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- PDB-6aaf: Crystal structure of fission yeast Atg8 complexed with the helica... -

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Basic information

Entry
Database: PDB / ID: 6aaf
TitleCrystal structure of fission yeast Atg8 complexed with the helical AIM of Hfl1.
Components
  • Autophagy-related protein 8
  • Transmembrane protein 184 homolog C30D11.06c
KeywordsMEMBRANE PROTEIN / vacuole / autophagy
Function / homology
Function and homology information


TBC/RABGAPs / Receptor Mediated Mitophagy / Macroautophagy / vacuole organization / autophagy of mitochondrion / fungal-type vacuole / phosphatidylethanolamine binding / phagophore assembly site / fungal-type vacuole membrane / cellular response to nitrogen starvation ...TBC/RABGAPs / Receptor Mediated Mitophagy / Macroautophagy / vacuole organization / autophagy of mitochondrion / fungal-type vacuole / phosphatidylethanolamine binding / phagophore assembly site / fungal-type vacuole membrane / cellular response to nitrogen starvation / autophagosome membrane / autophagosome assembly / transmembrane transporter activity / autophagosome maturation / macroautophagy / transmembrane transport / protein transport / cytoplasmic vesicle / membrane fusion / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Organic solute transporter subunit alpha/Transmembrane protein 184 / Organic solute transporter Ostalpha / Organic solute transporter Ostalpha / 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 8 / Vacuole membrane protein hfl11
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.197 Å
AuthorsYamasaki, A. / Noda, N.N.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science25111004 Japan
CitationJournal: Elife / Year: 2018
Title: Lipidation-independent vacuolar functions of Atg8 rely on its noncanonical interaction with a vacuole membrane protein
Authors: Liu, X.M. / Yamasaki, A. / Du, X.M. / Coffman, V.C. / Ohsumi, Y. / Nakatogawa, H. / Wu, J.Q. / Noda, N.N. / Du, L.L.
History
DepositionJul 18, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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-related protein 8
B: Transmembrane protein 184 homolog C30D11.06c


Theoretical massNumber of molelcules
Total (without water)17,7372
Polymers17,7372
Non-polymers00
Water724
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-13 kcal/mol
Surface area7610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.798, 108.866, 35.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Autophagy-related protein 8 / Autophagy-related ubiquitin-like modifier atg8


Mass: 13876.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: atg8, SPBP8B7.24c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O94272
#2: Protein/peptide Transmembrane protein 184 homolog C30D11.06c / Hfl1(386-409)


Mass: 3860.346 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: SPAC30D11.06c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q09906
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 1.82 Å3/Da / Density % sol: 32.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 27.5% PEG8000, 0.2 M sodium acetate, 0.1 M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.197→35.12 Å / Num. obs: 7091 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.4 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 8.1
Reflection shellResolution: 2.197→2.33 Å / Rmerge(I) obs: 1.331 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 1101 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZPN

2zpn


Resolution: 2.197→35.12 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 37.59
RfactorNum. reflection% reflection
Rfree0.2593 702 9.97 %
Rwork0.2112 --
obs0.2161 7038 99.48 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.197→35.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1085 0 0 4 1089
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041107
X-RAY DIFFRACTIONf_angle_d0.731490
X-RAY DIFFRACTIONf_dihedral_angle_d14.37424
X-RAY DIFFRACTIONf_chiral_restr0.03163
X-RAY DIFFRACTIONf_plane_restr0.003190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1966-2.36620.47151310.37811228X-RAY DIFFRACTION99
2.3662-2.60430.42021470.32591226X-RAY DIFFRACTION99
2.6043-2.98090.34781340.27881250X-RAY DIFFRACTION100
2.9809-3.7550.28981410.22241274X-RAY DIFFRACTION100
3.755-35.12450.19451490.16241358X-RAY DIFFRACTION100
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)
11.43450.7296-1.80381.9969-0.60332.158-0.3465-1.8681-0.89690.72880.1958-2.19660.92181.09230.23890.59360.0568-0.05350.68590.14470.756122.144319.03217.3627
28.21073.59072.21648.2943-0.11722.9141-0.18841.0090.4402-0.75420.5932-0.5071-0.64690.66460.02420.5778-0.10320.08610.64610.01670.731519.176726.89646.1932
39.11662.9746-0.3614.7621.90445.6065-0.19350.7253-0.351-0.87080.5722-0.05960.7821-0.02210.0820.37010.0296-0.02660.4648-0.03230.481812.015517.49446.2073
48.69893.3379-0.58968.8009-0.58953.5927-0.08420.1583-1.4858-0.45120.0622-0.41540.91870.5674-0.00090.48560.09040.04260.5184-0.03670.54849.07668.52139.175
57.1154.10311.46312.40610.15545.08060.2458-0.0122-1.36950.00220.5711-1.39750.98450.48760.02360.7620.01110.01450.49360.02130.98974.41461.658914.7158
68.57341.98030.01777.91320.05626.90190.21090.22020.26860.0395-0.21090.92280.0686-0.3527-0.08230.35910.0347-0.01130.4509-0.00220.54491.588319.890512.793
72.6655-0.7679-3.07072.595-1.75246.853-0.7756-1.56890.20541.38410.377-0.2626-0.18190.57910.04830.4312-0.03120.00030.5197-0.02840.637413.060326.011613.0665
80.6341-0.69270.15052.24451.55622.27020.0563-0.789-0.5810.6981-0.5280.65570.89980.48230.28310.44940.0295-0.08890.51050.11030.81388.904810.974317.8019
90.70791.57152.10478.79323.80015.9845-1.13332.8771-1.73220.42351.265-3.37161.31120.8012-0.46841.1640.04150.35561.1753-0.52321.513719.657615.82341.7524
102.18732.4258-1.42349.677-1.54229.34420.92760.5043-1.3277-1.73150.0999-1.21720.5278-1.11370.01770.8974-0.14970.03750.9002-0.14940.75844.49427.8418-0.9274
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 24 )
3X-RAY DIFFRACTION3chain 'A' and (resid 25 through 35 )
4X-RAY DIFFRACTION4chain 'A' and (resid 36 through 68 )
5X-RAY DIFFRACTION5chain 'A' and (resid 69 through 79 )
6X-RAY DIFFRACTION6chain 'A' and (resid 80 through 98 )
7X-RAY DIFFRACTION7chain 'A' and (resid 99 through 104 )
8X-RAY DIFFRACTION8chain 'A' and (resid 105 through 113 )
9X-RAY DIFFRACTION9chain 'B' and (resid 386 through 391 )
10X-RAY DIFFRACTION10chain 'B' and (resid 392 through 407 )

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