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- PDB-2ncn: Solution Structure of the Autophagy-Related Protein LC3C -

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Basic information

Entry
Database: PDB / ID: 2ncn
TitleSolution Structure of the Autophagy-Related Protein LC3C
ComponentsAutophagy-Related Protein LC3C
KeywordsPROTEIN TRANSPORT
Function / homology
Function and homology information


protein exit from endoplasmic reticulum / aggrephagy / cellular response to nitrogen starvation / phosphatidylethanolamine binding / Macroautophagy / autophagosome maturation / autophagosome membrane / organelle membrane / autophagosome assembly / autophagosome ...protein exit from endoplasmic reticulum / aggrephagy / cellular response to nitrogen starvation / phosphatidylethanolamine binding / Macroautophagy / autophagosome maturation / autophagosome membrane / organelle membrane / autophagosome assembly / autophagosome / endomembrane system / cellular response to starvation / macroautophagy / cytoplasmic ribonucleoprotein granule / cytoplasmic vesicle / microtubule / ubiquitin protein ligase binding / cytosol
Similarity search - Function
Microtubule-associated protein 1A/1B light chain 3C / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Microtubule-associated proteins 1A/1B light chain 3C
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsKrichel, C. / Weiergraeber, O.H. / Willbold, D. / Neudecker, P.
CitationJournal: Sci Rep / Year: 2019
Title: Solution structure of the autophagy-related protein LC3C reveals a polyproline II motif on a mobile tether with phosphorylation site.
Authors: Krichel, C. / Mockel, C. / Schillinger, O. / Huesgen, P.F. / Sticht, H. / Strodel, B. / Weiergraber, O.H. / Willbold, D. / Neudecker, P.
History
DepositionApr 11, 2016Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2Jun 14, 2023Group: Database references / Other / Category: database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Autophagy-Related Protein LC3C


Theoretical massNumber of molelcules
Total (without water)14,8021
Polymers14,8021
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Autophagy-Related Protein LC3C / Autophagy-related protein LC3 C / Autophagy-related ubiquitin-like modifier LC3 C / MAP1 light ...Autophagy-related protein LC3 C / Autophagy-related ubiquitin-like modifier LC3 C / MAP1 light chain 3-like protein 3 / MAP1A/MAP1B light chain 3 C / MAP1A/MAP1B LC3 C / Microtubule-associated protein 1 light chain 3 gamma


Mass: 14802.249 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3C / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BXW4

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1132D 1H-1H TOCSY
1232D 1H-1H NOESY
1312D 1H-15N HSQC
1413D 1H-15N TOCSY
1513D 1H-15N NOESY
1613D 1H-15N 1H-15N NOESY
1723D HNHA
1832D 1H-13C HSQC
1923D HNCO
11023D HNCA
11123D HN(CA)CB
11223D CBCA(CO)NH
11323D HBHA(CO)NH
11423D C(CO)NH
11523D H(CCO)NH
11633D (H)CCH-COSY
11733D (H)CCH-COSY
11833D (H)CCH-TOCSY
11933D 1H-13C NOESY
12023D 1H-13C 1H-15N NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.35-0.7 mM [U-15N] Microtubule-associated protein light chain 3C (LC3C), 20 mM PIPES, 150 mM sodium chloride, 0.1 mM EDTA, 2% [U-2H] glycerol, 90% H2O, 10% D2O, 90% H2O/10% D2O90% H2O/10% D2O
20.35-0.7 mM [U-13C; U-15N] Microtubule-associated protein light chain 3C (LC3C), 20 mM PIPES, 150 mM sodium chloride, 0.1 mM EDTA, 2% [U-2H] glycerol, 90% H2O, 10% D2O, 90% H2O/10% D2O90% H2O/10% D2O
30.35-0.7 mM [U-13C; U-15N] Microtubule-associated protein light chain 3C (LC3C), 20 mM PIPES, 150 mM sodium chloride, 0.1 mM EDTA, 2% [U-2H] glycerol, 100% D2O, 100% D2O100% D2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mMMicrotubule-associated protein light chain 3C (LC3C)-1[U-15N]0.35-0.71
20 mMPIPES-21
150 mMsodium chloride-31
0.1 mMEDTA-41
2 %glycerol-5[U-2H]1
90 %H2O-61
10 %D2O-71
mMMicrotubule-associated protein light chain 3C (LC3C)-8[U-13C; U-15N]0.35-0.72
20 mMPIPES-92
150 mMsodium chloride-102
0.1 mMEDTA-112
2 %glycerol-12[U-2H]2
90 %H2O-132
10 %D2O-142
mMMicrotubule-associated protein light chain 3C (LC3C)-15[U-13C; U-15N]0.35-0.73
20 mMPIPES-163
150 mMsodium chloride-173
0.1 mMEDTA-183
2 %glycerol-19[U-2H]3
100 %D2O-203
Sample conditionsIonic strength: 171 / pH: 6.0 / Pressure: 1 atm / Temperature: 293.15 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE6001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameVersionDeveloperClassification
ARIA2Linge, O'Donoghue and Nilgesstructure solution
ARIA2Linge, O'Donoghue and Nilgesrefinement
NMRViewJohnson, One Moon Scientificchemical shift assignment
AnalysisCCPNchemical shift assignment
AnalysisCCPNdata analysis
AnalysisCornilescu, Delaglio and Baxchemical shift assignment
AnalysisCornilescu, Delaglio and Baxdata analysis
AnalysisCCPNchemical shift assignment
AnalysisCCPNdata analysis
AnalysisCornilescu, Delaglio and Baxchemical shift assignment
AnalysisCornilescu, Delaglio and Baxdata analysis
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readstructure solution
CNS1.21Brunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1162 / NOE intraresidue total count: 202 / NOE long range total count: 307 / NOE medium range total count: 266 / NOE sequential total count: 387 / Hydrogen bond constraints total count: 102 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 123 / Protein psi angle constraints total count: 91
NMR representativeSelection criteria: lowest energy
NMR ensembleAverage torsion angle constraint violation: 0.129 °
Conformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10 / Maximum lower distance constraint violation: 0.25 Å / Maximum torsion angle constraint violation: 3.77 ° / Maximum upper distance constraint violation: 0.34 Å / Torsion angle constraint violation method: CING
NMR ensemble rmsDistance rms dev: 0.017 Å / Distance rms dev error: 0.002 Å

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