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- PDB-4zdv: Crystal structure of LC3 in complex with FAM134B LIR -

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Basic information

Entry
Database: PDB / ID: 4zdv
TitleCrystal structure of LC3 in complex with FAM134B LIR
ComponentsMicrotubule-associated proteins 1A/1B light chain 3A
KeywordsPROTEIN TRANSPORT / Autophagy / ER-phagy / Complex
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 starvation / autophagosome / cellular response to amino acid 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 / 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 3A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKhaminets, A. / Grumati, P. / Dikic, I. / Akutsu, M.
CitationJournal: Nature / Year: 2015
Title: Regulation of endoplasmic reticulum turnover by selective autophagy.
Authors: Khaminets, A. / Heinrich, T. / Mari, M. / Grumati, P. / Huebner, A.K. / Akutsu, M. / Liebmann, L. / Stolz, A. / Nietzsche, S. / Koch, N. / Mauthe, M. / Katona, I. / Qualmann, B. / Weis, J. / ...Authors: Khaminets, A. / Heinrich, T. / Mari, M. / Grumati, P. / Huebner, A.K. / Akutsu, M. / Liebmann, L. / Stolz, A. / Nietzsche, S. / Koch, N. / Mauthe, M. / Katona, I. / Qualmann, B. / Weis, J. / Reggiori, F. / Kurth, I. / Hubner, C.A. / Dikic, I.
History
DepositionApr 19, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Jun 24, 2015Group: Database references
Revision 2.0Jan 10, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)15,3891
Polymers15,3891
Non-polymers00
Water2,090116
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.170, 62.170, 74.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-274-

HOH

21A-282-

HOH

31A-312-

HOH

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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: 15389.448 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 8% Tacsimate (Hampton Research) pH 8.0, 20% Poly ethylene glycol 3350

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→62.17 Å / Num. obs: 14123 / % possible obs: 100 % / Redundancy: 11.3 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 17.1
Reflection shellResolution: 1.8→1.9 Å / Rmerge(I) obs: 0.527 / Num. unique all: 2004

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ECI

3eci


Resolution: 1.8→47.709 Å / FOM work R set: 0.85 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.09 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2227 701 4.98 %
Rwork0.1843 13387 -
obs0.1861 14088 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.55 Å2 / Biso mean: 26.72 Å2 / Biso min: 11.34 Å2
Refinement stepCycle: final / Resolution: 1.8→47.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1045 0 0 116 1161
Biso mean---33.85 -
Num. residues----126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071067
X-RAY DIFFRACTIONf_angle_d1.0691439
X-RAY DIFFRACTIONf_chiral_restr0.09156
X-RAY DIFFRACTIONf_plane_restr0.005190
X-RAY DIFFRACTIONf_dihedral_angle_d14.127419
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8001-1.93910.26261410.204526072748
1.9391-2.13420.21851360.190126262762
2.1342-2.4430.20951520.186126232775
2.443-3.07790.24821310.206526812812
3.0779-47.7260.21051410.170528502991
Refinement TLS params.Method: refined / Origin x: 21.0685 Å / Origin y: -10.5138 Å / Origin z: 14.5465 Å
111213212223313233
T0.1189 Å2-0.0094 Å20.0137 Å2-0.168 Å20.0116 Å2--0.1507 Å2
L1.482 °2-0.0402 °20.3345 °2-0.7421 °20.0742 °2--1.1082 °2
S0.0565 Å °-0.0356 Å °-0.1539 Å °-0.0245 Å °-0.004 Å °-0.1293 Å °0.1371 Å °-0.0924 Å °-0.0547 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-6 - 119
2X-RAY DIFFRACTION1allB1 - 116

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