[English] 日本語
Yorodumi
- PDB-8gu7: Selective targeting of the Beclin 2-Atg14L coiled coil complex by... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gu7
TitleSelective targeting of the Beclin 2-Atg14L coiled coil complex by stapled peptides promotes autophagy and endolysosomal trafficking of GPCRs
Components
  • Beclin 1-associated autophagy-related key regulator
  • Beclin-2
KeywordsSTRUCTURAL PROTEIN / PI3KC3 complex / Beclin 2 / Autophagy
Function / homology
Function and homology information


G protein-coupled receptor catabolic process / extrinsic component of omegasome membrane / phosphatidylinositol 3-kinase inhibitor activity / regulation of triglyceride metabolic process / Macroautophagy / extrinsic component of phagophore assembly site membrane / phosphatidylinositol 3-kinase complex, class III / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / response to mitochondrial depolarisation ...G protein-coupled receptor catabolic process / extrinsic component of omegasome membrane / phosphatidylinositol 3-kinase inhibitor activity / regulation of triglyceride metabolic process / Macroautophagy / extrinsic component of phagophore assembly site membrane / phosphatidylinositol 3-kinase complex, class III / phosphatidylinositol 3-kinase complex, class III, type II / phosphatidylinositol 3-kinase complex, class III, type I / response to mitochondrial depolarisation / mitochondria-associated endoplasmic reticulum membrane contact site / early endosome to late endosome transport / phosphatidylinositol 3-kinase regulator activity / protein targeting to lysosome / late endosome to vacuole transport / phagophore assembly site / phosphatidylinositol-3-phosphate biosynthetic process / cellular response to nitrogen starvation / post-transcriptional regulation of gene expression / endosome to lysosome transport / autophagosome membrane docking / negative regulation of protein phosphorylation / autophagosome membrane / axoneme / autophagosome assembly / autophagosome maturation / regulation of macroautophagy / phosphatidylinositol 3-kinase binding / cellular response to glucose starvation / mitophagy / phagocytic vesicle / protein-membrane adaptor activity / autophagosome / cellular response to starvation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / autophagy / positive regulation of protein phosphorylation / glucose homeostasis / GTPase binding / protein-macromolecule adaptor activity / defense response to virus / innate immune response / endoplasmic reticulum membrane / protein-containing complex binding
Similarity search - Function
UV radiation resistance protein/autophagy-related protein 14 / Vacuolar sorting 38 and autophagy-related subunit 14 / Atg6/Beclin / Atg6/Beclin C-terminal domain superfamily / Atg6, BARA domain / Atg6/beclin, coiled-coil domain / Apg6 BARA domain / Apg6 coiled-coil region
Similarity search - Domain/homology
Beclin-2 / Beclin 1-associated autophagy-related key regulator
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsQiu, X. / Zhao, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32000864 China
CitationJournal: Autophagy / Year: 2023
Title: The potent BECN2-ATG14 coiled-coil interaction is selectively critical for endolysosomal degradation of GPRASP1/GASP1-associated GPCRs.
Authors: Qiu, X. / Li, N. / Yang, Q. / Wu, S. / Li, X. / Pan, X. / Yamamoto, S. / Zhang, X. / Zeng, J. / Liao, J. / He, C. / Wang, R. / Zhao, Y.
History
DepositionSep 11, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beclin 1-associated autophagy-related key regulator
B: Beclin 1-associated autophagy-related key regulator
C: Beclin-2
D: Beclin-2


Theoretical massNumber of molelcules
Total (without water)35,9844
Polymers35,9844
Non-polymers00
Water1086
1
A: Beclin 1-associated autophagy-related key regulator
D: Beclin-2


Theoretical massNumber of molelcules
Total (without water)17,9922
Polymers17,9922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-16 kcal/mol
Surface area5390 Å2
MethodPISA
2
B: Beclin 1-associated autophagy-related key regulator
C: Beclin-2


Theoretical massNumber of molelcules
Total (without water)17,9922
Polymers17,9922
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1680 Å2
ΔGint-17 kcal/mol
Surface area5450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.500, 72.500, 68.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Beclin 1-associated autophagy-related key regulator / Barkor / Autophagy-related protein 14-like protein / Atg14L


Mass: 7021.218 Da / Num. of mol.: 2 / Mutation: C22L,C34S,G36L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Atg14, Atg14L, D14Ertd436e, Kiaa0831 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CDJ3
#2: Protein Beclin-2 / Beclin-1 autophagy-related pseudogene 1 / Beclin-1-like protein 1


Mass: 10970.921 Da / Num. of mol.: 2 / Mutation: R243L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BECN2, BECN1L1, BECN1P1 / Production host: Escherichia coli (E. coli) / References: UniProt: A8MW95
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.8 M Ammonium citrate tribasic, pH 7.0

-
Data collection

DiffractionMean temperature: 289 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.5→51.26 Å / Num. obs: 6736 / % possible obs: 99.8 % / Redundancy: 12.2 % / CC1/2: 0.995 / Net I/σ(I): 14.1
Reflection shellResolution: 2.5→2.64 Å / Num. unique obs: 951 / CC1/2: 0.972 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
PDB_EXTRACT3.27data extraction
SCALEITdata reduction
SCALAdata scaling
Arcimboldophasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8GT9

8gt9


Resolution: 2.6→41.11 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.909 / SU B: 0.012 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.252 / ESU R Free: 0.278 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2397 280 4.7 %RANDOM
Rwork0.2174 ---
obs0.2183 5705 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 172.69 Å2 / Biso mean: 66.999 Å2 / Biso min: 33.89 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å20 Å2
2---0.83 Å20 Å2
3---1.66 Å2
Refinement stepCycle: final / Resolution: 2.6→41.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1093 0 0 6 1099
Biso mean---59.6 -
Num. residues----132
LS refinement shellResolution: 2.6→2.667 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 16 -
Rwork0.189 410 -
all-426 -
obs--100 %

+
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