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- PDB-6vzf: Crystal Structure of Atg11 Coiled-Coil 3 -

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Basic information

Entry
Database: PDB / ID: 6vzf
TitleCrystal Structure of Atg11 Coiled-Coil 3
ComponentsAutophagy-related protein 11
KeywordsSTRUCTURAL PROTEIN / coiled-coil / autophagy / scaffold
Function / homology
Function and homology information


regulation of cellular response to phosphate starvation / autophagy of peroxisome / Atg1/ULK1 kinase complex / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / positive regulation of autophagosome assembly / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus / phagophore assembly site membrane / autophagy of mitochondrion ...regulation of cellular response to phosphate starvation / autophagy of peroxisome / Atg1/ULK1 kinase complex / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / positive regulation of autophagosome assembly / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus / phagophore assembly site membrane / autophagy of mitochondrion / protein-containing complex localization / phagophore assembly site / reticulophagy / vacuolar membrane / extrinsic component of membrane / autophagosome assembly / SNARE binding / autophagy / molecular adaptor activity / positive regulation of protein phosphorylation / protein kinase binding
Similarity search - Function
Autophagy protein ATG17-like domain / Autophagy protein ATG17-like domain / Autophagy-related protein 11, C-terminal / Autophagy-related protein 11 / Autophagy-related protein 11
Similarity search - Domain/homology
Autophagy-related protein 11
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.03 Å
AuthorsMargolis, H.K. / Ragusa, M.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM128663 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM113132 United States
CitationJournal: J.Mol.Biol. / Year: 2020
Title: The Third Coiled Coil Domain of Atg11 Is Required for Shaping Mitophagy Initiation Sites.
Authors: Margolis, H.K. / Katzenell, S. / Leary, K.A. / Ragusa, M.J.
History
DepositionFeb 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 6, 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

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Assembly

Deposited unit
A: Autophagy-related protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,3102
Polymers12,2141
Non-polymers961
Water41423
1
A: Autophagy-related protein 11
hetero molecules

A: Autophagy-related protein 11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6194
Polymers24,4272
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area3730 Å2
ΔGint-53 kcal/mol
Surface area14000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.105, 103.105, 37.520
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-901-

SO4

21A-1007-

HOH

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Components

#1: Protein Autophagy-related protein 11 / Cytoplasm to vacuole targeting protein 9


Mass: 12213.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ATG11, CVT9, YPR049C, YP9499.07c / Plasmid: phis2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q12527
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 4.71 Å3/Da / Density % sol: 73.91 % / Description: rods
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 90 mM LiNaK, 0.1 M Buffer system 4 pH 6.5 (MOPSO + Bis Tris), 50% v/v precipitant mix 6 (25% w/v PEG 4000, 40% w/v 1,2,6-hexanetriol)

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Data collection

Diffraction
IDMean temperature (K)Ambient temp detailsCrystal-IDSerial crystal experiment
180cryo stream1N
280cryo stream1N
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 24-ID-C10.9791
SYNCHROTRONNSLS-II 17-ID-220.979344
Detector
TypeIDDetectorDate
DECTRIS PILATUS3 6M1PIXELNov 2, 2018
DECTRIS EIGER X 16M2PIXELOct 11, 2018
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.9793441
ReflectionResolution: 2.03→44.65 Å / Num. obs: 15063 / % possible obs: 99.9 % / Redundancy: 20.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.024 / Rrim(I) all: 0.109 / Net I/σ(I): 16.7 / Num. measured all: 303942
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.03-2.0819.51.8522169811100.6610.4271.9012100
9.08-44.6517.40.05932921890.9990.0140.0657.697.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.03→34.61 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.842 / SU ML: 0.078 / SU R Cruickshank DPI: 0.119 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.115
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2459 781 5.2 %RANDOM
Rwork0.2263 ---
obs0.2273 14270 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 175.3 Å2 / Biso mean: 88 Å2 / Biso min: 23.13 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.08 Å2-0 Å2
2---0.15 Å20 Å2
3---0.5 Å2
Refinement stepCycle: final / Resolution: 2.03→34.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms706 0 5 23 734
Biso mean--37.67 63.68 -
Num. residues----86
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.013715
X-RAY DIFFRACTIONr_bond_other_d0.0010.017648
X-RAY DIFFRACTIONr_angle_refined_deg1.7191.642960
X-RAY DIFFRACTIONr_angle_other_deg1.2841.5781519
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.723585
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67425.21746
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.93515148
X-RAY DIFFRACTIONr_dihedral_angle_4_deg29.307154
X-RAY DIFFRACTIONr_chiral_restr0.0990.295
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.02787
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02125
LS refinement shellResolution: 2.03→2.083 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 49 -
Rwork0.268 1061 -
all-1110 -
obs--100 %

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