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- PDB-8t35: Crystal structure of K51 acetylated LC3A in complex with the LIR ... -

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Basic information

Entry
Database: PDB / ID: 8t35
TitleCrystal structure of K51 acetylated LC3A in complex with the LIR of TP53INP2/DOR
ComponentsTumor protein p53-inducible nuclear protein 2,Microtubule-associated proteins 1A/1B light chain 3ANeoplasm
KeywordsPROTEIN BINDING / Autophagy / LC3A acetylation / DOR LIR / TP53IP2 LIR
Function / homology
Function and homology information


negative regulation of protein localization / cellular response to oxygen-glucose deprivation / autophagy of mitochondrion / tissue homeostasis / cellular response to nitrogen starvation / SMAD protein signal transduction / response to iron(II) ion / autolysosome / Macroautophagy / Receptor Mediated Mitophagy ...negative regulation of protein localization / cellular response to oxygen-glucose deprivation / autophagy of mitochondrion / tissue homeostasis / cellular response to nitrogen starvation / SMAD protein signal transduction / response to iron(II) ion / autolysosome / Macroautophagy / Receptor Mediated Mitophagy / p38MAPK cascade / autophagosome membrane / organelle membrane / autophagosome maturation / autophagosome assembly / autophagosome / JNK cascade / cellular response to copper ion / PINK1-PRKN Mediated Mitophagy / cellular response to amino acid starvation / cellular response to starvation / ubiquitin binding / macroautophagy / response to lead ion / protein localization / phospholipid binding / PML body / cellular response to hydrogen peroxide / osteoblast differentiation / late endosome / cytoplasmic vesicle / ubiquitin-dependent protein catabolic process / microtubule binding / microtubule / intracellular membrane-bounded organelle / glutamatergic synapse / ubiquitin protein ligase binding / positive regulation of DNA-templated transcription / nucleus / 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
Tumor protein p53-inducible nuclear protein 2 / Microtubule-associated proteins 1A/1B light chain 3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.902 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tumor protein p53-inducible nuclear protein 2,Microtubule-associated proteins 1A/1B light chain 3A
B: Tumor protein p53-inducible nuclear protein 2,Microtubule-associated proteins 1A/1B light chain 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,76610
Polymers31,2702
Non-polymers4978
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.356, 49.927, 69.784
Angle α, β, γ (deg.)90.00, 94.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tumor protein p53-inducible nuclear protein 2,Microtubule-associated proteins 1A/1B light chain 3A / Neoplasm / Diabetes and obesity-regulated gene / p53-inducible protein U / PIG-U / Autophagy-related protein ...Diabetes and obesity-regulated gene / p53-inducible protein U / PIG-U / Autophagy-related protein LC3 A / Autophagy-related ubiquitin-like modifier LC3 A / MAP1 light chain 3-like protein 1 / MAP1A/MAP1B light chain 3 A / MAP1A/MAP1B LC3 A / Microtubule-associated protein 1 light chain 3 alpha


Mass: 15634.854 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TP53INP2, C20orf110, DOR, PINH, MAP1LC3A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8IXH6, UniProt: Q9H492
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.07 Å3/Da / Density % sol: 40.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% PEG4000, 0.1M Na-citrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9768 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9768 Å / Relative weight: 1
ReflectionResolution: 1.902→37.235 Å / Num. obs: 19838 / % possible obs: 98.28 % / Redundancy: 3.3 % / CC1/2: 0.997 / Net I/σ(I): 8.26
Reflection shellResolution: 1.926→1.995 Å / Num. unique obs: 1751 / CC1/2: 0.693

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Processing

Software
NameVersionClassification
PHENIX(1.11.1-2575_1496: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.902→37.235 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2588 974 4.91 %
Rwork0.2277 --
obs0.2292 19838 97.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.902→37.235 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2095 0 32 37 2164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062172
X-RAY DIFFRACTIONf_angle_d0.8862909
X-RAY DIFFRACTIONf_dihedral_angle_d16.1061344
X-RAY DIFFRACTIONf_chiral_restr0.05314
X-RAY DIFFRACTIONf_plane_restr0.006378
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.902-2.00210.38541230.35912410X-RAY DIFFRACTION88
2.0021-2.12760.36171320.30872686X-RAY DIFFRACTION99
2.1276-2.29180.34931610.28382700X-RAY DIFFRACTION99
2.2918-2.52240.3181580.24712741X-RAY DIFFRACTION100
2.5224-2.88730.29951320.24892744X-RAY DIFFRACTION99
2.8873-3.63720.25741290.24332772X-RAY DIFFRACTION100
3.6372-37.2350.21161390.19052811X-RAY DIFFRACTION99
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)
13.22210.21780.52791.4572-0.24141.4653-0.0917-0.06210.05550.13010.10840.0578-0.1220.0911-0.02480.359-0.00130.03640.22030.02310.43136.57930.78290.7392
25.79250.39222.00830.97880.55763.2683-0.27490.01840.0424-0.110.12530.1913-0.30140.09510.14710.36190.00790.01450.38660.07110.180512.0086-15.984226.3532
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid -6 through 118)
2X-RAY DIFFRACTION2(chain 'B' and resid -9 through 117)

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