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- PDB-4tq1: Crystal structure of human ATG5-TECAIR -

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Basic information

Entry
Database: PDB / ID: 4tq1
TitleCrystal structure of human ATG5-TECAIR
Components
  • Autophagy protein 5
  • Tectonin beta-propeller repeat-containing protein 1
KeywordsPROTEIN BINDING / autophagy protein complex
Function / homology
Function and homology information


otolith development / regulation of autophagosome maturation / response to fluoride / regulation of cytokine production involved in immune response / positive regulation of viral translation / Atg8-family ligase activity / Atg12-Atg5-Atg16 complex / antigen processing and presentation of endogenous antigen / phagophore / negative regulation of autophagic cell death ...otolith development / regulation of autophagosome maturation / response to fluoride / regulation of cytokine production involved in immune response / positive regulation of viral translation / Atg8-family ligase activity / Atg12-Atg5-Atg16 complex / antigen processing and presentation of endogenous antigen / phagophore / negative regulation of autophagic cell death / positive regulation of stress granule assembly / cellular response to nitrosative stress / negative regulation of defense response to virus / ventricular cardiac muscle cell development / mitochondria-associated endoplasmic reticulum membrane contact site / regulation of cilium assembly / aggrephagy / transferase complex / mucus secretion / response to fungus / negative thymic T cell selection / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / cellular response to nitrogen starvation / regulation of release of sequestered calcium ion into cytosol / phosphatidylinositol-3-phosphate binding / negative stranded viral RNA replication / response to iron(II) ion / negative regulation of phagocytosis / negative regulation of cardiac muscle cell apoptotic process / positive regulation of mucus secretion / negative regulation of type I interferon production / chaperone-mediated autophagy / Macroautophagy / Receptor Mediated Mitophagy / heart contraction / axoneme / autophagosome membrane / autophagosome maturation / mitophagy / autophagosome assembly / negative regulation of reactive oxygen species metabolic process / autophagosome / blood vessel remodeling / cardiac muscle cell apoptotic process / negative regulation of protein ubiquitination / PINK1-PRKN Mediated Mitophagy / negative regulation of innate immune response / post-translational protein modification / establishment of localization in cell / Negative regulators of DDX58/IFIH1 signaling / macroautophagy / autophagy / vasodilation / phagocytic vesicle membrane / chromatin organization / cytoplasmic vesicle / protein ubiquitination / response to xenobiotic stimulus / lysosomal membrane / axon / intracellular membrane-bounded organelle / protein-containing complex / nucleoplasm / membrane / cytosol / cytoplasm
Similarity search - Function
Peroxin domain / Integral peroxisomal membrane peroxin / Propeller / Tectonin domain / Autophagy protein Apg5, helix rich domain / Ubiquitin-like (UB roll) - #620 / Peroxin/Ferlin domain / : / : / : ...Peroxin domain / Integral peroxisomal membrane peroxin / Propeller / Tectonin domain / Autophagy protein Apg5, helix rich domain / Ubiquitin-like (UB roll) - #620 / Peroxin/Ferlin domain / : / : / : / Autophagy protein ATG5, alpha-helical bundle region / Autophagy protein ATG5, UblA domain / Dysferlin domain, N-terminal region. / Dysferlin domain, C-terminal region. / Autophagy-related protein 5 / Autophagy protein Atg5, helix rich domain / Autophagy protein Atg5, UblA domain / Autophagy protein ATG5, UblB domain / Beta-propeller repeat TECPR / Beta propeller repeats in Physarum polycephalum tectonins, Limulus lectin L-6 and animal hypothetical proteins. / Serum Albumin; Chain A, Domain 1 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / PH-like domain superfamily / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Tectonin beta-propeller repeat-containing protein 1 / Autophagy protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.802 Å
AuthorsKim, J.H. / Hong, S.B. / Song, H.K.
CitationJournal: Autophagy / Year: 2015
Title: Insights into autophagosome maturation revealed by the structures of ATG5 with its interacting partners
Authors: Kim, J.H. / Hong, S.B. / Lee, J.K. / Han, S. / Roh, K.H. / Lee, K.E. / Kim, Y.K. / Choi, E.J. / Song, H.K.
History
DepositionJun 10, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Data collection / Derived calculations / Source and taxonomy
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Autophagy protein 5
B: Tectonin beta-propeller repeat-containing protein 1


Theoretical massNumber of molelcules
Total (without water)38,8842
Polymers38,8842
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-15 kcal/mol
Surface area13960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.618, 71.919, 96.354
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Autophagy protein 5 / / APG5-like / Apoptosis-specific protein


Mass: 34039.812 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATG5, APG5L, ASP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9H1Y0
#2: Protein/peptide Tectonin beta-propeller repeat-containing protein 1


Mass: 4844.444 Da / Num. of mol.: 1 / Fragment: UNP residues 503-540
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TECPR1, KIAA1358 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q7Z6L1
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 1.94 Å3/Da / Density % sol: 36.71 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: MPD, PEG 1000, PEG 3350, alcohols, MES-imdazole / PH range: 6.5

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 28746 / % possible obs: 100 % / Redundancy: 7.8 % / Net I/σ(I): 34

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementResolution: 1.802→34.78 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2224 1926 6.97 %
Rwork0.178 --
obs0.1811 27641 96.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.802→34.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2425 0 0 190 2615
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072495
X-RAY DIFFRACTIONf_angle_d1.0413378
X-RAY DIFFRACTIONf_dihedral_angle_d14.393931
X-RAY DIFFRACTIONf_chiral_restr0.072355
X-RAY DIFFRACTIONf_plane_restr0.004431
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8017-1.84680.27721220.21941658X-RAY DIFFRACTION87
1.8468-1.89670.24461240.2081660X-RAY DIFFRACTION89
1.8967-1.95250.20761340.18891730X-RAY DIFFRACTION92
1.9525-2.01550.20211350.19121769X-RAY DIFFRACTION95
2.0155-2.08750.22021370.18291816X-RAY DIFFRACTION96
2.0875-2.17110.2711340.17971829X-RAY DIFFRACTION96
2.1711-2.26990.24431370.17621825X-RAY DIFFRACTION98
2.2699-2.38960.23361360.17991856X-RAY DIFFRACTION98
2.3896-2.53920.23351410.18681872X-RAY DIFFRACTION98
2.5392-2.73520.21721410.18931878X-RAY DIFFRACTION98
2.7352-3.01030.22251410.17941890X-RAY DIFFRACTION99
3.0103-3.44560.2411450.17791927X-RAY DIFFRACTION100
3.4456-4.33980.21321440.15471944X-RAY DIFFRACTION100
4.3398-34.7870.19311550.17682061X-RAY DIFFRACTION100

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