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- PDB-8t4t: Crystal structure of LC3A in complex with the LIR of TP53INP2/DOR -

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Basic information

Entry
Database: PDB / ID: 8t4t
TitleCrystal structure of LC3A in complex with the LIR of TP53INP2/DOR
ComponentsTumor protein p53-inducible nuclear protein 2,Microtubule-associated proteins 1A/1B light chain 3A chimeraNeoplasm
KeywordsPROTEIN BINDING / LC3A / Autophagy / DOR LIR / TP53INP2 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: 2.359 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 10, 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 chimera
B: Tumor protein p53-inducible nuclear protein 2,Microtubule-associated proteins 1A/1B light chain 3A chimera


Theoretical massNumber of molelcules
Total (without water)31,4462
Polymers31,4462
Non-polymers00
Water18010
1
A: Tumor protein p53-inducible nuclear protein 2,Microtubule-associated proteins 1A/1B light chain 3A chimera


Theoretical massNumber of molelcules
Total (without water)15,7231
Polymers15,7231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tumor protein p53-inducible nuclear protein 2,Microtubule-associated proteins 1A/1B light chain 3A chimera


Theoretical massNumber of molelcules
Total (without water)15,7231
Polymers15,7231
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.004, 47.740, 72.902
Angle α, β, γ (deg.)90.00, 95.49, 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 chimera / 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: 15722.941 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.04 Å3/Da / Density % sol: 39.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 12.5% PEG3350, 0.2M NH4-citrate, 5% isopropanol, 0.1M MES pH6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.359→39.883 Å / Num. obs: 9618 / % possible obs: 89.74 % / Redundancy: 3 % / CC1/2: 0.995 / Net I/σ(I): 7.91
Reflection shellResolution: 2.359→2.444 Å / Num. unique obs: 508 / CC1/2: 0.123

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.359→39.883 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 35.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2715 951 9.99 %
Rwork0.2029 --
obs0.2101 9520 89.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.359→39.883 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2065 0 0 10 2075
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012109
X-RAY DIFFRACTIONf_angle_d1.2312846
X-RAY DIFFRACTIONf_dihedral_angle_d17.4061316
X-RAY DIFFRACTIONf_chiral_restr0.063310
X-RAY DIFFRACTIONf_plane_restr0.009371
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3592-2.48360.4221720.3308658X-RAY DIFFRACTION48
2.4836-2.63920.37171260.33761136X-RAY DIFFRACTION84
2.6392-2.84290.39581460.29241311X-RAY DIFFRACTION98
2.8429-3.12890.33721480.26451343X-RAY DIFFRACTION99
3.1289-3.58140.30311510.23761346X-RAY DIFFRACTION99
3.5814-4.51120.25281510.17251364X-RAY DIFFRACTION100
4.5112-39.8830.21161570.15351411X-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)
12.81760.63591.47440.2110.40970.6243-0.0642-0.00330.21070.13360.0670.14120.0846-0.0022-0.00030.5561-0.04510.01120.60090.00040.661-17.247-8.926-4.838
20.1203-0.5078-0.57734.47652.95143.04810.6433-0.42630.1741-0.9846-0.1446-0.4554-0.7817-0.03790.25860.2492-0.0368-0.0140.46380.04830.5517-1.735-5.1871.985
30.6685-0.8847-0.38142.4061-0.79233.1711-0.0284-0.16830.14360.7868-0.1071-0.1790.43070.16480.0010.4114-0.01260.04010.45960.0560.5264-7.279-12.3115.528
40.3613-0.78480.31021.7308-0.65420.25390.42130.44480.5626-0.3423-0.1536-0.1914-0.1011-0.58560.03740.94780.30980.02691.1060.00110.521818.155-28.02335.481
50.0222-0.12380.02061.11370.13350.1611-0.2445-0.0188-0.3586-0.1765-0.24-1.416-0.22570.52170.00640.6655-0.26810.17231.0872-0.14250.64111.202-33.57326.343
60.7812-0.4020.73840.3022-0.35640.74330.7356-0.789-1.19361.28610.09150.93761.0664-0.86730.05760.9091-0.15770.05720.69340.03110.8004-9.289-40.2726.778
70.61740.7365-0.10893.01822.1762.4199-0.2508-0.26510.25230.37950.03730.6375-0.4799-0.35930.00130.8006-0.0147-0.07530.7630.15480.5518-8.805-23.66928.849
83.60810.68921.5570.31310.20170.72750.1908-0.89050.7244-1.109-0.43511.7479-0.2462-1.3472-0.01271.43820.4297-0.12730.7478-0.1460.973-14.723-16.49431.274
96.6075-0.194-1.32621.1276-0.48320.50680.27420.5741.95370.67710.0744-0.0124-2.0583-1.04260.93321.620.1245-0.27380.79540.29520.7481-8.646-8.7830.528
100.23320.20370.08070.562-0.20450.4702-0.15661.74210.82-0.9745-0.21840.6252-0.6063-0.40440.00010.8692-0.107-0.08850.7895-0.00440.8403-12.225-19.63318.015
110.5704-0.3308-0.58731.59450.11260.6179-0.7250.88560.74010.37160.13380.4559-0.51690.0378-0.06640.8843-0.051-0.13180.62090.06330.6162-10.332-26.44420.379
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID -5:50 )A-5 - 50
2X-RAY DIFFRACTION2( CHAIN A AND RESID 51:70 )A51 - 70
3X-RAY DIFFRACTION3( CHAIN A AND RESID 71:116 )A71 - 116
4X-RAY DIFFRACTION4( CHAIN B AND RESID -10:6 )B-10 - 6
5X-RAY DIFFRACTION5( CHAIN B AND RESID 7:12 )B7 - 12
6X-RAY DIFFRACTION6( CHAIN B AND RESID 13:26 )B13 - 26
7X-RAY DIFFRACTION7( CHAIN B AND RESID 27:59 )B27 - 59
8X-RAY DIFFRACTION8( CHAIN B AND RESID 60:70 )B60 - 70
9X-RAY DIFFRACTION9( CHAIN B AND RESID 71:80 )B71 - 80
10X-RAY DIFFRACTION10( CHAIN B AND RESID 81:94 )B81 - 94
11X-RAY DIFFRACTION11( CHAIN B AND RESID 95:116 )B95 - 116

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