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- PDB-2lue: LC3B OPTN-LIR Ptot complex structure -

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Basic information

Entry
Database: PDB / ID: 2lue
TitleLC3B OPTN-LIR Ptot complex structure
Components
  • Microtubule-associated proteins 1A/1B light chain 3B
  • Optineurin
KeywordsPROTEIN BINDING / Selective autophagy / LC3 proteins / Signaling protein / Protein-peptide complex / Phosphoserine
Function / homology
Function and homology information


SARS-CoV-2 modulates autophagy / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / ceramide binding / Golgi ribbon formation / negative regulation of receptor recycling / cell death / protein localization to Golgi apparatus / positive regulation of xenophagy / Golgi to plasma membrane protein transport / cellular response to nitrogen starvation ...SARS-CoV-2 modulates autophagy / parkin-mediated stimulation of mitophagy in response to mitochondrial depolarization / ceramide binding / Golgi ribbon formation / negative regulation of receptor recycling / cell death / protein localization to Golgi apparatus / positive regulation of xenophagy / Golgi to plasma membrane protein transport / cellular response to nitrogen starvation / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / regulation of canonical NF-kappaB signal transduction / TNFR1-induced proapoptotic signaling / K63-linked polyubiquitin modification-dependent protein binding / Macroautophagy / Receptor Mediated Mitophagy / Golgi organization / axoneme / organelle membrane / autophagosome membrane / mitophagy / autophagosome maturation / autophagosome assembly / autophagosome / polyubiquitin modification-dependent protein binding / cellular response to unfolded protein / endomembrane system / positive regulation of autophagy / negative regulation of canonical NF-kappaB signal transduction / PINK1-PRKN Mediated Mitophagy / Pexophagy / cellular response to starvation / TNFR1-induced NF-kappa-B signaling pathway / mitochondrial membrane / macroautophagy / Regulation of TNFR1 signaling / trans-Golgi network / autophagy / recycling endosome membrane / Regulation of PLK1 Activity at G2/M Transition / KEAP1-NFE2L2 pathway / protein-macromolecule adaptor activity / Translation of Replicase and Assembly of the Replication Transcription Complex / cytoplasmic vesicle / microtubule binding / defense response to Gram-negative bacterium / microtubule / Golgi membrane / intracellular membrane-bounded organelle / innate immune response / ubiquitin protein ligase binding / perinuclear region of cytoplasm / Golgi apparatus / signal transduction / mitochondrion / nucleoplasm / identical protein binding / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
C2H2 type zinc-finger / NF-kappa-B essential modulator NEMO, N-terminal / NF-kappa-B essential modulator NEMO / NEMO, Zinc finger / Zinc finger CCHC NOA-type profile. / NF-kappa-B essential modulator NEMO, CC2-LZ domain / Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 ...C2H2 type zinc-finger / NF-kappa-B essential modulator NEMO, N-terminal / NF-kappa-B essential modulator NEMO / NEMO, Zinc finger / Zinc finger CCHC NOA-type profile. / NF-kappa-B essential modulator NEMO, CC2-LZ domain / Leucine zipper of domain CC2 of NEMO, NF-kappa-B essential modulator / 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
Optineurin / Microtubule-associated proteins 1A/1B light chain 3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / restrained energy refinement
Model detailsclosest to the average, model2
AuthorsRogov, V.V. / Rozenknop, A. / Loehr, F. / Guentert, P. / Doetsch, V.
CitationJournal: Biochem.J. / Year: 2013
Title: Structural basis for phosphorylation-triggered autophagic clearance of Salmonella.
Authors: Rogov, V.V. / Suzuki, H. / Fiskin, E. / Wild, P. / Kniss, A. / Rozenknop, A. / Kato, R. / Kawasaki, M. / McEwan, D.G. / Lohr, F. / Guntert, P. / Dikic, I. / Wakatsuki, S. / Dotsch, V.
History
DepositionJun 13, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Data collection / Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_conn / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Microtubule-associated proteins 1A/1B light chain 3B
B: Optineurin


Theoretical massNumber of molelcules
Total (without water)16,2112
Polymers16,2112
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 #1closest to the average

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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: 13965.106 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 5-119
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3B, MAP1ALC3 / Production host: Escherichia coli (E. coli) / Strain (production host): NEB T7 Express / References: UniProt: Q9GZQ8
#2: Protein/peptide Optineurin / E3-14.7K-interacting protein / FIP-2 / Huntingtin yeast partner L / Huntingtin-interacting protein ...E3-14.7K-interacting protein / FIP-2 / Huntingtin yeast partner L / Huntingtin-interacting protein 7 / HIP-7 / Huntingtin-interacting protein L / NEMO-related protein / Optic neuropathy-inducing protein / Transcription factor IIIA-interacting protein / TFIIIA-IntP


Mass: 2245.813 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 169-185 / Source method: obtained synthetically / Details: The peptide was chemically synthesized. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96CV9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: Complex structure of the autophagy modifier LC3B with synthetic OPTN-LIR peptide in totally phosphorylated form (all five serines are phosphoserines)
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1312D 1H-13C HSQC aromatic
1413D HN(CA)CB
1513D HNCO
1613D (H)CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY aliphatic
1913D 1H-13C NOESY aromatic
11013D NOESY-[13C,1H]-HSQC 13C/15N filtered in F1
11122D 1H-1H NOESY F1,F2 13C/15N filtered
11213D NOESY-[15N,1H]-FHSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [U-98% 13C; U-98% 15N] entity_1-1, 4.9 mM entity_2-2, 70 mM sodium phosphate-3, 30 mM sodium chloride-4, 0.3 mM DSS-5, 5 mM Protease inhibitors cocktail-6, 95% H2O/5% D2O95% H2O/5% D2O
22.5 mM [U-98% 13C; U-98% 15N] entity_1-7, 0.4 mM entity_2-8, 70 mM sodium phosphate-9, 30 mM sodium chloride-10, 0.3 mM DSS-11, 5 mM Protease inhibitors cocktail-12, 95% H2O/5% D2O95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMentity_1-1[U-98% 13C; U-98% 15N]1
4.9 mMentity_2-21
70 mMsodium phosphate-31
30 mMsodium chloride-41
0.3 mMDSS-51
5 mMProtease inhibitors cocktail-61
2.5 mMentity_1-7[U-98% 13C; U-98% 15N]2
0.4 mMentity_2-82
70 mMsodium phosphate-92
30 mMsodium chloride-102
0.3 mMDSS-112
5 mMProtease inhibitors cocktail-122
Sample conditionsIonic strength: 0.05 / pH: 6.8 / Pressure: ambient / Temperature: 288 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE9001
Bruker AvanceBrukerAVANCE8002
Bruker AvanceBrukerAVANCE7003
Bruker AvanceBrukerAVANCE6004
Bruker AvanceBrukerAVANCE5005

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin2Bruker Biospincollection
TopSpin2Bruker Biospinchemical shift calculation
TopSpin2Bruker Biospinprocessing
Sparky3.114Goddarddata analysis
Sparky3.114Goddardchemical shift assignment
Sparky3.114Goddardpeak picking
CYANA2Guntert, Mumenthaler and Wuthrichstructure solution
OPALpKoradi, Billeter and Guntertrefinement
RefinementMethod: restrained energy refinement / Software ordinal: 1
NMR constraintsNOE constraints total: 3472 / NOE intraresidue total count: 750 / NOE long range total count: 1240 / NOE medium range total count: 715 / NOE sequential total count: 767 / Hydrogen bond constraints total count: 94 / Protein phi angle constraints total count: 126 / Protein psi angle constraints total count: 130
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Maximum upper distance constraint violation: 0.1 Å / Representative conformer: 2

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