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- PDB-2kz9: Structure of E1-69 of Yeast V-ATPase -

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Basic information

Entry
Database: PDB / ID: 2kz9
TitleStructure of E1-69 of Yeast V-ATPase
ComponentsV-type proton ATPase subunit E
KeywordsPROTON TRANSPORT / V-ATPase / Subunit E
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 / vacuolar proton-transporting V-type ATPase complex / proton-transporting V-type ATPase complex / vacuolar acidification ...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 / vacuolar proton-transporting V-type ATPase complex / proton-transporting V-type ATPase complex / vacuolar acidification / fungal-type vacuole membrane / proton-transporting ATPase activity, rotational mechanism / proton transmembrane transport / membrane raft / Golgi membrane
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1620 / V-type ATPase subunit E / V-type ATPase subunit E, C-terminal domain superfamily / ATP synthase (E/31 kDa) subunit / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special
Similarity search - Domain/homology
V-type proton ATPase subunit E
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model 1
AuthorsSankaranarayanan, N. / Gruber, G.
CitationJournal: To be Published
Title: NMR Solution Structure of Subunit E (E1-69) of the Saccharomyces cerevisiae V1VO ATPase
Authors: Sankaranarayanan, N. / Thaker, Y.R. / Gruber, G.
History
DepositionJun 14, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: V-type proton ATPase subunit E


Theoretical massNumber of molelcules
Total (without water)7,9081
Polymers7,9081
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 / 10all calculated structures submitted
RepresentativeModel #1lowest energy

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Components

#1: Protein V-type proton ATPase subunit E / V-ATPase subunit E / Vacuolar proton pump subunit E / V-ATPase 27 kDa subunit


Mass: 7907.938 Da / Num. of mol.: 1 / Fragment: UNP residues 1-69
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: O6241, VAT5, VMA4, YOR332W / Production host: Escherichia coli (E. coli) / References: UniProt: P22203
Sequence detailsRESIDUE S2A IS MUTAGENESIS ACCORDING TO REF 13 OF DATABASE UNIPROTKB/SWISS-PROT P22203 (VATE_YEAST).

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
1212D 1H-15N HSQC
1313D HNCO
1413D CBCA(CO)NH
1513D HN(CA)CB
1613D HCACO

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Sample preparation

DetailsContents: 2 mM [U-100% 13C; U-100% 15N] protein-1, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
SampleConc.: 2 mM / Component: protein-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 200 / pH: 7 / Pressure: AMBIENT / Temperature: 293 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
CYANA2.1P.GUNTERT ET AL.refinement
MOLMOLKoradi, Billeter and Wuthrichstructure solution
SparkyGoddardpeak picking
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10 / Representative conformer: 1

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