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- PDB-1kjt: Crystal Structure of the GABA(A) Receptor Associated Protein, GABARAP -

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Basic information

Entry
Database: PDB / ID: 1kjt
TitleCrystal Structure of the GABA(A) Receptor Associated Protein, GABARAP
ComponentsGABARAP
KeywordsTRANSPORT PROTEIN / ubiquitin-like fold / N-terminal alpha helical region
Function / homology
Function and homology information


TBC/RABGAPs / Macroautophagy / positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / phosphatidylethanolamine binding / cellular response to nitrogen starvation / microtubule associated complex / postsynaptic specialization, intracellular component / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane ...TBC/RABGAPs / Macroautophagy / positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / phosphatidylethanolamine binding / cellular response to nitrogen starvation / microtubule associated complex / postsynaptic specialization, intracellular component / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / beta-tubulin binding / autophagosome membrane / extrinsic apoptotic signaling pathway via death domain receptors / axoneme / autophagosome assembly / autophagosome maturation / smooth endoplasmic reticulum / mitophagy / sperm midpiece / autophagosome / GABA-ergic synapse / microtubule cytoskeleton organization / protein transport / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / actin cytoskeleton / cell body / microtubule binding / cytoplasmic vesicle / microtubule / lysosome / Golgi membrane / ubiquitin protein ligase binding / perinuclear region of cytoplasm / Golgi apparatus / plasma membrane
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
NICKEL (II) ION / Gamma-aminobutyric acid receptor-associated protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBavro, V.N. / Sola, M. / Bracher, A. / Kneussel, M. / Betz, H. / Weissenhorn, W.
CitationJournal: EMBO Rep. / Year: 2002
Title: Crystal structure of the GABA(A)-receptor-associated protein, GABARAP.
Authors: Bavro, V.N. / Sola, M. / Bracher, A. / Kneussel, M. / Betz, H. / Weissenhorn, W.
History
DepositionDec 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GABARAP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2414
Polymers14,1001
Non-polymers1403
Water93752
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)29.720, 56.040, 64.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14100.201 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: modified pMAL-c2g / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 codon + / References: UniProt: P60517
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.92 Å3/Da / Density % sol: 35.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 2000MME, Tris HCL, nickel chloride, sodium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7.2 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris1droppH7.2
2100 mM1dropNaCl
325 mg/mlprotein1drop
40.1 mMTris1reservoirpH8.5
530 %(w/v)PEG2000MME1reservoir
65 mM1reservoirNiCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9333 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 20, 2001
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9333 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 7790 / Num. obs: 7736
Reflection shellResolution: 2→2.07 Å
Reflection
*PLUS
Num. obs: 7790 / % possible obs: 99.4 % / Redundancy: 3.8 % / Num. measured all: 56243 / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 95.5 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 2.11

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Processing

Software
NameClassification
MOLREPphasing
CCP4model building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.261 -RANDOM
Rwork0.235 --
obs-7695 -
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 3 53 1007
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor obs: 0.235 / Rfactor Rfree: 0.261 / Rfactor Rwork: 0.235
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.006
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_deg1.146

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