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- PDB-7r9z: LC3A in complex with Fragment 2-3 -

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Basic information

Entry
Database: PDB / ID: 7r9z
TitleLC3A in complex with Fragment 2-3
ComponentsMicrotubule-associated proteins 1A/1B light chain 3A
KeywordsHYDROLASE / mAtg8 / autophagy
Function / homology
Function and homology information


cellular response to oxygen-glucose deprivation / SMAD protein signal transduction / phosphatidylethanolamine binding / response to iron(II) ion / cellular response to nitrogen starvation / autophagy of mitochondrion / Receptor Mediated Mitophagy / Macroautophagy / organelle membrane / autolysosome ...cellular response to oxygen-glucose deprivation / SMAD protein signal transduction / phosphatidylethanolamine binding / response to iron(II) ion / cellular response to nitrogen starvation / autophagy of mitochondrion / Receptor Mediated Mitophagy / Macroautophagy / organelle membrane / autolysosome / p38MAPK cascade / autophagosome membrane / autophagosome maturation / autophagosome assembly / JNK cascade / cellular response to copper ion / cellular response to amino acid starvation / autophagosome / cellular response to starvation / PINK1-PRKN Mediated Mitophagy / macroautophagy / response to lead ion / phospholipid binding / cellular response to hydrogen peroxide / late endosome / microtubule binding / microtubule / intracellular membrane-bounded organelle / glutamatergic synapse / ubiquitin protein ligase binding / cytosol
Similarity search - Function
Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
(5-fluoro-1H-indol-3-yl)acetic acid / Microtubule-associated proteins 1A/1B light chain 3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsRouge, L. / Steffek, M. / Helgason, E. / Dueber, E. / Mulvihill, M.
CitationJournal: Biochemistry / Year: 2023
Title: A Multifaceted Hit-Finding Approach Reveals Novel LC3 Family Ligands.
Authors: Steffek, M. / Helgason, E. / Popovych, N. / Rouge, L. / Bruning, J.M. / Li, K.S. / Burdick, D.J. / Cai, J. / Crawford, T. / Xue, J. / Decurtins, W. / Fang, C. / Grubers, F. / Holliday, M.J. ...Authors: Steffek, M. / Helgason, E. / Popovych, N. / Rouge, L. / Bruning, J.M. / Li, K.S. / Burdick, D.J. / Cai, J. / Crawford, T. / Xue, J. / Decurtins, W. / Fang, C. / Grubers, F. / Holliday, M.J. / Langley, A. / Petersen, A. / Satz, A.L. / Song, A. / Stoffler, D. / Strebel, Q. / Tom, J.Y.K. / Skelton, N. / Staben, S.T. / Wichert, M. / Mulvihill, M.M. / Dueber, E.C.
History
DepositionJun 29, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_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 3A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4842
Polymers14,2901
Non-polymers1931
Water1,24369
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.463, 93.463, 32.322
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Space group name HallI4bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2

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Components

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


Mass: 14290.405 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3A / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H492
#2: Chemical ChemComp-2LZ / (5-fluoro-1H-indol-3-yl)acetic acid


Mass: 193.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H8FNO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.2M Sodium formate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→46.73 Å / Num. obs: 15116 / % possible obs: 100 % / Redundancy: 12.9 % / Biso Wilson estimate: 32.05 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 2
Reflection shellResolution: 1.72→1.75 Å / Rmerge(I) obs: 1.25 / Num. unique obs: 1508

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WAL

3wal


Resolution: 1.72→46.73 Å / SU ML: 0.2509 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.5216
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2185 1508 9.98 %
Rwork0.1924 13608 -
obs0.195 15116 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.88 Å2
Refinement stepCycle: LAST / Resolution: 1.72→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 14 69 1040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00841001
X-RAY DIFFRACTIONf_angle_d0.97761351
X-RAY DIFFRACTIONf_chiral_restr0.0666145
X-RAY DIFFRACTIONf_plane_restr0.0055178
X-RAY DIFFRACTIONf_dihedral_angle_d18.4718394
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.780.37531360.30721230X-RAY DIFFRACTION100
1.78-1.840.32531350.26021230X-RAY DIFFRACTION100
1.84-1.910.29161370.241214X-RAY DIFFRACTION100
1.91-20.27921360.22911228X-RAY DIFFRACTION100
2-2.10.28861350.2231226X-RAY DIFFRACTION100
2.11-2.240.25611360.21771219X-RAY DIFFRACTION100
2.24-2.410.21731370.19681241X-RAY DIFFRACTION100
2.41-2.650.24031380.21721233X-RAY DIFFRACTION100
2.65-3.040.26321360.20781240X-RAY DIFFRACTION100
3.04-3.820.21561350.18641248X-RAY DIFFRACTION99.93
3.83-46.730.16461470.15751299X-RAY DIFFRACTION100

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