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- PDB-2lx4: NMR solution structure of peptide a2N(1-17) from Mus musculus V-ATPase -

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Basic information

Entry
Database: PDB / ID: 2lx4
TitleNMR solution structure of peptide a2N(1-17) from Mus musculus V-ATPase
ComponentsV-type proton ATPase 116 kDa subunit a isoform 2
KeywordsPROTON TRANSPORT / V-ATPase / subunit a / alpha helix / pH sensor / Sec7 binding motif
Function / homology
Function and homology information


Ion channel transport / Transferrin endocytosis and recycling / Insulin receptor recycling / cellular response to increased oxygen levels / intracellular organelle / ROS and RNS production in phagocytes / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / proton-transporting ATPase activity, rotational mechanism ...Ion channel transport / Transferrin endocytosis and recycling / Insulin receptor recycling / cellular response to increased oxygen levels / intracellular organelle / ROS and RNS production in phagocytes / vacuolar proton-transporting V-type ATPase, V0 domain / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / proton-transporting ATPase activity, rotational mechanism / acrosomal vesicle / ATPase binding / intracellular iron ion homeostasis / membrane => GO:0016020 / endosome membrane / perinuclear region of cytoplasm / plasma membrane
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 116 kDa subunit a2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsDip, P. / Gruber, G. / Marshansky, V.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: The N Termini of a-Subunit Isoforms Are Involved in Signaling between Vacuolar H+-ATPase (V-ATPase) and Cytohesin-2.
Authors: Hosokawa, H. / Dip, P.V. / Merkulova, M. / Bakulina, A. / Zhuang, Z. / Khatri, A. / Jian, X. / Keating, S.M. / Bueler, S.A. / Rubinstein, J.L. / Randazzo, P.A. / Ausiello, D.A. / Gruber, G. / Marshansky, V.
History
DepositionAug 14, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Mar 13, 2013Group: Database references
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
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
A: V-type proton ATPase 116 kDa subunit a isoform 2


Theoretical massNumber of molelcules
Total (without water)1,9341
Polymers1,9341
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)10 / 20structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide V-type proton ATPase 116 kDa subunit a isoform 2


Mass: 1934.328 Da / Num. of mol.: 1 / Fragment: N-terminus (residues 1-17) / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P15920

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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

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Sample preparation

DetailsContents: 2 mM a2N(1-17), 50 % [U-99% 2H] TFE, 25 mM sodium phosphate, 300 mM sodium chloride, trifluoroethanol/water
Solvent system: trifluoroethanol/water
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
2 mMa2N(1-17)-11
50 %TFE-2[U-99% 2H]1
25 mMsodium phosphate-31
300 mMsodium chloride-41
Sample conditionspH: 6.5 / 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
TopSpin2.1Bruker Biospincollection
TopSpin2.1Bruker Biospinprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardchemical shift calculation
SparkyGoddardpeak picking
SparkyGoddarddata analysis
TALOSCornilescu, Delaglio and Baxgeometry optimization
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
CYANAGuntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsProtein phi angle constraints total count: 10 / Protein psi angle constraints total count: 10
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 20 / Conformers submitted total number: 10

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