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- PDB-9jjd: Structural analysis of autophagy-related protein 8a in Drosophila... -

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Basic information

Entry
Database: PDB / ID: 9jjd
TitleStructural analysis of autophagy-related protein 8a in Drosophila melanogaster
ComponentsAutophagy-related 8a, isoform A
KeywordsLIPID TRANSPORT / LIPID TRAMSPORT / LIPID BINDING PROTEIN
Function / homology
Function and homology information


TBC/RABGAPs / type I terminal bouton / larval midgut cell programmed cell death / Macroautophagy / amphisome / GABA receptor binding / phosphatidylethanolamine binding / cellular response to nitrogen starvation / reticulophagy / autolysosome ...TBC/RABGAPs / type I terminal bouton / larval midgut cell programmed cell death / Macroautophagy / amphisome / GABA receptor binding / phosphatidylethanolamine binding / cellular response to nitrogen starvation / reticulophagy / autolysosome / autophagosome membrane / autophagosome assembly / autophagosome maturation / regulation of protein ubiquitination / mitophagy / autophagosome / determination of adult lifespan / macroautophagy / autophagy / protein tag activity / ubiquitin protein ligase binding / protein kinase binding
Similarity search - Function
Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Autophagy-related 8a, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsZhang, S.Q. / Luo, X. / Wu, D.X. / Liu, J. / Li, X.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32172461 China
CitationJournal: J.Agric.Food Chem. / Year: 2025
Title: Crystal Structure of Autophagy-Associated Protein 8 at 1.36 angstrom Resolution and Its Inhibitory Interactions with Indole Analogs.
Authors: Zhang, S. / Luo, X. / Yuan, X. / Wu, D. / Liu, J. / Zhao, K. / Xu, Y. / Zhou, J. / Li, X. / Li, Q.X.
History
DepositionSep 13, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 26, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Autophagy-related 8a, isoform A


Theoretical massNumber of molelcules
Total (without water)14,4171
Polymers14,4171
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.450, 58.990, 68.850
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-related 8a, isoform A / LD05816p


Mass: 14416.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly)
Gene: Atg8a, Atg-8a, ATG8, Atg8, atg8, ATG8/LC3, Atg8/LC3, ATG8a, Atg8A, atg8A, atg8a, Atg8alpha, BcDNA:LD05816, CG1534, dAtg8a, DmAtg8a, Dmel\CG32672, DrAtg8a, LC3, LC3/Atg8, CG32672, Dmel_CG32672
Production host: Escherichia coli (E. coli) / References: UniProt: Q9W2S2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.29 Å3/Da / Density % sol: 46.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-Tris pH=6.5, 26 (W/V) PEG MME 5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.36→29.73 Å / Num. obs: 29174 / % possible obs: 99.9 % / Redundancy: 11.7 % / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.025 / Rrim(I) all: 0.085 / Net I/σ(I): 14.7
Reflection shellResolution: 1.36→1.4 Å / Rmerge(I) obs: 0.967 / Num. unique obs: 2111 / Rpim(I) all: 0.395 / Rrim(I) all: 1.047 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XDSdata scaling
PHENIX(1.20.1_4487: ???)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.36→29.73 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 22.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2205 2000 6.87 %
Rwork0.1801 --
obs0.1828 29111 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.36→29.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1018 0 0 130 1148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011057
X-RAY DIFFRACTIONf_angle_d1.0981423
X-RAY DIFFRACTIONf_dihedral_angle_d5.523141
X-RAY DIFFRACTIONf_chiral_restr0.096144
X-RAY DIFFRACTIONf_plane_restr0.013185
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.390.45691390.35531882X-RAY DIFFRACTION99
1.39-1.430.33351410.28221911X-RAY DIFFRACTION100
1.43-1.470.25661400.2151904X-RAY DIFFRACTION100
1.47-1.520.25771400.17821903X-RAY DIFFRACTION100
1.52-1.580.20751410.17611901X-RAY DIFFRACTION100
1.58-1.640.24061430.18041932X-RAY DIFFRACTION100
1.64-1.710.23971410.18231915X-RAY DIFFRACTION100
1.71-1.80.24691420.1941925X-RAY DIFFRACTION100
1.8-1.920.20991420.18741928X-RAY DIFFRACTION100
1.92-2.060.25191430.18111928X-RAY DIFFRACTION100
2.06-2.270.21131430.17721945X-RAY DIFFRACTION100
2.27-2.60.18941440.17611959X-RAY DIFFRACTION100
2.6-3.280.1941470.17841992X-RAY DIFFRACTION100
3.28-29.730.22361540.16812086X-RAY DIFFRACTION100

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