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- PDB-2n9x: LC3 FUNDC1 complex structure -

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Basic information

Entry
Database: PDB / ID: 2n9x
TitleLC3 FUNDC1 complex structure
Components
  • FUN14 domain-containing protein 1
  • Microtubule-associated proteins 1A/1B light chain 3B
KeywordsPROTEIN BINDING/PEPTIDE / protein/peptide / LC3 interacting region (LIR) / PROTEIN BINDING-PEPTIDE complex
Function / homology
Function and homology information


SARS-CoV-2 modulates autophagy / ceramide binding / autophagy of mitochondrion / cellular response to nitrogen starvation / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / Macroautophagy / Receptor Mediated Mitophagy / axoneme ...SARS-CoV-2 modulates autophagy / ceramide binding / autophagy of mitochondrion / cellular response to nitrogen starvation / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / Macroautophagy / Receptor Mediated Mitophagy / axoneme / organelle membrane / autophagosome membrane / mitophagy / autophagosome maturation / autophagosome assembly / autophagosome / endomembrane system / PINK1-PRKN Mediated Mitophagy / Pexophagy / cellular response to starvation / mitochondrial membrane / macroautophagy / autophagy / KEAP1-NFE2L2 pathway / Translation of Replicase and Assembly of the Replication Transcription Complex / cytoplasmic vesicle / microtubule binding / microtubule / mitochondrial outer membrane / response to hypoxia / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / mitochondrion / cytosol
Similarity search - Function
FUN14 / FUN14 family / 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
FUN14 domain-containing protein 1 / Microtubule-associated proteins 1A/1B light chain 3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model1
AuthorsXia, B. / Kuang, Y.
CitationJournal: Autophagy / Year: 2016
Title: Structural basis for the phosphorylation of FUNDC1 LIR as a molecular switch of mitophagy.
Authors: Kuang, Y. / Ma, K. / Zhou, C. / Ding, P. / Zhu, Y. / Chen, Q. / Xia, B.
History
DepositionDec 14, 2015Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 7, 2017Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Microtubule-associated proteins 1A/1B light chain 3B
B: FUN14 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)16,2212
Polymers16,2212
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 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Microtubule-associated proteins 1A/1B light chain 3B / Autophagy-related protein LC3 B / Autophagy-related ubiquitin-like modifier LC3 B / MAP1 light ...Autophagy-related protein LC3 B / Autophagy-related ubiquitin-like modifier LC3 B / MAP1 light chain 3-like protein 2 / MAP1A/MAP1B light chain 3 B / MAP1A/MAP1B LC3 B / Microtubule-associated protein 1 light chain 3 beta


Mass: 14150.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3B, MAP1ALC3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GZQ8
#2: Protein/peptide FUN14 domain-containing protein 1


Mass: 2071.023 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 10-26 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8IVP5

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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
1313D CBCA(CO)NH
1413D HN(CA)CB
1513D HN(CO)CA
1613D HNCA
1713D HNCO
1813D HBHA(CO)NH
1913D (H)CCH-COSY
11013D (H)CCH-TOCSY
11113D 1H-15N NOESY
11213D 1H-13C NOESY
11313D 1H-13C NOESY aromatic
11412D 1H-1H TOCSY
11512D 1H-1H NOESY
11613D 1H-13C NOESY

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Sample preparation

DetailsContents: 0.9 mM [U-13C; U-15N] entity_1-1, 1.8 mM entity_2-2, 100 mM sodium chloride-3, 25 mM sodium phosphate-4, 10 % [U-2H] D2O-5, 1 % DSS-6, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.9 mMentity_1-1[U-13C; U-15N]1
1.8 mMentity_2-21
100 mMsodium chloride-31
25 mMsodium phosphate-41
10 %D2O-5[U-2H]1
1 %DSS-61
Sample conditionsIonic strength: 0.15 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Bruker AvanceBrukerAVANCE8002

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Processing

NMR software
NameDeveloperClassification
CYANAGuntert, Mumenthaler and Wuthrichstructure solution
AmberCase, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollmanrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsProtein chi angle constraints total count: 112 / Protein other angle constraints total count: 338 / Protein phi angle constraints total count: 102 / Protein psi angle constraints total count: 83
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 6.5 ° / Maximum upper distance constraint violation: 0.26 Å / Representative conformer: 1

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