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- PDB-7elg: LC3B modificated with a covalent probe -

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Basic information

Entry
Database: PDB / ID: 7elg
TitleLC3B modificated with a covalent probe
ComponentsMicrotubule-associated proteins 1A/1B light chain 3B
KeywordsPROTEIN BINDING / Inhibitor / Complex
Function / homology
Function and homology information


SARS-CoV-2 modulates autophagy / ceramide binding / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / cellular response to nitrogen starvation / autophagy of mitochondrion / Receptor Mediated Mitophagy / Macroautophagy / organelle membrane ...SARS-CoV-2 modulates autophagy / ceramide binding / phosphatidylethanolamine binding / Translation of Replicase and Assembly of the Replication Transcription Complex / TBC/RABGAPs / cellular response to nitrogen starvation / autophagy of mitochondrion / Receptor Mediated Mitophagy / Macroautophagy / organelle membrane / axoneme / autophagosome membrane / autophagosome maturation / autophagosome assembly / mitophagy / endomembrane system / autophagosome / Pexophagy / cellular response to starvation / PINK1-PRKN Mediated Mitophagy / macroautophagy / mitochondrial membrane / 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
Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Chem-8Z6 / Microtubule-associated proteins 1A/1B light chain 3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 Å
AuthorsFan, S. / Wan, W.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)81625022 China
National Natural Science Foundation of China (NSFC)91853205 China
National Natural Science Foundation of China (NSFC)81821005 China
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Inhibition of Autophagy by a Small Molecule through Covalent Modification of the LC3 Protein.
Authors: Fan, S. / Yue, L. / Wan, W. / Zhang, Y. / Zhang, B. / Otomo, C. / Li, Q. / Lin, T. / Hu, J. / Xu, P. / Zhu, M. / Tao, H. / Chen, Z. / Li, L. / Ding, H. / Yao, Z. / Lu, J. / Wen, Y. / Zhang, ...Authors: Fan, S. / Yue, L. / Wan, W. / Zhang, Y. / Zhang, B. / Otomo, C. / Li, Q. / Lin, T. / Hu, J. / Xu, P. / Zhu, M. / Tao, H. / Chen, Z. / Li, L. / Ding, H. / Yao, Z. / Lu, J. / Wen, Y. / Zhang, N. / Tan, M. / Chen, K. / Xie, Y. / Otomo, T. / Zhou, B. / Jiang, H. / Dang, Y. / Luo, C.
History
DepositionApr 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7823
Polymers14,4801
Non-polymers3022
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-11 kcal/mol
Surface area7730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.108, 54.766, 60.792
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 14479.567 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3B, MAP1ALC3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9GZQ8
#2: Chemical ChemComp-8Z6 / 2-methylidene-5-thiophen-2-yl-cyclohexane-1,3-dione


Mass: 206.261 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H10O2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.02 Å3/Da / Density % sol: 39.05 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 2.0M ammonium sulfate, 0.1M tri-sodium citrate (pH 5.6), 0.2M potassium sodium tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.599→30.402 Å / Num. obs: 16025 / % possible obs: 99.69 % / Redundancy: 12.8 % / Rmerge(I) obs: 0.03709 / Net I/σ(I): 36.72
Reflection shellResolution: 1.599→1.656 Å / Rmerge(I) obs: 0.469 / Num. unique obs: 1562

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VTU

3vtu


Resolution: 1.599→30.402 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2308 770 4.8 %
Rwork0.1929 15255 -
obs0.1948 16025 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.24 Å2 / Biso mean: 33.5022 Å2 / Biso min: 16.21 Å2
Refinement stepCycle: final / Resolution: 1.599→30.402 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1015 0 19 77 1111
Biso mean--43.79 40.93 -
Num. residues----122
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071056
X-RAY DIFFRACTIONf_angle_d1.0131423
X-RAY DIFFRACTIONf_chiral_restr0.058155
X-RAY DIFFRACTIONf_plane_restr0.005183
X-RAY DIFFRACTIONf_dihedral_angle_d16.493651
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.599-1.72250.2561310.21093002
1.7225-1.89580.22651470.20463023
1.8958-2.17010.2181720.19163006
2.1701-2.73380.2451510.20443056
Refinement TLS params.Method: refined / Origin x: 12.8016 Å / Origin y: -2.7713 Å / Origin z: -3.296 Å
111213212223313233
T0.1716 Å2-0.0053 Å20.0119 Å2-0.164 Å20.0212 Å2--0.1797 Å2
L1.5216 °20.3864 °20.3419 °2-1.4787 °20.393 °2--2.4187 °2
S-0.0254 Å °0.0482 Å °-0.0154 Å °-0.0111 Å °0.0668 Å °-0.0466 Å °-0.0463 Å °0.1495 Å °0.0001 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 123
2X-RAY DIFFRACTION1allB1
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allS1 - 81

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