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- PDB-5d7g: Structure of human ATG5 E122D-ATG16L1 complex at 3.0 Angstroms -

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Basic information

Entry
Database: PDB / ID: 5d7g
TitleStructure of human ATG5 E122D-ATG16L1 complex at 3.0 Angstroms
Components
  • Autophagy protein 5
  • Autophagy-related protein 16-1
KeywordsAPOPTOSIS / Autophagy
Function / homology
Function and homology information


otolith development / regulation of autophagosome maturation / positive regulation of viral translation / response to fluoride / regulation of cytokine production involved in immune response / C-terminal protein lipidation / Atg8-family ligase activity / Atg12-Atg5-Atg16 complex / antigen processing and presentation of endogenous antigen / phagophore ...otolith development / regulation of autophagosome maturation / positive regulation of viral translation / response to fluoride / regulation of cytokine production involved in immune response / C-terminal protein lipidation / Atg8-family ligase activity / Atg12-Atg5-Atg16 complex / antigen processing and presentation of endogenous antigen / phagophore / vacuole-isolation membrane contact site / ubiquitin-like protein transferase activity / negative regulation of defense response to virus / cellular response to nitrosative stress / ventricular cardiac muscle cell development / positive regulation of stress granule assembly / microautophagy / negative regulation of autophagic cell death / regulation of cilium assembly / mitochondria-associated endoplasmic reticulum membrane contact site / aggrephagy / transferase complex / mucus secretion / response to fungus / xenophagy / negative thymic T cell selection / corpus callosum development / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / negative stranded viral RNA replication / regulation of release of sequestered calcium ion into cytosol / endolysosome membrane / cellular response to nitrogen starvation / response to iron(II) ion / negative regulation of phagocytosis / positive regulation of mucus secretion / negative regulation of cardiac muscle cell apoptotic process / negative regulation of type I interferon production / chaperone-mediated autophagy / Receptor Mediated Mitophagy / Macroautophagy / 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 / sperm midpiece / cardiac muscle cell apoptotic process / negative regulation of protein ubiquitination / negative regulation of innate immune response / PINK1-PRKN Mediated Mitophagy / post-translational protein modification / establishment of localization in cell / Negative regulators of DDX58/IFIH1 signaling / 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 / identical protein binding / membrane / 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. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / 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 / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsQiu, Y. / Schulman, B.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Elife / Year: 2016
Title: Mutation in ATG5 reduces autophagy and leads to ataxia with developmental delay.
Authors: Kim, M. / Sandford, E. / Gatica, D. / Qiu, Y. / Liu, X. / Zheng, Y. / Schulman, B.A. / Xu, J. / Semple, I. / Ro, S.H. / Kim, B. / Mavioglu, R.N. / Tolun, A. / Jipa, A. / Takats, S. / ...Authors: Kim, M. / Sandford, E. / Gatica, D. / Qiu, Y. / Liu, X. / Zheng, Y. / Schulman, B.A. / Xu, J. / Semple, I. / Ro, S.H. / Kim, B. / Mavioglu, R.N. / Tolun, A. / Jipa, A. / Takats, S. / Karpati, M. / Li, J.Z. / Yapici, Z. / Juhasz, G. / Lee, J.H. / Klionsky, D.J. / Burmeister, M.
History
DepositionAug 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
G: Autophagy protein 5
H: Autophagy-related protein 16-1


Theoretical massNumber of molelcules
Total (without water)165,4898
Polymers165,4898
Non-polymers00
Water181
1
A: Autophagy protein 5
B: Autophagy-related protein 16-1
C: Autophagy protein 5
D: Autophagy-related protein 16-1


Theoretical massNumber of molelcules
Total (without water)82,7454
Polymers82,7454
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5990 Å2
ΔGint-52 kcal/mol
Surface area26660 Å2
MethodPISA
2
E: Autophagy protein 5
F: Autophagy-related protein 16-1
G: Autophagy protein 5
H: Autophagy-related protein 16-1


Theoretical massNumber of molelcules
Total (without water)82,7454
Polymers82,7454
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-47 kcal/mol
Surface area27460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.114, 84.478, 151.849
Angle α, β, γ (deg.)90.00, 133.81, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 32878.621 Da / Num. of mol.: 4 / Mutation: E122D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATG5, APG5L, ASP / Cell line (production host): Hi5 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q9H1Y0
#2: Protein
Autophagy-related protein 16-1 / APG16-like 1


Mass: 8493.685 Da / Num. of mol.: 4 / Fragment: UNP residues 1-69
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATG16L1, APG16L, UNQ9393/PRO34307 / Cell line (production host): Hi5 / Production host: Baculovirus expression vector pFastBac1-HM / References: UniProt: Q676U5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 3.04 Å3/Da / Density % sol: 59.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Micro crystal: 37.5 mM MES, pH 5.2 to pH 5.8, 0.2 M sodium tartrate, and 11 to 13% polyethylene glycol 3350; Micor seeding condition:40 mM MES, pH 5.5, 0.2M sodium tartrate, 8.5% PEG3350, 10 mM DTT
PH range: 5.2-5.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 20, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 39496 / % possible obs: 98.9 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 14.3
Reflection shellResolution: 3→3.12 Å / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 2.3 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TQ0

4tq0


Resolution: 3→49.535 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2438 1920 4.86 %
Rwork0.1981 --
obs0.2003 39496 98.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→49.535 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9416 0 0 1 9417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089697
X-RAY DIFFRACTIONf_angle_d0.99413250
X-RAY DIFFRACTIONf_dihedral_angle_d13.7693353
X-RAY DIFFRACTIONf_chiral_restr0.0381463
X-RAY DIFFRACTIONf_plane_restr0.0061701
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.0750.41591470.30872666X-RAY DIFFRACTION99
3.075-3.15820.38231280.29962711X-RAY DIFFRACTION99
3.1582-3.25110.32811270.26822667X-RAY DIFFRACTION99
3.2511-3.3560.35691550.24952650X-RAY DIFFRACTION98
3.356-3.47590.28321620.22842625X-RAY DIFFRACTION99
3.4759-3.6150.32171250.21962708X-RAY DIFFRACTION100
3.615-3.77950.24971460.21182703X-RAY DIFFRACTION99
3.7795-3.97870.24381080.20722679X-RAY DIFFRACTION99
3.9787-4.22780.22261150.19232691X-RAY DIFFRACTION98
4.2278-4.55410.24631060.17882704X-RAY DIFFRACTION99
4.5541-5.0120.18441580.1672681X-RAY DIFFRACTION99
5.012-5.73630.24141660.18312634X-RAY DIFFRACTION98
5.7363-7.22350.2431660.20062696X-RAY DIFFRACTION99
7.2235-49.54180.19081110.17772761X-RAY DIFFRACTION97

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