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- PDB-6lan: Structure of CCDC50 and LC3B complex -

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Basic information

Entry
Database: PDB / ID: 6lan
TitleStructure of CCDC50 and LC3B complex
ComponentsCoiled-coil domain-containing protein 50,Microtubule-associated proteins 1A/1B light chain 3B
KeywordsPEPTIDE BINDING PROTEIN / autophagy / complex
Function / homology
Function and homology information


SARS-CoV-2 modulates autophagy / ceramide binding / 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 ...SARS-CoV-2 modulates autophagy / ceramide binding / 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 / sensory perception of sound / autophagy / KEAP1-NFE2L2 pathway / Translation of Replicase and Assembly of the Replication Transcription Complex / cytoplasmic vesicle / microtubule binding / microtubule / intracellular membrane-bounded organelle / ubiquitin protein ligase binding / mitochondrion / cytosol
Similarity search - Function
Coiled-coil domain-containing protein 50, N-terminal / Coiled-coil domain-containing protein 50 / Coiled-coil domain-containing protein 50 N-terminus / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Coiled-coil domain-containing protein 50 / Microtubule-associated proteins 1A/1B light chain 3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsLiu, L. / Li, J. / Hou, P.
CitationJournal: Cell Res. / Year: 2021
Title: A novel selective autophagy receptor, CCDC50, delivers K63 polyubiquitination-activated RIG-I/MDA5 for degradation during viral infection.
Authors: Hou, P. / Yang, K. / Jia, P. / Liu, L. / Lin, Y. / Li, Z. / Li, J. / Chen, S. / Guo, S. / Pan, J. / Wu, J. / Peng, H. / Zeng, W. / Li, C. / Liu, Y. / Guo, D.
History
DepositionNov 12, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 22, 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
A: Coiled-coil domain-containing protein 50,Microtubule-associated proteins 1A/1B light chain 3B


Theoretical massNumber of molelcules
Total (without water)15,8831
Polymers15,8831
Non-polymers00
Water5,152286
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8810 Å2
Unit cell
Length a, b, c (Å)65.776, 46.804, 46.154
Angle α, β, γ (deg.)90.000, 101.269, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-357-

HOH

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Components

#1: Protein Coiled-coil domain-containing protein 50,Microtubule-associated proteins 1A/1B light chain 3B / Protein Ymer / Autophagy-related protein LC3 B / Autophagy-related ubiquitin-like modifier LC3 B / ...Protein Ymer / 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: 15883.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The fusion protein of CCDC50 peptide (residues -7-1) and LC3B protein (residues 2-125).
Source: (gene. exp.) Homo sapiens (human) / Gene: CCDC50, C3orf6, MAP1LC3B, MAP1ALC3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8IVM0, UniProt: Q9GZQ8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / 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: 43.92 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 20% v/v 2-Propanol, 0.1 M sodium citrate pH 5.6, 20% w/v PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.41→50 Å / Num. obs: 24956 / % possible obs: 97.5 % / Redundancy: 12 % / Biso Wilson estimate: 13.89 Å2 / CC1/2: 0.997 / Rsym value: 0.048 / Net I/σ(I): 49.9
Reflection shellResolution: 1.41→1.43 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1672 / CC1/2: 0.902 / Rsym value: 0.65 / % possible all: 91.3

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Processing

Software
NameVersionClassification
Coot1.17_3644model building
PHENIX1.17_3644refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WAO

3wao


Resolution: 1.41→23.4 Å / SU ML: 0.1757 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.3261
RfactorNum. reflection% reflection
Rfree0.2189 1990 7.98 %
Rwork0.1916 --
obs0.1938 24952 93.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 24 Å2
Refinement stepCycle: LAST / Resolution: 1.41→23.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 0 286 1392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00441189
X-RAY DIFFRACTIONf_angle_d0.80071614
X-RAY DIFFRACTIONf_chiral_restr0.0718175
X-RAY DIFFRACTIONf_plane_restr0.0041214
X-RAY DIFFRACTIONf_dihedral_angle_d30.4593467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.41-1.450.359910.33191059X-RAY DIFFRACTION60.49
1.45-1.480.29371150.27261326X-RAY DIFFRACTION77.14
1.48-1.530.3241410.27771632X-RAY DIFFRACTION93.81
1.53-1.580.33341460.2541688X-RAY DIFFRACTION96.78
1.58-1.630.24861470.24491692X-RAY DIFFRACTION97.25
1.63-1.70.28051480.23961696X-RAY DIFFRACTION97.41
1.7-1.780.28331480.24211702X-RAY DIFFRACTION97.42
1.78-1.870.25331470.23251707X-RAY DIFFRACTION97.78
1.87-1.990.23641490.22381716X-RAY DIFFRACTION98.26
1.99-2.140.24121480.19511714X-RAY DIFFRACTION98.62
2.14-2.360.23561510.17541745X-RAY DIFFRACTION98.6
2.36-2.70.20421520.17321736X-RAY DIFFRACTION99.32
2.7-3.390.17521510.15711743X-RAY DIFFRACTION99.32
3.4-23.40.16561560.15621806X-RAY DIFFRACTION99.75

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