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- PDB-7w36: Crystal structure of human Atg5 complexed with a stapled peptide -

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Basic information

Entry
Database: PDB / ID: 7w36
TitleCrystal structure of human Atg5 complexed with a stapled peptide
Components
  • Autophagy protein 5
  • Stapled ATG16L1-derived peptide
KeywordsLIGASE / Autophagy / Inhibitor / Complex / Stapled peptide
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 / 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 / C-terminal protein lipidation / negative regulation of autophagic cell death / cellular response to nitrosative stress / vacuole-isolation membrane contact site / 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 / negative thymic T cell selection / nucleophagy / protein localization to phagophore assembly site / corpus callosum development / phagophore assembly site membrane / cellular response to nitrogen starvation / negative stranded viral RNA replication / regulation of release of sequestered calcium ion into cytosol / endolysosome membrane / 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 / Macroautophagy / chaperone-mediated autophagy / Receptor Mediated Mitophagy / 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 / 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 / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
: / : / : / 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 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) / 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
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
AuthorsKurata, I. / Matoba, K. / Noda, N.N.
Funding support2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H05707
Japan Science and TechnologyJPMJCR20E3
CitationJournal: J.Am.Chem.Soc. / Year: 2022
Title: Targeting the ATG5-ATG16L1 Protein-Protein Interaction with a Hydrocarbon-Stapled Peptide Derived from ATG16L1 for Autophagy Inhibition.
Authors: Cui, J. / Ogasawara, Y. / Kurata, I. / Matoba, K. / Fujioka, Y. / Noda, N.N. / Shibasaki, M. / Watanabe, T.
History
DepositionNov 25, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 21, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Autophagy protein 5
B: Stapled ATG16L1-derived peptide


Theoretical massNumber of molelcules
Total (without water)35,3142
Polymers35,3142
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-14 kcal/mol
Surface area14080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.794, 73.083, 102.127
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: 32489.195 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 (E. coli) / References: UniProt: Q9H1Y0
#2: Protein/peptide Stapled ATG16L1-derived peptide / APG16-like 1


Mass: 2825.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q676U5
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: 2.31 Å3/Da / Density % sol: 46.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2M MgCl2, 0.1M Tris-HCl pH8.5

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Feb 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.87→40.249 Å / Num. obs: 14426 / % possible obs: 99.5 % / Redundancy: 3.6 % / Rrim(I) all: 0.14 / Net I/σ(I): 7.33
Reflection shellResolution: 2.87→3.03 Å / Num. unique obs: 2288 / CC1/2: 0.638

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TQ1

4tq1


Resolution: 3→40.249 Å / SU ML: 0.49 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 33.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2866 1274 10.09 %
Rwork0.2452 --
obs0.2494 12621 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→40.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2352 0 0 0 2352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042421
X-RAY DIFFRACTIONf_angle_d0.7923278
X-RAY DIFFRACTIONf_dihedral_angle_d13.3011448
X-RAY DIFFRACTIONf_chiral_restr0.043343
X-RAY DIFFRACTIONf_plane_restr0.005417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0002-3.12030.4051390.41821263X-RAY DIFFRACTION100
3.1203-3.26220.40861390.31241255X-RAY DIFFRACTION100
3.2622-3.43410.3561450.31411253X-RAY DIFFRACTION100
3.4341-3.64910.31061410.27361275X-RAY DIFFRACTION100
3.6491-3.93070.29851460.25371263X-RAY DIFFRACTION100
3.9307-4.32580.30091390.22161264X-RAY DIFFRACTION100
4.3258-4.95080.21671340.19931265X-RAY DIFFRACTION99
4.9508-6.23380.27221440.23541246X-RAY DIFFRACTION100
6.2338-40.2490.27371470.23141263X-RAY DIFFRACTION100

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