM7, UNP residues 728-748 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. This sequence occurs naturally in the yeast.
References: UniProt: P32563
Sequence detailsTHE LYSINE RESIDUES ON POSITION 1,2,24 AND 25 WERE ADDED TO THIS CHEMICALLY SYNTHESIZED PEPTIDE IN ...THE LYSINE RESIDUES ON POSITION 1,2,24 AND 25 WERE ADDED TO THIS CHEMICALLY SYNTHESIZED PEPTIDE IN ORDER TO IMPROVE SOLUBILITY AND RECONSTITUTION IN SDS MICELLES AND LIPID BILAYERS.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-1H TOCSY
1212D 1H-1H NOESY
NMR detailsText: only 1H-1H NOE restraints were used for the structure determination

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Sample preparation

DetailsContents: 1mM KMTM7, 250mM [U-100% 2H] SDS, 10mM sodium phosphate, 0.3mM DSS, 10% D2O, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMKMTM71
250 mMSDS[U-100% 2H]1
10 mMsodium phosphate1
0.3 mMDSS1
10 %D2O1
Sample conditionspH: 5.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2.2Linge, O'Donoghue and Nilgesstructure solution
AQUA3.2Rullmann, Doreleijers and Kapteindata analysis
SparkyGoddardpeak picking
SparkyGoddardchemical shift assignment
ProcheckNMRLaskowski and MacArthurdata analysis
TopSpinBruker Biospincollection
ARIA2.2Linge, O'Donoghue and Nilgesrefinement
RefinementMethod: molecular dynamics / Software ordinal: 1
Details: Used the ARIA software defaults with some changes (see the paper)
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: 20 / Representative conformer: 12

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