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- PDB-5gmv: LC3B-FUNDC1 complex -

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Basic information

Entry
Database: PDB / ID: 5gmv
TitleLC3B-FUNDC1 complex
Components
  • Microtubule-associated proteins 1A/1B light chain 3B
  • Peptide from FUN14 domain-containing protein 1
KeywordsPROTEIN BINDING / LC3B / FUNDC1 / specific recognition / phosphorylation / selective mitophagy
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 / autophagosome membrane / organelle membrane / autophagosome maturation / mitophagy / 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)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsLv, M. / Wang, C. / Li, F.
CitationJournal: Protein Cell / Year: 2017
Title: Structural insights into the recognition of phosphorylated FUNDC1 by LC3B in mitophagy
Authors: Lv, M. / Wang, C. / Li, F. / Peng, J. / Wen, B. / Gong, Q. / Shi, Y. / Tang, Y.
History
DepositionJul 17, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
B: Microtubule-associated proteins 1A/1B light chain 3B
D: Peptide from FUN14 domain-containing protein 1
A: Microtubule-associated proteins 1A/1B light chain 3B
C: Peptide from FUN14 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)31,4864
Polymers31,4864
Non-polymers00
Water1,856103
1
B: Microtubule-associated proteins 1A/1B light chain 3B
D: Peptide from FUN14 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)15,7432
Polymers15,7432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-8 kcal/mol
Surface area7400 Å2
MethodPISA
2
A: Microtubule-associated proteins 1A/1B light chain 3B
C: Peptide from FUN14 domain-containing protein 1


Theoretical massNumber of molelcules
Total (without water)15,7432
Polymers15,7432
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-8 kcal/mol
Surface area7450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.537, 86.850, 40.537
Angle α, β, γ (deg.)90.000, 110.860, 90.000
Int Tables number4
Space group name H-MP1211

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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: 14710.027 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3B, MAP1ALC3 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q9GZQ8
#2: Protein/peptide Peptide from FUN14 domain-containing protein 1 / / FUNDC1 peptide


Mass: 1032.981 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8IVP5
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.19 Å3/Da / Density % sol: 43.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 30% PEG MME 2000, 0.1mM sodium cacodylate (pH 6.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.25→43.425 Å / Num. obs: 12052 / % possible obs: 96.8 % / Redundancy: 3.3 % / Rsym value: 0.076 / Net I/av σ(I): 4.728 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.25-2.373.30.3140.9195.6
2.37-2.523.30.1973.9196.5
2.52-2.693.30.1623.5196.4
2.69-2.93.30.1196.3197.5
2.9-3.183.40.0917.7197.8
3.18-3.563.30.0787.7197.8
3.56-4.113.20.0743.6197.4
4.11-5.033.40.04215.7194.6
5.03-7.123.50.05311.4198.7
7.12-37.8793.40.03220.5197.1

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VTU

3vtu


Resolution: 2.25→43.42 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.889 / SU B: 8.956 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.452 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2722 653 5.4 %RANDOM
Rwork0.2057 ---
obs0.2094 11381 96.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.08 Å2 / Biso mean: 33.026 Å2 / Biso min: 14.22 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-0.02 Å2
2--0 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.25→43.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 0 103 2225
Biso mean---34.77 -
Num. residues----256
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192158
X-RAY DIFFRACTIONr_bond_other_d0.0020.022114
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.9812906
X-RAY DIFFRACTIONr_angle_other_deg0.93334862
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2265252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.54723.889108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.66915414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0551518
X-RAY DIFFRACTIONr_chiral_restr0.0790.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212362
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02492
X-RAY DIFFRACTIONr_mcbond_it1.8233.1671020
X-RAY DIFFRACTIONr_mcbond_other1.8223.1641019
X-RAY DIFFRACTIONr_mcangle_it3.0584.731268
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 31 -
Rwork0.259 819 -
all-850 -
obs--95.61 %

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