[English] 日本語
Yorodumi
- PDB-6hoi: Structure of Beclin1 LIR motif bound to GABARAPL1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hoi
TitleStructure of Beclin1 LIR motif bound to GABARAPL1
Components
  • Beclin-1BECN1
  • Gamma-aminobutyric acid receptor-associated protein-like 1
KeywordsSIGNALING PROTEIN / Autophagy / ATG8 / LIR
Function / homology
Function and homology information


cellular response to aluminum ion / glycophagy / 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 / positive regulation of attachment of mitotic spindle microtubules to kinetochore / cytoplasmic side of mitochondrial outer membrane / negative regulation of lysosome organization ...cellular response to aluminum ion / glycophagy / 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 / positive regulation of attachment of mitotic spindle microtubules to kinetochore / cytoplasmic side of mitochondrial outer membrane / negative regulation of lysosome organization / positive regulation of autophagosome assembly / engulfment of apoptotic cell / negative regulation of autophagosome assembly / receptor catabolic process / Tat protein binding / GABA receptor binding / protein targeting to lysosome / suppression by virus of host autophagy / early endosome to late endosome transport / cellular response to nitrogen starvation / late endosome to vacuole transport / phagophore assembly site / Translation of Replicase and Assembly of the Replication Transcription Complex / response to iron(II) ion / negative regulation of programmed cell death / : / SMAD protein signal transduction / phosphatidylinositol-3-phosphate biosynthetic process / Macroautophagy / autophagy of mitochondrion / mitotic metaphase chromosome alignment / lysosome organization / beta-tubulin binding / positive regulation of cardiac muscle hypertrophy / mitophagy / neuron development / p38MAPK cascade / autophagosome maturation / autophagosome membrane / autophagosome assembly / autophagosome / negative regulation of reactive oxygen species metabolic process / regulation of macroautophagy / response to vitamin E / cellular response to glucose starvation / cellular defense response / phosphatidylinositol 3-kinase binding / phagocytic vesicle / amyloid-beta metabolic process / positive regulation of autophagy / JNK cascade / cellular response to epidermal growth factor stimulus / cellular response to copper ion / cellular response to amino acid starvation / positive regulation of intrinsic apoptotic signaling pathway / regulation of cytokinesis / regulation of autophagy / phospholipid binding / macroautophagy / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / response to lead ion / trans-Golgi network / cytoplasmic vesicle membrane / ISG15 antiviral mechanism / autophagy / cellular response to hydrogen peroxide / protein-macromolecule adaptor activity / GTPase binding / Translation of Replicase and Assembly of the Replication Transcription Complex / protein-containing complex assembly / defense response to virus / microtubule / response to hypoxia / nuclear body / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / endosome membrane / Ub-specific processing proteases / endosome / response to xenobiotic stimulus / negative regulation of cell population proliferation / cell division / dendrite / apoptotic process / ubiquitin protein ligase binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / protein kinase binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / Golgi apparatus / endoplasmic reticulum / identical protein binding / cytosol / cytoplasm
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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 / BECN1 / 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 / Ethylene glycol


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


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


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Processing

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more