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- PDB-8fkm: Human Atg3 with deletions of residues 1 to 25 and 90 to 190 -

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Basic information

Entry
Database: PDB / ID: 8fkm
TitleHuman Atg3 with deletions of residues 1 to 25 and 90 to 190
ComponentsUbiquitin-like-conjugating enzyme ATG3
KeywordsLIGASE / Conjugase / Atg3 / Autophagy
Function / homology
Function and homology information


Atg12 transferase activity / Atg8-family conjugating enzyme activity / Atg8-family ligase activity / Atg12-Atg5-Atg16 complex / ubiquitin-like protein transferase activity / regulation of cilium assembly / glycophagy / nucleophagy / mitochondrial fragmentation involved in apoptotic process / autophagy of mitochondrion ...Atg12 transferase activity / Atg8-family conjugating enzyme activity / Atg8-family ligase activity / Atg12-Atg5-Atg16 complex / ubiquitin-like protein transferase activity / regulation of cilium assembly / glycophagy / nucleophagy / mitochondrial fragmentation involved in apoptotic process / autophagy of mitochondrion / phagophore assembly site / Transferases; Acyltransferases; Aminoacyltransferases / protein targeting to membrane / negative regulation of phagocytosis / Macroautophagy / autophagosome assembly / protein transport / protein ubiquitination / enzyme binding / cytoplasm / cytosol
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 ATG3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsYe, Y.S. / Tian, F.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM127730 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM127954 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA222349 United States
CitationJournal: Nat Commun / Year: 2023
Title: Multifaceted membrane interactions of human Atg3 promote LC3-phosphatidylethanolamine conjugation during autophagy.
Authors: Ye, Y. / Tyndall, E.R. / Bui, V. / Bewley, M.C. / Wang, G. / Hong, X. / Shen, Y. / Flanagan, J.M. / Wang, H.G. / Tian, F.
History
DepositionDec 21, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Database references / Category: citation / database_2
Item: _citation.page_last / _citation.pdbx_database_id_PubMed ..._citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ubiquitin-like-conjugating enzyme ATG3


Theoretical massNumber of molelcules
Total (without water)22,0911
Polymers22,0911
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 50structures with the lowest energy
RepresentativeModel #1medoid

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Components

#1: Protein Ubiquitin-like-conjugating enzyme ATG3 / Autophagy-related protein 3 / APG3-like / hApg3 / Protein PC3-96


Mass: 22091.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ATG3, APG3, APG3L / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NT62

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D HNCO
141isotropic13D HNCA
151isotropic13D HN(CA)CO
191isotropic13D HN(CA)CB
181isotropic13D HN(COCA)CB
176isotropic23D 1H-13C NOESY
161isotropic23D 1H-15N NOESY
1106isotropic13D (H)CCH-TOCSY
1117anisotropic12D ARTSY
1152anisotropic12D ARTSY
1143anisotropic12D ARTSY
1134anisotropic12D ARTSY
1125anisotropic12D ARTSY
1161isotropic1HBHA(CO)NH
1176isotropic12D Hb(CbCgCd)Hd
1186isotropic12D Hb(CbCgCdCe)He
1196isotropic13D 1H-13C NOESY aromatic
1206isotropic12D 1H-13C HSQC aromatic

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent systemDetails
solution1150 mM NaCl, 50 mM HEPES, 2 mM TCEP, 0.5 mM [U-13C; U-15N] human Atg3, 96% H2O/4% D2O13C, 15N96% H2O/4% D2O
solution2150 mM NaCl, 50 mM HEPES, 2 mM TCEP, 0.5 mM [U-13C; U-15N] human Atg3, 6.5 mg/mL Pf1 phage, 96% H2O/4% D2O15N, 2H96% H2O/4% D2O6.5 mg/mL phage
solution3150 mM NaCl, 50 mM HEPES, 2 mM TCEP, 0.5 mM [U-13C; U-15N] human Atg3, 7 % positive gel, 96% H2O/4% D2O15N, 2H96% H2O/4% D2O7% positive gel
solution4150 mM NaCl, 50 mM HEPES, 2 mM TCEP, 0.5 mM [U-13C; U-15N] human Atg3, 5 % negative gel, 96% H2O/4% D2O15N, 2H96% H2O/4% D2O5% negative gel
solution5150 mM NaCl, 50 mM HEPES, 2 mM TCEP, 0.5 mM [U-13C; U-15N] human Atg3, 5 % neutral gel, 96% H2O/4% D2O15N, 2H96% H2O/4% D2O5% neutral gel
solution6150 mM NaCl, 50 mM HEPES, 2 mM TCEP, 0.5 mM [U-13C; U-15N] human Atg3, 100% D2O13C, 15N100% D2O
solution7150 mM NaCl, 50 mM HEPES, 2 mM TCEP, 0.5 mM [U-13C; U-15N] human Atg3, 92% H2O/8% D2O15N, 2H92% H2O/8% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
150 mMNaClnatural abundance1
50 mMHEPESnatural abundance1
2 mMTCEPnatural abundance1
0.5 mMhuman Atg3[U-13C; U-15N]1
150 mMNaClnatural abundance2
50 mMHEPESnatural abundance2
2 mMTCEPnatural abundance2
0.5 mMhuman Atg3[U-13C; U-15N]2
6.5 mg/mLPf1 phagenatural abundance2
150 mMNaClnatural abundance3
50 mMHEPESnatural abundance3
2 mMTCEPnatural abundance3
0.5 mMhuman Atg3[U-13C; U-15N]3
7 %positive gelnatural abundance3
150 mMNaClnatural abundance4
50 mMHEPESnatural abundance4
2 mMTCEPnatural abundance4
0.5 mMhuman Atg3[U-13C; U-15N]4
5 %negative gelnatural abundance4
150 mMNaClnatural abundance5
50 mMHEPESnatural abundance5
2 mMTCEPnatural abundance5
0.5 mMhuman Atg3[U-13C; U-15N]5
5 %neutral gelnatural abundance5
150 mMNaClnatural abundance6
50 mMHEPESnatural abundance6
2 mMTCEPnatural abundance6
0.5 mMhuman Atg3[U-13C; U-15N]6
150 mMNaClnatural abundance7
50 mMHEPESnatural abundance7
2 mMTCEPnatural abundance7
0.5 mMhuman Atg3[U-13C; U-15N]7
Sample conditionsIonic strength: NaCl 150 mM / Label: condition_1 / pH: 6.5 / Pressure: 1 Pa / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II6001
Bruker AVANCE IIIBrukerAVANCE III8502

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichchemical shift assignment
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NMRViewJohnson, One Moon Scientificpeak picking
RefinementMethod: simulated annealing / Software ordinal: 3
NMR representativeSelection criteria: medoid
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 10

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