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- PDB-6wy6: Crystal structure of S. cerevisiae Atg8 in complex with Ede1 (122... -

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Basic information

Entry
Database: PDB / ID: 6wy6
TitleCrystal structure of S. cerevisiae Atg8 in complex with Ede1 (1220-1247)
Components
  • Autophagy-related protein 8
  • EH domain-containing and endocytosis protein 1
KeywordsPROTEIN TRANSPORT / selective autophagy / clathrin-mediated endocytosis / intrinsic receptor / Atg8 / Ede1 / cryo-electron tomography / liquid-liquid phase separation / LLPS
Function / homology
Function and homology information


NRAGE signals death through JNK / G alpha (12/13) signalling events / CDC42 GTPase cycle / Clathrin-mediated endocytosis / RHOU GTPase cycle / Cvt vesicle membrane / RHOQ GTPase cycle / actin cortical patch organization / TBC/RABGAPs / Receptor Mediated Mitophagy ...NRAGE signals death through JNK / G alpha (12/13) signalling events / CDC42 GTPase cycle / Clathrin-mediated endocytosis / RHOU GTPase cycle / Cvt vesicle membrane / RHOQ GTPase cycle / actin cortical patch organization / TBC/RABGAPs / Receptor Mediated Mitophagy / regulation of membrane invagination / vacuole-isolation membrane contact site / protein targeting to vacuole involved in autophagy / Macroautophagy / actin cortical patch / cytoplasm to vacuole targeting by the Cvt pathway / cellular bud tip / nucleophagy / autophagy of mitochondrion / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus / cellular response to nitrogen starvation / phosphatidylethanolamine binding / cellular bud neck / mating projection tip / protein-containing complex localization / fungal-type vacuole membrane / phagophore assembly site / reticulophagy / endosomal transport / positive regulation of cytokinesis / autophagosome membrane / autophagosome assembly / autophagosome / regulation of macroautophagy / endoplasmic reticulum to Golgi vesicle-mediated transport / endoplasmic reticulum unfolded protein response / ubiquitin binding / mitochondrial membrane / macroautophagy / protein tag activity / autophagy / endocytosis / regulation of protein localization / protein transport / membrane fusion / calcium ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Cytoskeletal-regulatory complex EF hand / EH domain profile. / Eps15 homology domain / EH domain / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. ...Cytoskeletal-regulatory complex EF hand / EH domain profile. / Eps15 homology domain / EH domain / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / UBA/TS-N domain / Ubiquitin associated domain / Ubiquitin-associated domain / Ubiquitin-associated domain (UBA) profile. / UBA-like superfamily / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Autophagy-related protein 8 / EH domain-containing and endocytosis protein 1 / Autophagy-related protein 8
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.773 Å
AuthorsZheng, Y. / Wilfling, F. / Baumeister, W. / Schulman, B.A.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG) Germany
Max Planck Society Germany
European Research Council (ERC) Germany
CitationJournal: Mol.Cell / Year: 2020
Title: A Selective Autophagy Pathway for Phase-Separated Endocytic Protein Deposits.
Authors: Wilfling, F. / Lee, C.W. / Erdmann, P.S. / Zheng, Y. / Sherpa, D. / Jentsch, S. / Pfander, B. / Schulman, B.A. / Baumeister, W.
History
DepositionMay 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 16, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Oct 18, 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
B: Autophagy-related protein 8
A: Autophagy-related protein 8
C: EH domain-containing and endocytosis protein 1
D: EH domain-containing and endocytosis protein 1


Theoretical massNumber of molelcules
Total (without water)33,5524
Polymers33,5524
Non-polymers00
Water3,891216
1
B: Autophagy-related protein 8
D: EH domain-containing and endocytosis protein 1


Theoretical massNumber of molelcules
Total (without water)16,7762
Polymers16,7762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-8 kcal/mol
Surface area7740 Å2
MethodPISA
2
A: Autophagy-related protein 8
C: EH domain-containing and endocytosis protein 1


Theoretical massNumber of molelcules
Total (without water)16,7762
Polymers16,7762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-7 kcal/mol
Surface area8090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.642, 49.642, 123.446
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Autophagy-related protein 8 / Autophagy-related ubiquitin-like modifier ATG8 / Cytoplasm to vacuole targeting protein 5


Mass: 13603.682 Da / Num. of mol.: 2 / Fragment: UNP residues 1-116
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ATG8, APG8, AUT7, CVT5, SCY_0144 / Production host: Escherichia coli (E. coli) / References: UniProt: A6ZKM4, UniProt: P38182*PLUS
#2: Protein/peptide EH domain-containing and endocytosis protein 1 / Bud site selection protein 15 / Ede1


Mass: 3172.261 Da / Num. of mol.: 2 / Fragment: UNP residues 1220-1247 / Mutation: D1247E / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P34216
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.27 Å3/Da / Density % sol: 45.74 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 1.1 M ammonium sulfate, 0.1 M sodium acetate, pH 4.8, 0.01 M sodium iodide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 11, 2017
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.773→46.06 Å / Num. obs: 28870 / % possible obs: 99.97 % / Redundancy: 8.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.032 / Rrim(I) all: 0.068 / Rsym value: 0.06 / Χ2: 1.586 / Net I/σ(I): 29.36
Reflection shellResolution: 1.773→1.836 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.409 / Num. unique obs: 2848 / CC1/2: 0.862 / Rpim(I) all: 0.297 / Rrim(I) all: 0.586 / Rsym value: 0.503 / Χ2: 0.883 / % possible all: 99.65

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Processing

Software
NameVersionClassification
REFMACccp4refinement
Cootmodel building
PDB_EXTRACT3.25data extraction
HKL-2000data scaling
PHASERccp4phasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ZNP

2znp


Resolution: 1.773→46.057 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 21.61
RfactorNum. reflection% reflection
Rfree0.2028 1478 5.12 %
Rwork0.1756 --
obs0.1771 28859 99.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.86 Å2 / Biso mean: 28.8951 Å2 / Biso min: 13.76 Å2
Refinement stepCycle: final / Resolution: 1.773→46.057 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2189 0 0 216 2405
Biso mean---36.58 -
Num. residues----277
LS refinement shellResolution: 1.773→1.836 Å /
Rfactor% reflection
Rfree0.2676 -
Rwork0.224 -
obs-99.94 %

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