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- PDB-3wim: GABARAP-LIR peptide complex -

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Basic information

Entry
Database: PDB / ID: 3wim
TitleGABARAP-LIR peptide complex
Components
  • Gamma-aminobutyric acid receptor-associated protein
  • WD repeat and FYVE domain-containing protein 3
KeywordsTRANSPORT PROTEIN / Ubiquitin like fold / Alpha helical region / Autophagy / Maturation of autophagosome / Atg7 / Atg3 / ALFY / GABA(A) receptor / Phosphatidylethanolamine / Autophagosome / Isolation membrane
Function / homology
Function and homology information


1-phosphatidylinositol binding / positive regulation of protein K48-linked ubiquitination / aggrephagy / regulation of Rac protein signal transduction / GABA receptor binding / cellular response to nitrogen starvation / phosphatidylethanolamine binding / TBC/RABGAPs / microtubule associated complex / Macroautophagy ...1-phosphatidylinositol binding / positive regulation of protein K48-linked ubiquitination / aggrephagy / 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 maturation / autophagosome assembly / extrinsic apoptotic signaling pathway via death domain receptors / smooth endoplasmic reticulum / autophagosome / protein targeting / inclusion body / sperm midpiece / PML body / microtubule cytoskeleton organization / protein transport / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / actin cytoskeleton / nuclear envelope / cytoplasmic vesicle / microtubule binding / chemical synaptic transmission / perikaryon / nuclear membrane / microtubule / lysosome / axon / Golgi membrane / ubiquitin protein ligase binding / synapse / nucleolus / nucleoplasm / membrane / metal ion binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
BEACH domain / PH-BEACH domain / BEACH domain superfamily / Beige/BEACH domain / PH domain associated with Beige/BEACH / BEACH domain profile. / BEACH-type PH domain profile. / Beige/BEACH domain / FYVE zinc finger / FYVE zinc finger ...BEACH domain / PH-BEACH domain / BEACH domain superfamily / Beige/BEACH domain / PH domain associated with Beige/BEACH / BEACH domain profile. / BEACH-type PH domain profile. / Beige/BEACH domain / FYVE zinc finger / FYVE zinc finger / Protein present in Fab1, YOTB, Vac1, and EEA1 / Zinc finger, FYVE-related / Zinc finger FYVE/FYVE-related type profile. / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Zinc finger, FYVE/PHD-type / Ubiquitin-like (UB roll) / Armadillo-like helical / Concanavalin A-like lectin/glucanase domain superfamily / PH-like domain superfamily / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type / Ubiquitin-like domain superfamily / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Gamma-aminobutyric acid receptor-associated protein / WD repeat and FYVE domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLystad, A. / Ichimura, Y. / Takagi, K. / Yang, Y. / Pankiv, S. / Mizushima, T. / Komatsu, M. / Simonsen, A.
CitationJournal: To be Published / Year: 2014
Title: GABARAP-LIR peptide complex
Authors: Lystad, A. / Ichimura, Y. / Takagi, K. / Yang, Y. / Pankiv, S. / Mizushima, T. / Komatsu, M. / Simonsen, A.
History
DepositionSep 19, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Gamma-aminobutyric acid receptor-associated protein
B: WD repeat and FYVE domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)15,5632
Polymers15,5632
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-6 kcal/mol
Surface area7150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.491, 53.491, 83.193
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-202-

HOH

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Components

#1: Protein Gamma-aminobutyric acid receptor-associated protein / GABA(A) receptor-associated protein / MM46


Mass: 13942.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAP, FLC3B, HT004 / Production host: Escherichia coli (E. coli) / References: UniProt: O95166
#2: Protein/peptide WD repeat and FYVE domain-containing protein 3 / Autophagy-linked FYVE protein / Alfy


Mass: 1620.693 Da / Num. of mol.: 1 / Fragment: UNP residues 3341-3354 / Source method: obtained synthetically / Details: Synthetic construct / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8IZQ1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 2.21 Å3/Da / Density % sol: 44.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 2M ammonium sulfate, 0.1M sodium citrate, 0.2M potassium sodium tartrate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 4595 / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 8.9
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 6.8 / Num. unique all: 219 / % possible all: 100

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GNU

1gnu


Resolution: 2.6→46.32 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.851 / SU B: 12.908 / SU ML: 0.283 / Cross valid method: THROUGHOUT / ESU R Free: 0.392 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29605 210 4.6 %RANDOM
Rwork0.21013 ---
obs0.21405 4353 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.429 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.13 Å20 Å2
2--0.26 Å20 Å2
3----0.38 Å2
Refinement stepCycle: LAST / Resolution: 2.6→46.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1087 0 0 12 1099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0221117
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9611.9641502
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9925127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.28123.2259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.73815201
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.588158
X-RAY DIFFRACTIONr_chiral_restr0.0930.2154
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021857
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0811.5645
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.06221046
X-RAY DIFFRACTIONr_scbond_it2.823472
X-RAY DIFFRACTIONr_scangle_it4.6224.5456
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.661 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 16 -
Rwork0.234 317 -
obs--99.4 %

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