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- PDB-2lpu: Solution structures of KmAtg10 -

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Basic information

Entry
Database: PDB / ID: 2lpu
TitleSolution structures of KmAtg10
ComponentsKmAtg10
KeywordsPROTEIN TRANSPORT / Autophagy / E2-like / Atg10 / proteolysis
Function / homology
Function and homology information


ubiquitin-like protein transferase activity / phagophore assembly site membrane / Transferases; Acyltransferases; Aminoacyltransferases / autophagy / protein transport
Similarity search - Function
Yope Regulator; Chain: A, - #50 / Ubiquitin-like-conjugating enzyme Atg3/Atg10 / Autophagocytosis associated protein, active-site domain / Yope Regulator; Chain: A, / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-like-conjugating enzyme ATG10
Similarity search - Component
Biological speciesKluyveromyces marxianus (yeast)
MethodSOLUTION NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsYamaguchi, M. / Noda, N.N. / Yamamoto, H. / Shima, T. / Kumeta, H. / Kobashigawa, Y. / Akada, R. / Ohsumi, Y. / Inagaki, F.
CitationJournal: Structure / Year: 2012
Title: Structural insights into atg10-mediated formation of the autophagy-essential atg12-atg5 conjugate
Authors: Yamaguchi, M. / Noda, N.N. / Yamamoto, H. / Shima, T. / Kumeta, H. / Kobashigawa, Y. / Akada, R. / Ohsumi, Y. / Inagaki, F.
History
DepositionFeb 19, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KmAtg10


Theoretical massNumber of molelcules
Total (without water)17,7781
Polymers17,7781
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1lowest energy

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Components

#1: Protein KmAtg10


Mass: 17778.168 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces marxianus (yeast) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: W0TH64*PLUS
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. N-TERMINAL RESIDUES GPLGS ...A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST. N-TERMINAL RESIDUES GPLGS ARE CLONING ARTIFACT.

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1312D 1H-13C HSQC aromatic
1413D HNCO
1513D HN(CO)CA
1613D HNCA
1713D HBHA(CO)NH
1813D HN(CA)HA
1913D CBCA(CO)NH
11013D HN(CA)CB
11113D C(CO)NH
11213D (H)CCH-TOCSY aliphatic
11312D (HB)CB(CGCD)HD
11412D (HB)CB(CGCDCE)HE
11513D (H)CCH-TOCSY aromatic
11613D 1H-15N NOESY
11713D 1H-13C NOESY aliphatic
11813D 1H-13C NOESY aromatic

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Sample preparation

DetailsContents: 0.5 mM [U-99% 13C; U-99% 15N] KmAtg10-1, 50 mM sodium phosphate-2, 100 mM sodium chloride-3, 5 mM DTT-4, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMKmAtg10-1[U-99% 13C; U-99% 15N]1
50 mMsodium phosphate-21
100 mMsodium chloride-31
5 mMDTT-41
Sample conditionsIonic strength: 0.15 / pH: 6.8 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Agilent Unity INOVAAgilentUnity INOVA8001
Agilent Unity INOVAAgilentUnity INOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe2010.176.13.55Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky3.113Goddardchemical shift assignment
Sparky3.113Goddardpeak picking
Sparky3.113Goddardrefinement
TALOS+1.01Shen, Delaglio, Cornilescu, Baxstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CYANA2.1Guntert, Mumenthaler and Wuthrichrefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR constraintsProtein chi angle constraints total count: 0 / Protein phi angle constraints total count: 111 / Protein psi angle constraints total count: 114
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.14 Å / Representative conformer: 1

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