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- PDB-3a7p: The crystal structure of Saccharomyces cerevisiae Atg16 -

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Basic information

Entry
Database: PDB / ID: 3a7p
TitleThe crystal structure of Saccharomyces cerevisiae Atg16
ComponentsAutophagy protein 16
KeywordsPROTEIN TRANSPORT / coiled-coil / Autophagy / Coiled coil / Cytoplasmic vesicle / Transport / Vacuole
Function / homology
Function and homology information


Atg12-Atg5-Atg16 complex / vacuole-isolation membrane contact site / phagophore / cytoplasm to vacuole targeting by the Cvt pathway / autophagosome organization / nucleophagy / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / autophagy of mitochondrion ...Atg12-Atg5-Atg16 complex / vacuole-isolation membrane contact site / phagophore / cytoplasm to vacuole targeting by the Cvt pathway / autophagosome organization / nucleophagy / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / phagophore assembly site / autophagy of mitochondrion / autophagosome assembly / macroautophagy / autophagy / protein-macromolecule adaptor activity / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Autophagy-related protein 16 domain / Autophagy protein 16 (ATG16) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Autophagy protein 16
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsFujioka, Y. / Noda, N.N. / Inagaki, F.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Dimeric coiled-coil structure of Saccharomyces cerevisiae Atg16 and its functional significance in autophagy.
Authors: Fujioka, Y. / Noda, N.N. / Nakatogawa, H. / Ohsumi, Y. / Inagaki, F.
History
DepositionOct 1, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.4Nov 1, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Autophagy protein 16
B: Autophagy protein 16


Theoretical massNumber of molelcules
Total (without water)34,6072
Polymers34,6072
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3790 Å2
ΔGint-37 kcal/mol
Surface area12260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.191, 114.191, 156.286
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-163-

HOH

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Components

#1: Protein Autophagy protein 16 / Atg16 / Cytoplasm to vacuole targeting protein 11 / SAP18 homolog


Mass: 17303.604 Da / Num. of mol.: 2 / Mutation: D101A, E102A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ATG16 / Plasmid: pGEX6P / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q03818
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 4.25 Å3/Da / Density % sol: 71.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.5M calcium chloride, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. all: 15085 / Num. obs: 15085 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 13.2 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.1
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.3 / Num. unique all: 1204 / % possible all: 81

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3A7O

3a7o


Resolution: 2.8→46.1 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1390 -RANDOM
Rwork0.253 ---
all0.254 13763 --
obs0.254 13763 89.2 %-
Displacement parametersBiso mean: 70.6 Å2
Baniso -1Baniso -2Baniso -3
1--18.59 Å2-25.59 Å20 Å2
2---18.59 Å20 Å2
3---37.18 Å2
Refinement stepCycle: LAST / Resolution: 2.8→46.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1293 0 0 28 1321
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d16.2
X-RAY DIFFRACTIONc_improper_angle_d0.68
X-RAY DIFFRACTIONc_mcbond_it1.29
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.04
RfactorNum. reflection% reflection
Rfree0.481 147 -
Rwork0.436 --
obs-1652 66.2 %

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