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- PDB-8t33: Crystal structure of K46 acetylated GABARAP in complex with the L... -

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Basic information

Entry
Database: PDB / ID: 8t33
TitleCrystal structure of K46 acetylated GABARAP in complex with the LIR of TP53INP2/DOR
Components
  • Gamma-aminobutyric acid receptor-associated protein
  • Tumor protein p53-inducible nuclear protein 2
KeywordsPROTEIN BINDING / Autophagy / GABARAP acetylation / DOR LIR / TP53INP2 LIR
Function / homology
Function and homology information


negative regulation of protein localization / positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / tissue homeostasis / phosphatidylethanolamine binding / TBC/RABGAPs / cellular response to nitrogen starvation / microtubule associated complex / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane ...negative regulation of protein localization / positive regulation of protein K48-linked ubiquitination / regulation of Rac protein signal transduction / GABA receptor binding / tissue homeostasis / phosphatidylethanolamine binding / TBC/RABGAPs / cellular response to nitrogen starvation / microtubule associated complex / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / Macroautophagy / beta-tubulin binding / autophagosome membrane / extrinsic apoptotic signaling pathway via death domain receptors / axoneme / autophagosome assembly / autophagosome maturation / smooth endoplasmic reticulum / protein targeting / mitophagy / sperm midpiece / autophagosome / ubiquitin binding / GABA-ergic synapse / PML body / microtubule cytoskeleton organization / osteoblast differentiation / intracellular protein localization / protein transport / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / actin cytoskeleton / ubiquitin-dependent protein catabolic process / microtubule binding / cytoplasmic vesicle / chemical synaptic transmission / microtubule / lysosome / Golgi membrane / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / positive regulation of DNA-templated transcription / nucleus / plasma membrane / cytosol
Similarity search - Function
Tumour protein p53-inducible nuclear protein / DOR family / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / Gamma-aminobutyric acid receptor-associated protein / Tumor protein p53-inducible nuclear protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 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 1.4Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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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: Tumor protein p53-inducible nuclear protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,56815
Polymers15,7432
Non-polymers82513
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-219 kcal/mol
Surface area7470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.488, 89.178, 63.967
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-310-

HOH

21A-463-

HOH

31A-485-

HOH

41A-486-

HOH

51B-114-

HOH

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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 Tumor protein p53-inducible nuclear protein 2 / Diabetes and obesity-regulated gene / p53-inducible protein U / PIG-U


Mass: 1615.738 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53INP2, C20orf110, DOR, PINH / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IXH6
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.42 Å3/Da / Density % sol: 49.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 10 % w/v PEG 3000, 0.2 M Zinc acetate dihydrate, 0.1 M Sodium acetate PH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.522 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.522 Å / Relative weight: 1
ReflectionResolution: 1.599→45.87 Å / Num. obs: 39016 / % possible obs: 99.84 % / Redundancy: 4.4 % / CC1/2: 0.999 / Net I/σ(I): 23.94
Reflection shellResolution: 1.599→1.657 Å / Num. unique obs: 3866 / CC1/2: 0.961

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.599→45.87 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 19.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2123 3756 9.63 %
Rwork0.1848 35260 -
obs0.1874 39016 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 59.1 Å2 / Biso mean: 20.9786 Å2 / Biso min: 8.71 Å2
Refinement stepCycle: final / Resolution: 1.599→45.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1054 0 25 200 1279
Biso mean--28.1 33.83 -
Num. residues----125
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.5995-1.61970.26831390.2338129997
1.6197-1.64110.25611480.25351268100
1.6411-1.66350.24261390.22671317100
1.6635-1.68730.27131290.21291312100
1.6873-1.71250.24461430.21771299100
1.7392-1.76780.22191400.19961306100
1.7678-1.79820.20961420.20591332100
1.7982-1.83090.22931600.2021274100
1.8309-1.86620.21551250.20121317100
1.8662-1.90430.25741350.19071288100
1.9043-1.94570.26151470.19341301100
1.9457-1.99090.21091400.19251326100
2.0407-2.09590.20821370.18341301100
2.0959-2.15760.21761430.17461329100
2.1576-2.22720.24261320.18971309100
2.2272-2.30680.23811450.19051290100
2.3068-2.39920.25631420.19221293100
2.3992-2.50830.2421290.19111319100
2.5083-2.64060.19731400.18621299100
2.6406-2.8060.22051510.19171297100
2.806-3.02260.21391410.17741323100
3.0226-3.32670.21671360.17451304100
3.3267-3.80790.18171490.16911301100
3.8079-4.79670.16891350.14891306100
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)
10.58060.4045-0.20361.99130.78320.7669-0.2920.24530.0047-0.21410.15160.2556-0.0694-0.3805-0.04920.20150.0537-0.01130.41730.00520.24881.196918.3541-7.0141
22.3162-2.44751.48012.6461-1.63142.9245-0.0764-0.1476-0.45310.26760.33160.7079-0.099-0.65370.77110.16670.05850.09150.17080.04190.20044.926512.98296.1592
31.09770.2229-1.2581.2961-0.08241.45190.02060.0148-0.16020.16610.04670.058-0.0355-0.14650.00170.102-0.0073-0.00110.0799-0.00020.114812.630610.3642-2.2218
42.111-1.21070.0080.86610.50581.7014-0.06220.4806-0.00690.03880.36430.2981-0.0409-0.78460.42190.20280.0213-0.03360.24480.0210.22178.047113.4521-18.3165
50.53910.0331-0.48851.43770.03740.62780.1424-0.1558-0.07710.1676-0.0857-0.08040.06830.01690.00010.1155-0.0074-0.00110.10890.01460.115617.35838.1554-3.0993
61.66570.1681-0.08661.3571-0.55441.5148-0.03790.2205-0.255-0.22120.01680.06920.19980.0332-0.00010.14390.0010.01060.1306-0.01930.14218.553310.2633-17.4016
71.00970.531-0.0420.6824-0.22033.2607-0.0492-0.21430.26790.1123-0.02130.0406-0.51120.03380.07120.1537-0.02550.00110.1077-0.00670.133821.282720.472-8.4955
80.6947-0.8321-0.56282.0431-0.54312.7375-0.0975-0.06130.11660.28440.0658-0.0651-0.36110.0224-0.00840.1439-0.00220.00680.10860.00460.111313.936518.2435-2.2468
90.52090.4332-0.52243.95092.07462.5464-0.25220.25010.1499-0.04880.23211.0511-0.3878-0.8596-0.19520.20170.0510.00960.30280.07280.257914.709424.3792-20.1533
101.52840.4619-0.09750.90560.19371.1698-0.1140.05140.08960.01880.00850.11560.1898-0.1887-0.01680.1402-0.0130.03920.09450.01210.176814.92322.8988-4.056
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )A1 - 10
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 24 )A11 - 24
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 35 )A25 - 35
4X-RAY DIFFRACTION4chain 'A' and (resid 36 through 47 )A36 - 47
5X-RAY DIFFRACTION5chain 'A' and (resid 48 through 56 )A48 - 56
6X-RAY DIFFRACTION6chain 'A' and (resid 57 through 79 )A57 - 79
7X-RAY DIFFRACTION7chain 'A' and (resid 80 through 90 )A80 - 90
8X-RAY DIFFRACTION8chain 'A' and (resid 91 through 110 )A91 - 110
9X-RAY DIFFRACTION9chain 'A' and (resid 111 through 117 )A111 - 117
10X-RAY DIFFRACTION10chain 'B' and (resid 34 through 41 )B34 - 41

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