- PDB-2rpw: Structure of a peptide derived from H+-V-ATPase subunit a -
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Basic information
Entry
Database: PDB / ID: 2rpw
Title
Structure of a peptide derived from H+-V-ATPase subunit a
Components
25 meric peptide from V-type proton ATPase subunit a, vacuolar isoform
Keywords
TRANSPORT 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
protein localization to vacuolar membrane / cellular response to alkaline pH / Insulin receptor recycling / Transferrin endocytosis and recycling / polyphosphate metabolic process / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / vacuolar proton-transporting V-type ATPase, V0 domain / fungal-type vacuole / cellular hyperosmotic response ...protein localization to vacuolar membrane / cellular response to alkaline pH / Insulin receptor recycling / Transferrin endocytosis and recycling / polyphosphate metabolic process / ROS and RNS production in phagocytes / Amino acids regulate mTORC1 / vacuolar proton-transporting V-type ATPase, V0 domain / fungal-type vacuole / cellular hyperosmotic response / vacuolar proton-transporting V-type ATPase complex / phosphatidylinositol-3,5-bisphosphate binding / vacuolar acidification / fungal-type vacuole membrane / proton transmembrane transport / Neutrophil degranulation / proton-transporting ATPase activity, rotational mechanism / ATPase binding / protein-containing complex assembly / membrane raft Similarity search - Function
25mericpeptidefromV-typeprotonATPasesubunita, vacuolarisoform / 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 details
THE 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
Experiment
Method: SOLUTION NMR
NMR experiment
Conditions-ID
Experiment-ID
Solution-ID
Type
1
1
1
2D 1H-1H TOCSY
1
2
1
2D 1H-1H NOESY
NMR details
Text: only 1H-1H NOE restraints were used for the structure determination
Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz
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Processing
NMR software
Name
Version
Developer
Classification
ARIA
2.2
Linge, O'DonoghueandNilges
structuresolution
AQUA
3.2
Rullmann, DoreleijersandKaptein
dataanalysis
Sparky
Goddard
peakpicking
Sparky
Goddard
chemicalshiftassignment
ProcheckNMR
LaskowskiandMacArthur
dataanalysis
TopSpin
BrukerBiospin
collection
ARIA
2.2
Linge, O'DonoghueandNilges
refinement
Refinement
Method: molecular dynamics / Software ordinal: 1 Details: Used the ARIA software defaults with some changes (see the paper)
NMR representative
Selection criteria: closest to the average
NMR ensemble
Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 12
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