[English] 日本語
Yorodumi
- PDB-6ojj: Structure of ScAtg3 with truncations in N-terminal and flexible r... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ojj
TitleStructure of ScAtg3 with truncations in N-terminal and flexible region (FR)
ComponentsAutophagy-related protein 3,Autophagy-related protein 3
KeywordsLIGASE / Autophagy / E2
Function / homology
Function and homology information


Atg8-family ligase activity / phagophore / C-terminal protein lipidation / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / piecemeal microautophagy of the nucleus / autophagy of mitochondrion / phagophore assembly site / protein targeting to membrane ...Atg8-family ligase activity / phagophore / C-terminal protein lipidation / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / piecemeal microautophagy of the nucleus / autophagy of mitochondrion / phagophore assembly site / protein targeting to membrane / autophagosome assembly / protein transport / mitochondrion / cytosol / cytoplasm
Similarity search - Function
: / Ubiquitin-like-conjugating enzyme Atg3/Atg10 / Autophagocytosis associated protein, active-site domain
Similarity search - Domain/homology
Autophagy-related protein 3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.406 Å
AuthorsZheng, Y. / Qiu, Y. / Schulman, B.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)5P30CA021765, RO1GM069530 United States
CitationJournal: Nat Commun / Year: 2019
Title: A switch element in the autophagy E2 Atg3 mediates allosteric regulation across the lipidation cascade.
Authors: Zheng, Y. / Qiu, Y. / Grace, C.R.R. / Liu, X. / Klionsky, D.J. / Schulman, B.A.
History
DepositionApr 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Autophagy-related protein 3,Autophagy-related protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9173
Polymers25,7331
Non-polymers1842
Water41423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.078, 44.557, 66.200
Angle α, β, γ (deg.)90.00, 102.98, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Autophagy-related protein 3,Autophagy-related protein 3 / Autophagy-related E2-like conjugation enzyme ATG3


Mass: 25733.066 Da / Num. of mol.: 1 / Mutation: C41A, C76A, C83A,C41A, C76A, C83A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: ATG3, APG3, AUT1, YNR007C, N2040 / Production host: Escherichia coli (E. coli) / Strain (production host): RIL / References: UniProt: P40344
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 9% PEG3350, 100 mM HEPES pH 7.2, 150 mM L-Malic acid.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 10013 / % possible obs: 97.9 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rpim(I) all: 0.094 / Rsym value: 0.15 / Net I/σ(I): 12.4
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 482 / CC1/2: 0.587 / Rpim(I) all: 0.527 / Rsym value: 0.766 / Χ2: 0.86 / % possible all: 92.7

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DYT

2dyt


Resolution: 2.406→26.408 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.06
RfactorNum. reflection% reflection
Rfree0.2432 498 4.98 %
Rwork0.2131 --
obs0.2146 10005 96.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.406→26.408 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1486 0 12 23 1521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021533
X-RAY DIFFRACTIONf_angle_d0.6742076
X-RAY DIFFRACTIONf_dihedral_angle_d15.057562
X-RAY DIFFRACTIONf_chiral_restr0.028230
X-RAY DIFFRACTIONf_plane_restr0.004260
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4056-2.64740.32071210.29912200X-RAY DIFFRACTION90
2.6474-3.03010.2831300.26082382X-RAY DIFFRACTION98
3.0301-3.81570.26161230.21692431X-RAY DIFFRACTION99
3.8157-26.40960.20281240.18232494X-RAY DIFFRACTION99

+
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