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- PDB-2kwy: Structure of G61-101 -

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Basic information

Entry
Database: PDB / ID: 2kwy
TitleStructure of G61-101
ComponentsV-type proton ATPase subunit G
KeywordsPROTON TRANSPORT / G61-101
Function / homology
Function and homology information


Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / proton-transporting V-type ATPase complex / fungal-type vacuole membrane / vacuolar proton-transporting V-type ATPase complex ...Insulin receptor recycling / Transferrin endocytosis and recycling / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / Golgi lumen acidification / endosomal lumen acidification / vacuolar proton-transporting V-type ATPase, V1 domain / proton-transporting V-type ATPase complex / fungal-type vacuole membrane / vacuolar proton-transporting V-type ATPase complex / vacuolar acidification / proton transmembrane transport / proton-transporting ATPase activity, rotational mechanism / Golgi membrane / ATP hydrolysis activity
Similarity search - Function
Single helix bin / Vacuolar (H+)-ATPase G subunit / Vacuolar (H+)-ATPase G subunit / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
V-type proton ATPase subunit G
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsRishikesan, S. / Gruber, G.
CitationJournal: To be Published
Title: Structure of G61-101
Authors: Rishikesan, S. / Gruber, G.
History
DepositionApr 22, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: V-type proton ATPase subunit G


Theoretical massNumber of molelcules
Total (without water)4,6041
Polymers4,6041
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 / 10structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein/peptide V-type proton ATPase subunit G / V-ATPase subunit G / Vacuolar proton pump subunit G / V-ATPase 13 kDa subunit


Mass: 4604.321 Da / Num. of mol.: 1 / Fragment: UNP residues 61-101
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Production host: Escherichia coli (E. coli) / References: UniProt: P48836

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR / Details: Structure of G61-101
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
1212D 1H-15N HSQC
1313D CBCA(CO)NH
1413D HNCO
1513D HN(CA)CB

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Sample preparation

DetailsContents: 7 % D2O-1, 30 % [U-100% 2H] TFE-2, 25 mM sodium phosphate-3, 200 mM sodium chloride-4, Phosphate Buffer pH 6.8
Solvent system: Phosphate Buffer pH 6.8
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
7 %D2O-11
30 %TFE-2[U-100% 2H]1
25 mMsodium phosphate-31
200 mMsodium chloride-41
Sample conditionsIonic strength: 200 / pH: 6.8 / Pressure: AMBIENT / Temperature: 308 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
Sparky2.1Goddardchemical shift assignment
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
TALOSCornilescu, Delaglio and Baxchemical shift calculation
TopSpinBruker Biospinprocessing
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 613 / NOE intraresidue total count: 192 / NOE long range total count: 0 / NOE medium range total count: 108 / NOE sequential total count: 201 / Protein phi angle constraints total count: 43 / Protein psi angle constraints total count: 34
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 10 / Conformers submitted total number: 10 / Representative conformer: 1

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