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- PDB-6a9e: Crystal structure of the N-terminal domain of Atg2 -

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Basic information

Entry
Database: PDB / ID: 6a9e
TitleCrystal structure of the N-terminal domain of Atg2
ComponentsEndolysin,Autophagy-related protein 2
KeywordsLIPID TRANSPORT
Function / homology
Function and homology information


: / lipid transfer activity / intermembrane lipid transfer / autophagy of mitochondrion / piecemeal microautophagy of the nucleus / phagophore assembly site membrane / phosphatidylinositol-3-phosphate binding / phagophore assembly site / reticulophagy / extrinsic component of membrane ...: / lipid transfer activity / intermembrane lipid transfer / autophagy of mitochondrion / piecemeal microautophagy of the nucleus / phagophore assembly site membrane / phosphatidylinositol-3-phosphate binding / phagophore assembly site / reticulophagy / extrinsic component of membrane / sporulation resulting in formation of a cellular spore / autophagosome assembly / viral release from host cell by cytolysis / peptidoglycan catabolic process / meiotic cell cycle / macroautophagy / autophagy / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium / endoplasmic reticulum membrane
Similarity search - Function
Autophagy-related protein 2, CAD motif / Autophagy-related protein 2, middle RBG modules / Autophagy-related protein 2/VPS13, C-terminal / Autophagy-related protein 2 / ATG2/VPS13, C terminal domain / Vacuolar protein sorting-associated protein 13-like, N-terminal domain / VPS13-like, N-terminal / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 ...Autophagy-related protein 2, CAD motif / Autophagy-related protein 2, middle RBG modules / Autophagy-related protein 2/VPS13, C-terminal / Autophagy-related protein 2 / ATG2/VPS13, C terminal domain / Vacuolar protein sorting-associated protein 13-like, N-terminal domain / VPS13-like, N-terminal / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily
Similarity search - Domain/homology
Endolysin / Autophagy-related protein 2 / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage RB59 (virus)
Schizosaccharomyces pombe (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.205 Å
AuthorsOsawa, T. / Noda, N.N.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2019
Title: Atg2 mediates direct lipid transfer between membranes for autophagosome formation.
Authors: Osawa, T. / Kotani, T. / Kawaoka, T. / Hirata, E. / Suzuki, K. / Nakatogawa, H. / Ohsumi, Y. / Noda, N.N.
History
DepositionJul 13, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title
Revision 1.2Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Apr 17, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endolysin,Autophagy-related protein 2
B: Endolysin,Autophagy-related protein 2


Theoretical massNumber of molelcules
Total (without water)88,1812
Polymers88,1812
Non-polymers00
Water0
1
A: Endolysin,Autophagy-related protein 2


Theoretical massNumber of molelcules
Total (without water)44,0901
Polymers44,0901
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Endolysin,Autophagy-related protein 2


Theoretical massNumber of molelcules
Total (without water)44,0901
Polymers44,0901
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.451, 62.695, 86.317
Angle α, β, γ (deg.)90.00, 91.83, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endolysin,Autophagy-related protein 2 / Lysis protein / Lysozyme / Muramidase / Meiotically up-regulated gene 36 protein


Mass: 44090.461 Da / Num. of mol.: 2 / Mutation: D20N, C54T, C97A
Source method: isolated from a genetically manipulated source
Details: The deleted regions in our structure were due to electron density disorder.
Source: (gene. exp.) Enterobacteria phage RB59 (virus), (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Gene: e, RB59_126, atg2, mug36, SPBC31E1.01c, SPBC660.18c / Strain: 972 / ATCC 24843 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A097J809, UniProt: O94649, UniProt: P00720*PLUS, lysozyme

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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: 2.83 Å3/Da / Density % sol: 56.5 %
Description: the entry contains Friedel pairs in F_Plus/Minus columns and I_Plus/Minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG400, ammonium sulfate, Bis-Tris

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.9692 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9692 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 29622 / % possible obs: 100 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 13.8
Reflection shellResolution: 3.2→3.26 Å / Rmerge(I) obs: 0.579

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.205→44.103 Å / Cross valid method: FREE R-VALUE / σ(F): 0.65 / Phase error: 26.34
Details: the entry contains Friedel pairs in F_Plus/Minus columns and I_Plus/Minus columns
RfactorNum. reflection% reflection
Rfree0.2664 1426 4.82 %
Rwork0.2239 --
obs0.2254 29590 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.205→44.103 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5023 0 0 0 5023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035075
X-RAY DIFFRACTIONf_angle_d0.6446882
X-RAY DIFFRACTIONf_dihedral_angle_d11.6521776
X-RAY DIFFRACTIONf_chiral_restr0.025855
X-RAY DIFFRACTIONf_plane_restr0.003872
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2229-3.3380.27752040.26052728X-RAY DIFFRACTION93
3.338-3.47150.29181000.23632837X-RAY DIFFRACTION97
3.4715-3.62920.28941440.22682734X-RAY DIFFRACTION95
3.6292-3.82030.31071740.24092752X-RAY DIFFRACTION94
3.8203-4.05920.2687940.21732810X-RAY DIFFRACTION97
4.0592-4.37180.25891460.21222791X-RAY DIFFRACTION95
4.3718-4.81030.18631460.1882810X-RAY DIFFRACTION95
4.8103-5.50320.29111280.20792731X-RAY DIFFRACTION96
5.5032-6.92110.24091120.25112852X-RAY DIFFRACTION96
6.9211-31.3490.27371770.21992716X-RAY DIFFRACTION93

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