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- PDB-1kot: Solution Structure of Human GABA Receptor Associated Protein GABARAP -

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Basic information

Entry
Database: PDB / ID: 1kot
TitleSolution Structure of Human GABA Receptor Associated Protein GABARAP
ComponentsGABARAP
KeywordsTRANSPORT PROTEIN / human GABA Receptor Targeting GABARAP
Function / homology
Function and homology information


positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / phosphatidylethanolamine binding / TBC/RABGAPs / cellular response to nitrogen starvation / microtubule associated complex / autophagy of mitochondrion / Macroautophagy / beta-tubulin binding ...positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / phosphatidylethanolamine binding / TBC/RABGAPs / cellular response to nitrogen starvation / microtubule associated complex / autophagy of mitochondrion / Macroautophagy / beta-tubulin binding / axoneme / autophagosome membrane / autophagosome maturation / extrinsic apoptotic signaling pathway via death domain receptors / autophagosome assembly / smooth endoplasmic reticulum / protein targeting / sperm midpiece / autophagosome / microtubule cytoskeleton organization / protein transport / actin cytoskeleton / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / cytoplasmic vesicle / microtubule binding / chemical synaptic transmission / microtubule / lysosome / Golgi membrane / ubiquitin protein ligase binding / synapse / plasma membrane / cytosol
Similarity search - Function
Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Gamma-aminobutyric acid receptor-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsStangler, T. / Luge, C. / Mayr, L.M. / Willbold, D.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Solution structure of human GABA(A) receptor-associated protein GABARAP: implications for biolgoical funcrion and its regulation.
Authors: Stangler, T. / Mayr, L.M. / Willbold, D.
History
DepositionDec 22, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GABARAP


Theoretical massNumber of molelcules
Total (without water)14,0861
Polymers14,0861
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)15 / 400structures with the least restraint violations
RepresentativeModel #2lowest energy

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Components

#1: Protein GABARAP / GABA-A receptor-associated protein


Mass: 14086.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-GABARAP / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O95166

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
1323D 13C-separated NOESY
1423D 13C -seperated(aromatics) NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.8mM GABARAP U-15N,13C; 25mM sodium oxalate, pH 6.9 100mM NaCl 100mM KCl 100uM PMSF 0.02% sodium azide 50uM EDTA 5% D2O, 95% H2O95% H2O/5% D2O
20.8mM GABARAP U-15N,13C; 25mM sodium phosphate, pH 6.9 100mM NaCl 100mM KCl 100uM PMSF 0.02% sodium azide 50uM EDTA 100% D2O100% D2O
Sample conditionsIonic strength: 100mM NaCl 100mM KCl / pH: 6.9 / Pressure: ambient / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA7502
Bruker DMXBrukerDMX6003

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Processing

NMR software
NameVersionDeveloperClassification
VNMR5.3Variancollection
NMRPipeDelaglioprocessing
NMRView5.0.3Johnsondata analysis
ARIA1Nilgesrefinement
CNS1Brungerrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 400 / Conformers submitted total number: 15

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