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- SASDCL3: Atg1-Atg13 Subcomplex (Serine/threonine-protein kinase ATG1, Atg1... -

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Basic information

Entry
Database: SASBDB / ID: SASDCL3
SampleAtg1-Atg13 Subcomplex
  • Serine/threonine-protein kinase ATG1 (protein), Atg1, Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
  • Autophagy-related protein 13 (protein), Atg13Autophagy-related protein 13, Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Function / homology
Function and homology information


: / Cvt vesicle assembly / : / phagophore / vacuole-isolation membrane contact site / protein targeting to vacuole involved in autophagy / Atg1/ULK1 kinase complex / cytoplasm to vacuole targeting by the Cvt pathway / autophagy of mitochondrion / protein localization to phagophore assembly site ...: / Cvt vesicle assembly / : / phagophore / vacuole-isolation membrane contact site / protein targeting to vacuole involved in autophagy / Atg1/ULK1 kinase complex / cytoplasm to vacuole targeting by the Cvt pathway / autophagy of mitochondrion / protein localization to phagophore assembly site / phagophore assembly site membrane / piecemeal microautophagy of the nucleus / protein kinase regulator activity / phagophore assembly site / reticulophagy / extrinsic component of membrane / activation of protein kinase activity / autophagosome assembly / molecular adaptor activity / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / ATP binding / cytosol
Similarity search - Function
Autophagy-related protein 13, N-terminal / Autophagy-related protein 13 / Autophagy-related protein 13 / Serine/threonine-protein kinase Atg1-like, tMIT domain / Atg1-like, MIT domain 1 / Serine/threonine-protein kinase Atg1-like / HORMA domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Autophagy-related protein 13, N-terminal / Autophagy-related protein 13 / Autophagy-related protein 13 / Serine/threonine-protein kinase Atg1-like, tMIT domain / Atg1-like, MIT domain 1 / Serine/threonine-protein kinase Atg1-like / HORMA domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase ATG1 / Autophagy-related protein 13
Similarity search - Component
Biological speciesKluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37) (yeast)
CitationJournal: Structure / Year: 2015
Title: Solution structure of the Atg1 complex: implications for the architecture of the phagophore assembly site.
Authors: Jürgen Köfinger / Michael J Ragusa / Il-Hyung Lee / Gerhard Hummer / James H Hurley /
Abstract: The biogenesis of autophagosomes commences at the phagophore assembly site (PAS), a protein-vesicle ultrastructure that is organized by the Atg1 complex. The Atg1 complex consists of the Atg1 ...The biogenesis of autophagosomes commences at the phagophore assembly site (PAS), a protein-vesicle ultrastructure that is organized by the Atg1 complex. The Atg1 complex consists of the Atg1 protein kinase, the intrinsically disordered region-rich Atg13, and the dimeric double crescent-shaped Atg17-Atg31-Atg29 subcomplex. We show that the PAS contains a relatively uniform ∼28 copies of Atg17, and upon autophagy induction, similar numbers of Atg1 and Atg13 molecules. We then apply ensemble refinement of small-angle X-ray scattering to determine the solution structures of the Atg1-Atg13 and Atg17-Atg31-Atg29 subcomplexes and the Atg1 complex, using a trimmed minipentamer tractable to biophysical studies. We observe tetramers of Atg1 pentamers that assemble via Atg17-Atg31-Atg29. This leads to a model for the higher organization of the Atg1 complex in PAS scaffolding.
Contact author
  • Michael Ragusa (Dartmouth College)

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Structure visualization

Downloads & links

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Models

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Sample

SampleName: Atg1-Atg13 Subcomplex / Specimen concentration: 1.00-5.20 / Entity id: 633 / 634
BufferName: 20 mM Tris, 200 mM NaCl, 2% glycerol / pH: 8
Entity #633Name: Atg1 / Type: protein / Description: Serine/threonine-protein kinase ATG1 / Formula weight: 30.664 / Num. of mol.: 2
Source: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
References: UniProt: Q6CSX2
Sequence: DSNITPAVES LAAKAFVMYS FAEMKFSQIL PTPPSSTDYD PLSDKRLSNG SCAIEDEEDL DQGRPPSNQT LTSATTKISS ATNVDTQIPA PELKKLCTES LLLYLKALTI LAASMKLTSK WWYENESKNC TLKLNILVQW IRDRFNECLD KAEFLRLKLH AINTSPNSQW ...Sequence:
DSNITPAVES LAAKAFVMYS FAEMKFSQIL PTPPSSTDYD PLSDKRLSNG SCAIEDEEDL DQGRPPSNQT LTSATTKISS ATNVDTQIPA PELKKLCTES LLLYLKALTI LAASMKLTSK WWYENESKNC TLKLNILVQW IRDRFNECLD KAEFLRLKLH AINTSPNSQW SDDDPVIFVE KLIYDRALDI SRNAARMEME SGNYNTCELA YATSLWMLEI LLDENFQFNE VYDDEYASNI TSLDESDKEM IKKYISSIAN RLKALKSKMV
Entity #634Name: Atg13Autophagy-related protein 13 / Type: protein / Description: Autophagy-related protein 13 / Formula weight: 8.726 / Num. of mol.: 2
Source: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
References: UniProt: Q6CWK2
Sequence:
FDRTAKPRKS TENPPEDLLE FVKLLEDKKE LNMKPNTILP QQDISNSLMR FQSMKSNNDA LSDNLSMSMS IDQPNV

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Experimental information

BeamInstrument name: Advanced Light Source (ALS) 12.3.1 (SIBYLS)
City: Berkeley, CA / 国: USA / Type of source: X-ray synchrotronSynchrotron
DetectorName: Pilatus3 X 2M / Pixsize x: 172 mm
Scan
Title: Atg1-Atg13 Subcomplex / Measurement date: Dec 10, 2013 / Cell temperature: 22 °C / Unit: 1/A /
MinMax
Q0.0089 0.2719
Distance distribution function P(R)
Sofotware P(R): GNOM 5.0 / Number of points: 449 /
MinMax
Q0.013936 0.240948
P(R) point1 449
R0 108.6
Result
Type of curve: single_conc /
ExperimentalPorod
MW78.5 kDa-
Volume-160 nm3

P(R)P(R) errorGuinierGuinier error
Forward scattering, I01013 2.2 1019.45 2.2
Radius of gyration, Rg3.3 nm-3.32 nm0.2

MinMax
D-10.9
Guinier point11 60

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