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- PDB-6j04: Crystal structure of full length human LC3B delta G120 mutant (2_125) -

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Basic information

Entry
Database: PDB / ID: 6j04
TitleCrystal structure of full length human LC3B delta G120 mutant (2_125)
ComponentsMicrotubule-associated proteins 1A/1B light chain 3B
KeywordsPROTEIN BINDING / LC3B / microtubule-associated protein light chain-3 / Autophage
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 / 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 / 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 3B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.899 Å
AuthorsDing, Y. / Lu, B.X. / Wang, Z.Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Science Foundation (China)31470764 China
National Science Foundation (China)91527305 China
CitationJournal: Nature / Year: 2019
Title: Allele-selective lowering of mutant HTT protein by HTT-LC3 linker compounds
Authors: Li, Z.Y. / Wang, C. / Wang, Z.Y. / Zhu, C.G. / Li, J. / Sha, T. / Ma, L.X. / Gao, C. / Yang, Y. / Sun, Y.M. / Wang, J. / Sun, X.L. / Lu, C.Q. / Difiglia, M. / Mein, Y. / Ding, C. / Luo, S.Q. ...Authors: Li, Z.Y. / Wang, C. / Wang, Z.Y. / Zhu, C.G. / Li, J. / Sha, T. / Ma, L.X. / Gao, C. / Yang, Y. / Sun, Y.M. / Wang, J. / Sun, X.L. / Lu, C.Q. / Difiglia, M. / Mein, Y. / Ding, C. / Luo, S.Q. / Dang, Y.J. / Ding, Y. / Fei, Y.Y. / Lu, B.X.
History
DepositionDec 21, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
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

Downloads & links

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Assembly

Deposited unit
A: Microtubule-associated proteins 1A/1B light chain 3B
B: Microtubule-associated proteins 1A/1B light chain 3B
C: Microtubule-associated proteins 1A/1B light chain 3B
D: Microtubule-associated proteins 1A/1B light chain 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5076
Polymers58,3154
Non-polymers1922
Water4,450247
1
A: Microtubule-associated proteins 1A/1B light chain 3B
hetero molecules

C: Microtubule-associated proteins 1A/1B light chain 3B


Theoretical massNumber of molelcules
Total (without water)29,2543
Polymers29,1582
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area1240 Å2
ΔGint-22 kcal/mol
Surface area13480 Å2
MethodPISA
2
D: Microtubule-associated proteins 1A/1B light chain 3B

B: Microtubule-associated proteins 1A/1B light chain 3B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2543
Polymers29,1582
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_665x+1,y+1,z1
Buried area1300 Å2
ΔGint-22 kcal/mol
Surface area13500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.644, 56.475, 67.040
Angle α, β, γ (deg.)99.270, 97.450, 109.940
Int Tables number1
Space group name H-MP1

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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: 14578.832 Da / Num. of mol.: 4 / Fragment: UNP residues 2-125 / Mutation: deletion mutant G120
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP1LC3B, MAP1ALC3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9GZQ8
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.46 Å3/Da / Density % sol: 49.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.16M ammonium sulfate, 0.08M sodium acetate pH4.6, 20% (w/v) PEG4000; 20% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97892 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 1.899→30 Å / Num. obs: 40763 / % possible obs: 93.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.055 / Rrim(I) all: 0.108 / Χ2: 2.837 / Net I/σ(I): 6.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.973.60.56241310.7590.3390.6570.59994.4
1.97-2.053.50.4140900.8390.2470.480.66194.4
2.05-2.143.50.2940650.9070.1750.340.75993.1
2.14-2.253.40.21439700.9370.1320.2520.90691
2.25-2.393.70.17641550.9480.1040.2051.0995
2.39-2.583.60.14841310.9570.0880.1721.30494.6
2.58-2.843.50.12239480.9650.0740.1431.76690.8
2.84-3.253.70.09341930.9810.0550.1082.2196.1
3.25-4.093.60.08540350.9680.050.0994.31892.2
4.09-303.80.06240450.9840.0370.07313.9793

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX(1.12_2829: ???)refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UGM

1ugm


Resolution: 1.899→27.621 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 26.08
RfactorNum. reflection% reflection
Rfree0.262 2052 5.04 %
Rwork0.2094 --
obs0.212 40727 92.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.56 Å2 / Biso mean: 32.9684 Å2 / Biso min: 17.09 Å2
Refinement stepCycle: final / Resolution: 1.899→27.621 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3950 0 10 247 4207
Biso mean--38.43 39.84 -
Num. residues----474
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074030
X-RAY DIFFRACTIONf_angle_d0.7845419
X-RAY DIFFRACTIONf_chiral_restr0.052606
X-RAY DIFFRACTIONf_plane_restr0.005691
X-RAY DIFFRACTIONf_dihedral_angle_d6.7652505
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8987-1.94290.3061320.25452384251687
1.9429-1.99150.27821240.24092669279394
1.9915-2.04530.2661430.23112599274294
2.0453-2.10540.24941380.21622613275194
2.1054-2.17340.28451430.20912519266291
2.1734-2.2510.26061550.2112520267592
2.251-2.34110.28191310.20892628275995
2.3411-2.44760.2661330.20962677281095
2.4476-2.57650.2871470.21372597274495
2.5765-2.73780.26581430.21552584272793
2.7378-2.9490.30611360.22032513264991
2.949-3.24540.26311340.20862665279996
3.2454-3.7140.22231370.22637277495
3.714-4.67560.23321260.18312529265590
4.6756-27.62380.2791300.22362541267192

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