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- PDB-8t32: Crystal structure of K48 acetylated GABARAP in complex with the L... -

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Basic information

Entry
Database: PDB / ID: 8t32
TitleCrystal structure of K48 acetylated GABARAP in complex with the LIR of TP53INP2/DOR
Components
  • Gamma-aminobutyric acid receptor-associated protein
  • LIR of DOR
KeywordsPROTEIN BINDING / Autophagy / GABARAP acetylation / DOR LIR / TP53INP2 LIR
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 / Macroautophagy / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / smooth endoplasmic reticulum ...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 / Macroautophagy / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / smooth endoplasmic reticulum / autophagosome membrane / axoneme / extrinsic apoptotic signaling pathway via death domain receptors / autophagosome assembly / autophagosome maturation / protein targeting / beta-tubulin binding / mitophagy / sperm midpiece / autophagosome / GABA-ergic synapse / microtubule cytoskeleton organization / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / protein transport / actin cytoskeleton / cytoplasmic vesicle / microtubule binding / chemical synaptic transmission / microtubule / lysosome / Golgi membrane / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / plasma membrane / cytosol
Similarity search - Function
Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
TRIETHYLENE GLYCOL / Gamma-aminobutyric acid receptor-associated protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.051 Å
AuthorsAli, M.G.H. / Wahba, H.M. / Cyr, N. / Omichinski, J.G.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Autophagy / Year: 2024
Title: Structural and functional characterization of the role of acetylation on the interactions of the human Atg8-family proteins with the autophagy receptor TP53INP2/DOR.
Authors: Ali, M.G. / Wahba, H.M. / Igelmann, S. / Cyr, N. / Ferbeyre, G. / Omichinski, J.G.
History
DepositionJun 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Database references / Category: citation / Item: _citation.page_first / _citation.page_last
Revision 1.2Sep 4, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Sep 11, 2024Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gamma-aminobutyric acid receptor-associated protein
B: LIR of DOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8063
Polymers15,6562
Non-polymers1501
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.179, 44.179, 128.859
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

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


Mass: 14127.205 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 BL21(DE3) (bacteria) / References: UniProt: O95166
#2: Protein/peptide LIR of DOR


Mass: 1528.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.01 Å3/Da / Density % sol: 38.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 28 % (w/v) PEG 2000 MME, 0.1 M Bis-Tris: HCl, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 0.9687 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9687 Å / Relative weight: 1
ReflectionResolution: 2.051→30.8 Å / Num. obs: 8486 / % possible obs: 97.31 % / Redundancy: 20 % / CC1/2: 0.999 / Net I/σ(I): 16.91
Reflection shellResolution: 2.051→2.124 Å / Num. unique obs: 648 / CC1/2: 0.408

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.051→30.8 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2709 842 10.02 %
Rwork0.2549 --
obs0.2566 8401 97.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.051→30.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1064 0 10 13 1087
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021102
X-RAY DIFFRACTIONf_angle_d0.4631482
X-RAY DIFFRACTIONf_dihedral_angle_d13.94663
X-RAY DIFFRACTIONf_chiral_restr0.045153
X-RAY DIFFRACTIONf_plane_restr0.003189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.051-2.17910.42531210.3931058X-RAY DIFFRACTION85
2.1791-2.34720.3191380.3191260X-RAY DIFFRACTION99
2.3472-2.58340.37181390.31531253X-RAY DIFFRACTION100
2.5834-2.95690.33221420.3061283X-RAY DIFFRACTION100
2.9569-3.72440.27861450.27861300X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.05222.30990.16563.28972.88347.6252-0.6672-1.4114-1.1642-0.0273-0.32670.60652.1993-1.34090.0970.81760.03990.27330.90750.21.0818-1.1172-11.886123.1586
23.2931-0.9342-2.74116.0763-0.51757.1886-0.4596-1.45660.19611.99940.7535-0.1909-0.42760.7226-0.00781.06610.1445-0.06361.0296-0.01980.586310.7041-7.099326.6588
37.22330.0912-4.29666.9524-0.90049.3649-0.6579-0.5375-0.44320.33750.1985-0.1711.30910.4904-0.12380.6610.2050.00410.66030.10350.490311.4101-15.022312.267
42.35233.16751.0846.4077-2.67369.6705-0.2223-0.5258-0.0797-0.11280.4194-0.60220.04370.85520.02510.37680.00340.03890.52120.01470.525410.2941-7.5468.4596
53.37730.017-2.80442.3995-2.47354.5448-0.2226-0.4420.20790.71310.2950.2208-0.33310.3047-0.00040.61610.08840.0230.49160.10710.50785.863-5.645519.1834
68.02481.2277-5.43662.0009-8.89259.355-0.0210.82910.197-2.06661.20483.9262.0288-4.52412.17790.6914-0.12920.04131.05410.31790.8277-0.2679-10.9112.2761
72.6763-1.59490.9012.5338-0.76222.4303-0.3336-1.0349-0.87931.0152-0.0888-0.8668-0.13091.68810.02211.10990.2667-0.19591.3570.1731.003417.8994-15.96622.5889
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 35 )
3X-RAY DIFFRACTION3chain 'A' and (resid 36 through 68 )
4X-RAY DIFFRACTION4chain 'A' and (resid 69 through 98 )
5X-RAY DIFFRACTION5chain 'A' and (resid 99 through 110 )
6X-RAY DIFFRACTION6chain 'A' and (resid 111 through 115 )
7X-RAY DIFFRACTION7chain 'B' and (resid 30 through 41 )

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