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- PDB-6hoi: Structure of Beclin1 LIR motif bound to GABARAPL1 -

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Basic information

Entry
Database: PDB / ID: 6hoi
TitleStructure of Beclin1 LIR motif bound to GABARAPL1
Components
  • Beclin-1
  • Gamma-aminobutyric acid receptor-associated protein-like 1
KeywordsSIGNALING PROTEIN / Autophagy / ATG8 / LIR
Function / homology
Function and homology information


cellular response to aluminum ion / positive regulation of stress granule assembly / phosphatidylinositol 3-kinase complex, class III / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / response to mitochondrial depolarisation / glycophagy / positive regulation of attachment of mitotic spindle microtubules to kinetochore / negative regulation of lysosome organization ...cellular response to aluminum ion / positive regulation of stress granule assembly / phosphatidylinositol 3-kinase complex, class III / cellular response to oxygen-glucose deprivation / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / response to mitochondrial depolarisation / glycophagy / positive regulation of attachment of mitotic spindle microtubules to kinetochore / negative regulation of lysosome organization / engulfment of apoptotic cell / positive regulation of autophagosome assembly / early endosome to late endosome transport / cytoplasmic side of mitochondrial outer membrane / negative regulation of autophagosome assembly / receptor catabolic process / protein targeting to lysosome / SMAD protein signal transduction / late endosome to vacuole transport / GABA receptor binding / Tat protein binding / phosphatidylethanolamine binding / phagophore assembly site / Translation of Replicase and Assembly of the Replication Transcription Complex / phosphatidylinositol-3-phosphate biosynthetic process / cellular response to nitrogen starvation / negative regulation of programmed cell death / lysosome organization / response to vitamin E / mitotic metaphase chromosome alignment / cytoplasmic pattern recognition receptor signaling pathway / response to iron(II) ion / positive regulation of cardiac muscle hypertrophy / Macroautophagy / RSV-host interactions / p38MAPK cascade / autophagosome membrane / autophagosome assembly / autophagosome maturation / amyloid-beta metabolic process / regulation of macroautophagy / cellular defense response / neuron development / beta-tubulin binding / phosphatidylinositol 3-kinase binding / cellular response to glucose starvation / mitophagy / positive regulation of intrinsic apoptotic signaling pathway / phagocytic vesicle / JNK cascade / positive regulation of autophagy / autophagosome / cytoplasmic vesicle membrane / cellular response to epidermal growth factor stimulus / cellular response to amino acid starvation / cellular response to copper ion / regulation of cytokinesis / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / macroautophagy / trans-Golgi network / circadian rhythm / phospholipid binding / response to lead ion / ISG15 antiviral mechanism / autophagy / cellular response to hydrogen peroxide / GTPase binding / protein-containing complex assembly / Translation of Replicase and Assembly of the Replication Transcription Complex / protein-macromolecule adaptor activity / defense response to virus / molecular adaptor activity / microtubule / response to hypoxia / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endosome / endosome membrane / Ub-specific processing proteases / regulation of autophagy / nuclear body / cilium / ciliary basal body / response to xenobiotic stimulus / negative regulation of cell population proliferation / cell division / intracellular membrane-bounded organelle / apoptotic process / dendrite / ubiquitin protein ligase binding / endoplasmic reticulum membrane / protein kinase binding / negative regulation of apoptotic process / SARS-CoV-2 activates/modulates innate and adaptive immune responses / endoplasmic reticulum / Golgi apparatus / identical protein binding / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Beclin-1, BH3 domain / Beclin-1 BH3 domain, Bcl-2-interacting / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain / Atg6/beclin, coiled-coil domain / Apg6 BARA domain / Apg6 coiled-coil region / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like ...Beclin-1, BH3 domain / Beclin-1 BH3 domain, Bcl-2-interacting / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain / Atg6/beclin, coiled-coil domain / Apg6 BARA domain / Apg6 coiled-coil region / 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
ACETATE ION / Beclin-1 / Gamma-aminobutyric acid receptor-associated protein-like 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.14 Å
AuthorsMouilleron, S. / Birgisdottir, A.B. / Bhujbal, Z. / Wirth, M. / Sjottem, E. / Evjen, G. / Zhang, W. / Lee, R. / O'Reilly, N. / Tooze, S. ...Mouilleron, S. / Birgisdottir, A.B. / Bhujbal, Z. / Wirth, M. / Sjottem, E. / Evjen, G. / Zhang, W. / Lee, R. / O'Reilly, N. / Tooze, S. / Lamark, T. / Johansen, T.
Funding support Norway, 2items
OrganizationGrant numberCountry
Research Council of Norway214448 Norway
Research Council of Norway249884 Norway
CitationJournal: Autophagy / Year: 2019
Title: Members of the autophagy class III phosphatidylinositol 3-kinase complex I interact with GABARAP and GABARAPL1 via LIR motifs.
Authors: Birgisdottir, A.B. / Mouilleron, S. / Bhujabal, Z. / Wirth, M. / Sjottem, E. / Evjen, G. / Zhang, W. / Lee, R. / O'Reilly, N. / Tooze, S.A. / Lamark, T. / Johansen, T.
History
DepositionSep 17, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jul 10, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 24, 2024Group: 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: Gamma-aminobutyric acid receptor-associated protein-like 1
B: Gamma-aminobutyric acid receptor-associated protein-like 1
F: Beclin-1
G: Beclin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5138
Polymers31,2744
Non-polymers2394
Water3,297183
1
A: Gamma-aminobutyric acid receptor-associated protein-like 1
G: Beclin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7584
Polymers15,6372
Non-polymers1212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1360 Å2
ΔGint-7 kcal/mol
Surface area7000 Å2
MethodPISA
2
B: Gamma-aminobutyric acid receptor-associated protein-like 1
F: Beclin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7554
Polymers15,6372
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-8 kcal/mol
Surface area6550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.990, 54.000, 138.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Gamma-aminobutyric acid receptor-associated protein-like 1 / Early estrogen-regulated protein / GABA(A) receptor-associated protein-like 1 / Glandular ...Early estrogen-regulated protein / GABA(A) receptor-associated protein-like 1 / Glandular epithelial cell protein 1 / GEC-1


Mass: 14598.667 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GABARAPL1, GEC1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H0R8
#2: Protein/peptide Beclin-1 / Coiled-coil myosin-like BCL2-interacting protein / Protein GT197


Mass: 1038.110 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q14457
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 1.94 Å3/Da / Density % sol: 36.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium acetate, 0.1M Hepes pH 7.5, 12% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.14→35.161 Å / Num. obs: 88324 / % possible obs: 99.34 % / Redundancy: 4.1 % / Biso Wilson estimate: 14 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.03 / Rpim(I) all: 0.01 / Rrim(I) all: 0.03 / Net I/σ(I): 18.2
Reflection shellResolution: 1.14→1.18 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 8545 / CC1/2: 0.58 / Rpim(I) all: 0.44 / Rrim(I) all: 0.78 / % possible all: 97.51

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R2Q

2r2q


Resolution: 1.14→35.161 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.32
RfactorNum. reflection% reflection
Rfree0.1657 4387 4.97 %
Rwork0.1448 --
obs0.1459 88324 99.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.14→35.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2076 0 16 183 2275
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092244
X-RAY DIFFRACTIONf_angle_d1.1433050
X-RAY DIFFRACTIONf_dihedral_angle_d23.522873
X-RAY DIFFRACTIONf_chiral_restr0.096313
X-RAY DIFFRACTIONf_plane_restr0.008400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.14-1.1530.26161370.26592596X-RAY DIFFRACTION95
1.153-1.16650.27241550.25082715X-RAY DIFFRACTION98
1.1665-1.18080.25761350.22082807X-RAY DIFFRACTION100
1.1808-1.19570.221460.19462738X-RAY DIFFRACTION99
1.1957-1.21140.21961500.18152756X-RAY DIFFRACTION100
1.2114-1.2280.22521420.17592812X-RAY DIFFRACTION100
1.228-1.24560.21241660.16742699X-RAY DIFFRACTION100
1.2456-1.26420.19721350.15922811X-RAY DIFFRACTION100
1.2642-1.28390.18311710.14972793X-RAY DIFFRACTION100
1.2839-1.3050.19911330.13792734X-RAY DIFFRACTION100
1.305-1.32750.15521420.12322831X-RAY DIFFRACTION100
1.3275-1.35160.15221330.12562793X-RAY DIFFRACTION100
1.3516-1.37760.17421200.12182804X-RAY DIFFRACTION100
1.3776-1.40570.17131440.11682774X-RAY DIFFRACTION100
1.4057-1.43630.14851500.11262778X-RAY DIFFRACTION100
1.4363-1.46970.16421520.10972807X-RAY DIFFRACTION100
1.4697-1.50650.14991450.10852796X-RAY DIFFRACTION100
1.5065-1.54720.13971410.1022811X-RAY DIFFRACTION100
1.5472-1.59270.15061460.10172809X-RAY DIFFRACTION100
1.5927-1.64410.16161540.10462787X-RAY DIFFRACTION100
1.6441-1.70290.13761280.10732830X-RAY DIFFRACTION100
1.7029-1.77110.151430.11772801X-RAY DIFFRACTION100
1.7711-1.85170.16191540.12092822X-RAY DIFFRACTION100
1.8517-1.94930.15291700.12362782X-RAY DIFFRACTION100
1.9493-2.07140.1411570.12592819X-RAY DIFFRACTION99
2.0714-2.23130.17851400.13192836X-RAY DIFFRACTION99
2.2313-2.45580.18771580.15282854X-RAY DIFFRACTION99
2.4558-2.81110.1671320.16122840X-RAY DIFFRACTION99
2.8111-3.54110.16071600.15782872X-RAY DIFFRACTION98
3.5411-35.17740.15741480.16583030X-RAY DIFFRACTION98

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