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- PDB-4xc2: Crystal structure of GABARAP in complex with KBTBD6 LIR peptide -

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Basic information

Entry
Database: PDB / ID: 4xc2
TitleCrystal structure of GABARAP in complex with KBTBD6 LIR peptide
Components
  • GABA(A) receptor-associated protein
  • Kelch repeat and BTB domain-containing protein 6
KeywordsIMMUNE SYSTEM / autophagy / complex
Function / homology
Function and homology information


positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / cellular response to nitrogen starvation / phosphatidylethanolamine binding / TBC/RABGAPs / microtubule associated complex / Macroautophagy / beta-tubulin binding / axoneme ...positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / cellular response to nitrogen starvation / phosphatidylethanolamine binding / TBC/RABGAPs / microtubule associated complex / Macroautophagy / beta-tubulin binding / axoneme / autophagosome membrane / autophagosome assembly / extrinsic apoptotic signaling pathway via death domain receptors / smooth endoplasmic reticulum / autophagosome / protein targeting / sperm midpiece / post-translational protein modification / macroautophagy / autophagy / microtubule cytoskeleton organization / actin cytoskeleton / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / protein transport / Neddylation / cell body / cytoplasmic vesicle / microtubule binding / chemical synaptic transmission / microtubule / lysosome / Golgi membrane / synapse / ubiquitin protein ligase binding / perinuclear region of cytoplasm / Golgi apparatus / plasma membrane / cytosol
Similarity search - Function
Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch repeat type 1 / Kelch motif / Kelch-type beta propeller ...Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / BTB-kelch protein / BTB/Kelch-associated / BTB And C-terminal Kelch / BTB And C-terminal Kelch / Kelch / Kelch repeat type 1 / Kelch motif / Kelch-type beta propeller / BTB/POZ domain / BTB domain profile. / Broad-Complex, Tramtrack and Bric a brac / BTB/POZ domain / SKP1/BTB/POZ domain superfamily / 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 / Epididymis secretory sperm binding protein / Kelch repeat and BTB domain-containing protein 6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHuber, J. / Genau, H.M. / Baschieri, F. / Doetsch, V. / Farhan, H. / Rogov, V.V. / Behrends, C. / Akutsu, M.
Funding support Germany, 6items
OrganizationGrant numberCountry
DKTK Germany
Cluster of excellence Frankfurt Germany
German Research FoundationBE 4685/1-1 Germany
European Research Council282333 Germany
LOEWE Program of the State of Hesse Germany
Leibniz award Germany
CitationJournal: Mol.Cell / Year: 2015
Title: CUL3-KBTBD6/KBTBD7 Ubiquitin Ligase Cooperates with GABARAP Proteins to Spatially Restrict TIAM1-RAC1 Signaling.
Authors: Genau, H.M. / Huber, J. / Baschieri, F. / Akutsu, M. / Dotsch, V. / Farhan, H. / Rogov, V. / Behrends, C.
History
DepositionDec 17, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 2.0Sep 6, 2017Group: Atomic model / Author supporting evidence / Category: atom_site / pdbx_audit_support
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_audit_support.funding_organization
Revision 2.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GABA(A) receptor-associated protein
B: GABA(A) receptor-associated protein
C: GABA(A) receptor-associated protein
D: GABA(A) receptor-associated protein
E: Kelch repeat and BTB domain-containing protein 6
F: Kelch repeat and BTB domain-containing protein 6
G: Kelch repeat and BTB domain-containing protein 6
H: Kelch repeat and BTB domain-containing protein 6


Theoretical massNumber of molelcules
Total (without water)60,5418
Polymers60,5418
Non-polymers00
Water3,369187
1
A: GABA(A) receptor-associated protein
E: Kelch repeat and BTB domain-containing protein 6


Theoretical massNumber of molelcules
Total (without water)15,1352
Polymers15,1352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1400 Å2
ΔGint-6 kcal/mol
Surface area7230 Å2
MethodPISA
2
B: GABA(A) receptor-associated protein
F: Kelch repeat and BTB domain-containing protein 6


Theoretical massNumber of molelcules
Total (without water)15,1352
Polymers15,1352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-5 kcal/mol
Surface area7170 Å2
MethodPISA
3
C: GABA(A) receptor-associated protein
G: Kelch repeat and BTB domain-containing protein 6


Theoretical massNumber of molelcules
Total (without water)15,1352
Polymers15,1352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1460 Å2
ΔGint-6 kcal/mol
Surface area7190 Å2
MethodPISA
4
D: GABA(A) receptor-associated protein
H: Kelch repeat and BTB domain-containing protein 6


Theoretical massNumber of molelcules
Total (without water)15,1352
Polymers15,1352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-5 kcal/mol
Surface area7040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.893, 57.353, 67.310
Angle α, β, γ (deg.)65.300, 77.340, 89.950
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
GABA(A) receptor-associated protein / GABARAP protein / HCG1987397 / isoform CRA_b


Mass: 13827.839 Da / Num. of mol.: 4 / Fragment: UNP residues 3-116
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAP, hCG_1987397 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6IAW1, UniProt: O95166*PLUS
#2: Protein/peptide
Kelch repeat and BTB domain-containing protein 6


Mass: 1307.388 Da / Num. of mol.: 4 / Fragment: UNP residues 663-673 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q86V97
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.19 Å3/Da / Density % sol: 43.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.2 M Ammonium acetate, 0.01 M Magnesium acetate tetrahydrate, 30% Poly ethylene glycol 8000, 0.1 M Tris-HCl, pH 8.0

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→37.75 Å / Num. obs: 37496 / % possible obs: 92.7 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 12.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.365 / Mean I/σ(I) obs: 2.5 / Num. measured obs: 13090 / Num. unique all: 5380 / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D32

3d32


Resolution: 1.9→32.73 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.492 / SU ML: 0.153 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2582 1881 5 %RANDOM
Rwork0.1982 35614 --
obs0.2013 35614 92.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 97.94 Å2 / Biso mean: 33.186 Å2 / Biso min: 12.66 Å2
Baniso -1Baniso -2Baniso -3
1-5.04 Å20.47 Å20.75 Å2
2---1.19 Å20.96 Å2
3----2.04 Å2
Refinement stepCycle: final / Resolution: 1.9→32.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4254 0 0 187 4441
Biso mean---34.67 -
Num. residues----508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194393
X-RAY DIFFRACTIONr_bond_other_d00.024142
X-RAY DIFFRACTIONr_angle_refined_deg1.1621.9575927
X-RAY DIFFRACTIONr_angle_other_deg0.63539549
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8575504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.43722.991234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.58615757
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3961536
X-RAY DIFFRACTIONr_chiral_restr0.0790.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0214878
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021074
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 134 -
Rwork0.348 2632 -
all-2766 -
obs--91.62 %

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