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- PDB-3a7o: The crystal structure of the coiled-coil domain of Saccharomyces ... -

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Basic information

Entry
Database: PDB / ID: 3a7o
TitleThe crystal structure of the coiled-coil domain 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 / SAD / Resolution: 2.5 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 1.2Oct 18, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / struct_ref_seq_dif
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
C: Autophagy protein 16
D: Autophagy protein 16
E: Autophagy protein 16
F: Autophagy protein 16


Theoretical massNumber of molelcules
Total (without water)50,1036
Polymers50,1036
Non-polymers00
Water1,47782
1
A: Autophagy protein 16
B: Autophagy protein 16


Theoretical massNumber of molelcules
Total (without water)16,7012
Polymers16,7012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-27 kcal/mol
Surface area8350 Å2
MethodPISA
2
C: Autophagy protein 16
D: Autophagy protein 16


Theoretical massNumber of molelcules
Total (without water)16,7012
Polymers16,7012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-22 kcal/mol
Surface area8130 Å2
MethodPISA
3
E: Autophagy protein 16
F: Autophagy protein 16


Theoretical massNumber of molelcules
Total (without water)16,7012
Polymers16,7012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-25 kcal/mol
Surface area8700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.891, 127.891, 77.808
Angle α, β, γ (deg.)90, 90, 90
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11F-130-

HOH

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Components

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


Mass: 8350.517 Da / Num. of mol.: 6 / Fragment: coiled-coil domain
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.: 82 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.8M ammonium chloride, 0.1M sodium acetate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1951
21101
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU11.1
ROTATING ANODERIGAKU MICROMAX-00721.5418
Detector
TypeIDDetectorDate
RAYONIX MX-2251CCDJul 8, 2008
RIGAKU RAXIS VII2IMAGE PLATEJul 23, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.11
21.54181
ReflectionResolution: 2.5→50 Å / Num. all: 22847 / Num. obs: 22847 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 17.9 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 19.4
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.282 / Num. unique all: 2240 / % possible all: 100

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Processing

Software
NameClassification
HKL-2000data collection
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.5→46.08 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.299 1094 -RANDOM
Rwork0.272 ---
all0.273 22516 --
obs0.273 22516 98.4 %-
Displacement parametersBiso mean: 56.5 Å2
Baniso -1Baniso -2Baniso -3
1-5.66 Å20 Å20 Å2
2--5.66 Å20 Å2
3----11.32 Å2
Refinement stepCycle: LAST / Resolution: 2.5→46.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2662 0 0 82 2744
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d16.2
X-RAY DIFFRACTIONc_improper_angle_d0.66
X-RAY DIFFRACTIONc_mcbond_it1.53
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.034
RfactorNum. reflection% reflection
Rfree0.431 160 -
Rwork0.346 --
obs-3534 94.7 %

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