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- SASDC73: Atg1-Atg13-Atg17-Atg31-Atg29 Minipentamer Complex (Serine/threoni... -

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Basic information

Entry
Database: SASBDB / ID: SASDC73
SampleAtg1-Atg13-Atg17-Atg31-Atg29 Minipentamer Complex
  • 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)
  • Autophagy-related protein 17 (protein), Atg17, Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
  • Autophagy-related protein 29 (protein), Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
  • KLLA0A10637p (protein), Atg31, Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
Function / homology
Function and homology information


positive regulation of autophagosome size / : / autophagy of peroxisome / Cvt vesicle assembly / : / phagophore / vacuole-isolation membrane contact site / Atg1/ULK1 kinase complex / protein targeting to vacuole involved in autophagy / cytoplasm to vacuole targeting by the Cvt pathway ...positive regulation of autophagosome size / : / autophagy of peroxisome / Cvt vesicle assembly / : / phagophore / vacuole-isolation membrane contact site / Atg1/ULK1 kinase complex / protein targeting to vacuole involved in autophagy / 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 kinase regulator activity / phagophore assembly site / reticulophagy / extrinsic component of membrane / protein kinase activator activity / activation of protein kinase activity / autophagosome assembly / SNARE binding / autophagy / protein transport / 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 17 / Autophagy-related protein 31 / Autophagy-related protein 29 / Autophagy-related protein 29 superfamily / Atg29, N-terminal / Autophagy-related protein 31 / Atg29 N-terminal domain / Autophagy protein ATG17-like domain / Autophagy protein ATG17-like domain / Serine/threonine-protein kinase Atg1-like, tMIT domain ...Autophagy-related protein 17 / Autophagy-related protein 31 / Autophagy-related protein 29 / Autophagy-related protein 29 superfamily / Atg29, N-terminal / Autophagy-related protein 31 / Atg29 N-terminal domain / Autophagy protein ATG17-like domain / Autophagy protein ATG17-like domain / Serine/threonine-protein kinase Atg1-like, tMIT domain / Atg1-like, MIT domain 1 / Serine/threonine-protein kinase Atg1-like / Autophagy-related protein 13, N-terminal / Autophagy-related protein 13 / Autophagy-related protein 13 / 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
Autophagy-related protein 17 / Serine/threonine-protein kinase ATG1 / Autophagy-related protein 29 / Autophagy-related protein 13 / KLLA0A10637p
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

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Models

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Sample

SampleName: Atg1-Atg13-Atg17-Atg31-Atg29 Minipentamer Complex / Specimen concentration: 0.70-2.60 / Entity id: 633 / 634 / 635 / 636 / 637
BufferName: 20 mM Tris, 200 mM NaCl / 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
Entity #635Name: Atg17 / Type: protein / Description: Autophagy-related protein 17 / Formula weight: 49.864 / Num. of mol.: 2
Source: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
References: UniProt: Q6CS99
Sequence: MSDAATTIPS DEIDKLWNKA RNQLVEAQVE CEESLKILSK VRTEMDSSQK SRFKLKFILN CLVNQVEFFK NIMLEKCIST ELIDNEWSKL VLVEIVNDVS YWQNEITTKM KILQGTKYDL TDDHSSLSDF ICMDHVDILQ QKIDEIPIIK QQVTNIRQHY KSIKDRIENQ ...Sequence:
MSDAATTIPS DEIDKLWNKA RNQLVEAQVE CEESLKILSK VRTEMDSSQK SRFKLKFILN CLVNQVEFFK NIMLEKCIST ELIDNEWSKL VLVEIVNDVS YWQNEITTKM KILQGTKYDL TDDHSSLSDF ICMDHVDILQ QKIDEIPIIK QQVTNIRQHY KSIKDRIENQ LVAVKLKKLR TYFDSHFSRD SKNNLFKLLE SDYVTELNEF ENELADFLRS ITDHFDKCTI LKEQQIPLPD LKELFQIVKK DDTQLENIRE LVFETGLEVK AFSKKVNETI SEIMDKIGGF HLLASKIVTE LEKCEEYLSI FQKIANLVFV YKESCIKKIE QVQQLCEFYD KFKLGYKNLL RERDRRKATA LQMEKILKEC QEKLQALSDA DLDQRQQFLL ENGDYLPENI WPGYIDDMES MYSFEYSIHN VPN
Entity #636Type: protein / Description: Autophagy-related protein 29 / Formula weight: 10.031 / Num. of mol.: 2
Source: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
References: UniProt: Q6CTU8
Sequence:
MNNDNTKVYV RVAGKRPENF VETKPFIWDS RRDKILWTKI SKIDSLEDMD WQELGADLGA PEPFLKKRSY TLFQNQLKVL SNQID
Entity #637Name: Atg31 / Type: protein / Description: KLLA0A10637p / Formula weight: 16.071 / Num. of mol.: 2
Source: Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 1267 / NRRL Y-1140 / WM37)
References: UniProt: Q6CX74
Sequence:
MESPVLLVKN ANAATNASNL GLLGQKQNSY TVDENTWFLN NISFIFEDDD PSQHDEDQLD YENVIIIDSE PSGTVNNVEM LSERWQLLAF DQNPRDNCIS LTVMNELSAD LGQNTDISGL DNLSKLYHER NAQIRKLLDS IAP

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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-Atg17-Atg31-Atg29 Minipentamer Complex / Measurement date: Dec 20, 2013 / Storage temperature: 10 °C / Cell temperature: 22 °C / Exposure time: 0.6 sec. / Unit: 1/A /
MinMax
Q0.0109 0.2719
Distance distribution function P(R)
Sofotware P(R): GNOM 4.5a / Number of points: 260 /
MinMax
Q0.009628 0.2719
P(R) point1 260
R0 340
Result
Experimental MW: 234 kDa / Type of curve: single_conc
P(R)P(R) errorGuinierGuinier error
Forward scattering, I0768.6 14 967.1 618
Radius of gyration, Rg9.97 nm0.1 10.29 nm5.8

MinMax
D-34
Guinier point1 6

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