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- PDB-4tq0: Crystal structure of human ATG5-ATG16N69 -

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Basic information

Entry
Database: PDB / ID: 4tq0
TitleCrystal structure of human ATG5-ATG16N69
Components
  • Autophagy protein 5
  • Autophagy-related protein 16-1
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 / C-terminal protein lipidation / vacuole-isolation membrane contact site ...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 / C-terminal protein lipidation / vacuole-isolation membrane contact site / negative regulation of autophagic cell death / cellular response to nitrosative stress / ubiquitin-like protein transferase activity / negative regulation of defense response to virus / ventricular cardiac muscle cell development / microautophagy / mitochondria-associated endoplasmic reticulum membrane contact site / regulation of cilium assembly / aggrephagy / transferase complex / mucus secretion / response to fungus / xenophagy / nucleophagy / negative thymic T cell selection / protein localization to phagophore assembly site / phagophore assembly site membrane / corpus callosum development / cellular response to nitrogen starvation / negative stranded viral RNA replication / regulation of release of sequestered calcium ion into cytosol / endolysosome membrane / negative regulation of phagocytosis / response to iron(II) ion / negative regulation of cardiac muscle cell apoptotic process / positive regulation of mucus secretion / negative regulation of type I interferon production / Macroautophagy / Receptor Mediated Mitophagy / chaperone-mediated autophagy / heart contraction / axoneme / autophagosome membrane / mitophagy / autophagosome assembly / autophagosome / negative regulation of reactive oxygen species metabolic process / blood vessel remodeling / positive regulation of autophagy / protein-membrane adaptor activity / negative regulation of protein ubiquitination / cardiac muscle cell apoptotic process / sperm midpiece / PINK1-PRKN Mediated Mitophagy / negative regulation of innate immune response / post-translational protein modification / Negative regulators of DDX58/IFIH1 signaling / establishment of localization in cell / hippocampus development / macroautophagy / autophagy / vasodilation / phagocytic vesicle membrane / protein transport / GTPase binding / chromatin organization / defense response to virus / protein ubiquitination / response to xenobiotic stimulus / axon / protein-containing complex / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Autophagy protein Apg5, helix rich domain / Ubiquitin-like (UB roll) - #620 / : / : / : / Autophagy protein ATG5, alpha-helical bundle region / Autophagy protein ATG5, UblA domain / Autophagy-related protein 5 / Autophagy protein Atg5, helix rich domain / Autophagy protein Atg5, UblA domain ...Autophagy protein Apg5, helix rich domain / Ubiquitin-like (UB roll) - #620 / : / : / : / Autophagy protein ATG5, alpha-helical bundle region / Autophagy protein ATG5, UblA domain / Autophagy-related protein 5 / Autophagy protein Atg5, helix rich domain / Autophagy protein Atg5, UblA domain / Autophagy protein ATG5, UblB domain / Autophagy-related protein 16 / Autophagy-related protein 16 domain / Autophagy protein 16 (ATG16) / Serum Albumin; Chain A, Domain 1 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Autophagy-related protein 16-1 / Autophagy protein 5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.697 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: Autophagy-related protein 16-1
C: Autophagy protein 5
D: Autophagy-related protein 16-1
E: Autophagy protein 5
F: Autophagy-related protein 16-1


Theoretical massNumber of molelcules
Total (without water)127,1686
Polymers127,1686
Non-polymers00
Water2,918162
1
A: Autophagy protein 5
B: Autophagy-related protein 16-1


Theoretical massNumber of molelcules
Total (without water)42,3892
Polymers42,3892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-17 kcal/mol
Surface area14290 Å2
MethodPISA
2
C: Autophagy protein 5
D: Autophagy-related protein 16-1


Theoretical massNumber of molelcules
Total (without water)42,3892
Polymers42,3892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-16 kcal/mol
Surface area14170 Å2
MethodPISA
3
E: Autophagy protein 5
F: Autophagy-related protein 16-1


Theoretical massNumber of molelcules
Total (without water)42,3892
Polymers42,3892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-13 kcal/mol
Surface area14080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.094, 93.094, 245.577
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 34039.812 Da / Num. of mol.: 3
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 Autophagy-related protein 16-1 / APG16-like 1


Mass: 8349.556 Da / Num. of mol.: 3 / Fragment: UNP residues 1-69
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATG16L1, APG16L, UNQ9393/PRO34307 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q676U5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.09 Å3/Da / Density % sol: 41.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 400, MgCl2, KCl, Tris-HCl / PH range: 8.5

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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: Mar 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.697→50 Å / Num. obs: 28321 / % possible obs: 99.9 % / Redundancy: 15.8 % / Net I/σ(I): 39.1

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementResolution: 2.697→37.092 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 26.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2742 1829 6.46 %
Rwork0.2028 --
obs0.2074 28318 92.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.697→37.092 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7057 0 0 162 7219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017256
X-RAY DIFFRACTIONf_angle_d1.399834
X-RAY DIFFRACTIONf_dihedral_angle_d14.6362681
X-RAY DIFFRACTIONf_chiral_restr0.0631050
X-RAY DIFFRACTIONf_plane_restr0.0081248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6973-2.77020.40911080.28351655X-RAY DIFFRACTION76
2.7702-2.85170.40471160.26331741X-RAY DIFFRACTION80
2.8517-2.94370.35241180.25981712X-RAY DIFFRACTION79
2.9437-3.04890.37211280.24961840X-RAY DIFFRACTION85
3.0489-3.17090.32171370.23432012X-RAY DIFFRACTION93
3.1709-3.31510.28881520.2082179X-RAY DIFFRACTION99
3.3151-3.48980.25881510.19512153X-RAY DIFFRACTION99
3.4898-3.70830.25981510.18272172X-RAY DIFFRACTION99
3.7083-3.99430.23491420.1822120X-RAY DIFFRACTION96
3.9943-4.39560.22011520.15982130X-RAY DIFFRACTION96
4.3956-5.03040.22271530.15342158X-RAY DIFFRACTION97
5.0304-6.33260.23561560.19912230X-RAY DIFFRACTION98
6.3326-37.09520.28331650.22762387X-RAY DIFFRACTION99

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