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- PDB-5l83: Complex of potato ATG8 protein with a peptide from Irish potato f... -

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Basic information

Entry
Database: PDB / ID: 5l83
TitleComplex of potato ATG8 protein with a peptide from Irish potato famine pathogen effector protein PexRD54
Components
  • ASP-TRP-GLU-ILE-VAL
  • Autophagy-related protein
KeywordsIMMUNE SYSTEM / Autophagy-related protein 8 / ATG8 interacting moif / effector protein
Function / homology
Function and homology information


plant-type vacuole membrane / phosphatidylethanolamine binding / cellular response to nitrogen starvation / autophagosome membrane / autophagosome assembly / autophagosome maturation / defense response to fungus / mitophagy / cytoplasmic vesicle / cytoskeleton
Similarity search - Function
Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Autophagy-related protein 8C-like
Similarity search - Component
Biological speciesSolanum tuberosum (potato)
Phytophthora infestans (potato late blight agent)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMaqbool, A. / Hughes, R.K. / Banfield, M.J.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Basis of Host Autophagy-related Protein 8 (ATG8) Binding by the Irish Potato Famine Pathogen Effector Protein PexRD54.
Authors: Maqbool, A. / Hughes, R.K. / Dagdas, Y.F. / Tregidgo, N. / Zess, E. / Belhaj, K. / Round, A. / Bozkurt, T.O. / Kamoun, S. / Banfield, M.J.
History
DepositionJun 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Sep 28, 2016Group: Database references
Revision 1.3May 8, 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
C: ASP-TRP-GLU-ILE-VAL
D: ASP-TRP-GLU-ILE-VAL
A: Autophagy-related protein
B: Autophagy-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,10614
Polymers27,2474
Non-polymers85910
Water4,216234
1
C: ASP-TRP-GLU-ILE-VAL
B: Autophagy-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0367
Polymers13,6242
Non-polymers4125
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-43 kcal/mol
Surface area6750 Å2
MethodPISA
2
D: ASP-TRP-GLU-ILE-VAL
A: Autophagy-related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0707
Polymers13,6242
Non-polymers4465
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-55 kcal/mol
Surface area7130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.180, 172.180, 172.180
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number214
Space group name H-MI4132
Components on special symmetry positions
IDModelComponents
11A-422-

HOH

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Components

#1: Protein/peptide ASP-TRP-GLU-ILE-VAL


Mass: 660.715 Da / Num. of mol.: 2 / Source method: obtained synthetically
Source: (synth.) Phytophthora infestans (potato late blight agent)
#2: Protein Autophagy-related protein


Mass: 12962.998 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum tuberosum (potato) / Gene: PGSC0003DMG402022314, PGSC0003DMG400014422 / Production host: Escherichia coli (E. coli) / References: UniProt: M1C146
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 3.9 Å3/Da / Density % sol: 68.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M-ammonium sulphate, 0.1M Tris buffer, pH 8.0 and 36 % PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→86.09 Å / Num. obs: 32648 / % possible obs: 100 % / Redundancy: 32.8 % / Rsym value: 0.13 / Net I/σ(I): 27.4
Reflection shellResolution: 1.9→1.95 Å / Rsym value: 1.325

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→86.09 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.062 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.101 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19994 1715 5 %RANDOM
Rwork0.17476 ---
obs0.17604 32648 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.156 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.9→86.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1920 0 47 234 2201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192043
X-RAY DIFFRACTIONr_bond_other_d0.0010.021988
X-RAY DIFFRACTIONr_angle_refined_deg1.52.0052763
X-RAY DIFFRACTIONr_angle_other_deg0.79234600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6765242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.5623.40297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33415378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3681518
X-RAY DIFFRACTIONr_chiral_restr0.0850.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212204
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02434
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6772.173944
X-RAY DIFFRACTIONr_mcbond_other1.6622.171943
X-RAY DIFFRACTIONr_mcangle_it2.5573.2391176
X-RAY DIFFRACTIONr_mcangle_other2.5623.2411177
X-RAY DIFFRACTIONr_scbond_it2.7792.671099
X-RAY DIFFRACTIONr_scbond_other2.7782.671099
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2083.8721582
X-RAY DIFFRACTIONr_long_range_B_refined7.54418.9442499
X-RAY DIFFRACTIONr_long_range_B_other7.54318.9592500
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.951 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 117 -
Rwork0.242 2370 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
100000000000000-00.0068000.006800.0068000
20.381-0.1654-0.04290.3804-0.06472.3707-0.01450.0025-0.0199-0.0522-0.02010.0575-0.208-0.02070.03460.07610.0318-0.02460.02470.00810.059911.4647-13.5224-30.9853

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