[English] 日本語
Yorodumi
- PDB-3w1s: Crystal structure of Saccharomyces cerevisiae Atg12-Atg5 conjugat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3w1s
TitleCrystal structure of Saccharomyces cerevisiae Atg12-Atg5 conjugate bound to the N-terminal domain of Atg16
Components
  • Autophagy protein 16
  • Autophagy protein 5
  • Ubiquitin-like protein ATG12
KeywordsLIGASE / Ubiquitin fold / E3-like / Atg3 binding / Isopeptide bond between Atg12 Gly186 and Atg5 Lys149
Function / homology
Function and homology information


Receptor Mediated Mitophagy / cargo receptor ligand activity / Atg12-Atg5-Atg16 complex / vacuole-isolation membrane contact site / phagophore / Macroautophagy / cellular response to potassium ion starvation / transferase complex / aggrephagy / glycophagy ...Receptor Mediated Mitophagy / cargo receptor ligand activity / Atg12-Atg5-Atg16 complex / vacuole-isolation membrane contact site / phagophore / Macroautophagy / cellular response to potassium ion starvation / transferase complex / aggrephagy / glycophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / autophagosome organization / phagophore assembly site membrane / autophagy of mitochondrion / piecemeal microautophagy of the nucleus / phagophore assembly site / cellular response to nitrogen starvation / autophagosome membrane / autophagosome assembly / autophagosome maturation / mitophagy / autophagosome / macroautophagy / enzyme activator activity / autophagy / protein tag activity / protein-macromolecule adaptor activity / hydrolase activity / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Ubiquitin-like protein Atg12 / Ubiquitin-like autophagy protein Apg12 / Autophagy protein Apg5, helix rich domain / Ubiquitin-like (UB roll) - #620 / Autophagy-related protein 5 / Autophagy protein Atg5, helix rich domain / Autophagy protein Atg5, UblA domain / : / : / : ...Ubiquitin-like protein Atg12 / Ubiquitin-like autophagy protein Apg12 / Autophagy protein Apg5, helix rich domain / Ubiquitin-like (UB roll) - #620 / Autophagy-related protein 5 / Autophagy protein Atg5, helix rich domain / Autophagy protein Atg5, UblA domain / : / : / : / Autophagy protein ATG5, UblB domain / Autophagy protein ATG5, alpha-helical bundle region / Autophagy protein ATG5, UblA domain / Autophagy-related protein 16 domain / Autophagy protein 16 (ATG16) / Serum Albumin; Chain A, Domain 1 / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / Ubiquitin-like domain superfamily / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-like protein ATG12 / Autophagy protein 16 / Autophagy protein 5
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNoda, N.N. / Fujioka, Y. / Hanada, T. / Ohsumi, Y. / Inagaki, F.
CitationJournal: Embo Rep. / Year: 2013
Title: Structure of the Atg12-Atg5 conjugate reveals a platform for stimulating Atg8-PE conjugation
Authors: Noda, N.N. / Fujioka, Y. / Hanada, T. / Ohsumi, Y. / Inagaki, F.
History
DepositionNov 20, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Autophagy protein 5
B: Autophagy protein 16
C: Ubiquitin-like protein ATG12


Theoretical massNumber of molelcules
Total (without water)48,7543
Polymers48,7543
Non-polymers00
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Autophagy protein 5
B: Autophagy protein 16
C: Ubiquitin-like protein ATG12

A: Autophagy protein 5
B: Autophagy protein 16
C: Ubiquitin-like protein ATG12


Theoretical massNumber of molelcules
Total (without water)97,5096
Polymers97,5096
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area9900 Å2
ΔGint-46 kcal/mol
Surface area31400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.149, 106.084, 143.071
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein Autophagy protein 5


Mass: 32620.820 Da / Num. of mol.: 1 / Fragment: UNP residues 1-284
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / Gene: APG5, ATG5, Atg5(amino acids 1-284), P2601, YPL149W / Plasmid: pACYC184 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12380
#2: Protein/peptide Autophagy protein 16 / Cytoplasm to vacuole targeting protein 11 / SAP18 homolog


Mass: 5792.501 Da / Num. of mol.: 1 / Fragment: UNP residues 1-46
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Gene: APG15, APG16, ATG16, Atg16(amino acids 1-46), CVT11, SAP18, YM8520.08C, YMR159C
Plasmid: pGEX6p / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q03818
#3: Protein Ubiquitin-like protein ATG12 / Autophagy-related protein 12


Mass: 10341.172 Da / Num. of mol.: 1 / Fragment: UNP residues 100-186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Gene: APG12, ATG12, Atg12(amino acids 100-186), YBR1506, YBR217W
Plasmid: pACYC184 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P38316
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.81 Å3/Da / Density % sol: 56.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12% PEG10000, 0.5M potassium thiocyanate, 0.1M ADA, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 3, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→42.6 Å / Num. all: 17196 / Num. obs: 17173 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 53.8 Å2 / Rsym value: 0.055 / Net I/σ(I): 9.6
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 7.4 % / Num. unique all: 1691 / Rsym value: 0.303 / % possible all: 100

-
Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DYM, 1WZ3

2dym

1wz3


Resolution: 2.6→42.6 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 167335.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1679 10 %RANDOM
Rwork0.231 ---
obs0.231 16822 97.9 %-
all-17183 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.3649 Å2 / ksol: 0.38 e/Å3
Displacement parametersBiso mean: 51.6 Å2
Baniso -1Baniso -2Baniso -3
1-5.38 Å20 Å20 Å2
2---5.38 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.6→42.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2868 0 0 27 2895
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.51.5
X-RAY DIFFRACTIONc_mcangle_it2.562
X-RAY DIFFRACTIONc_scbond_it1.942
X-RAY DIFFRACTIONc_scangle_it2.872.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.339 247 9.5 %
Rwork0.31 2345 -
obs-2592 91.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5carbohydrate.paramcarbohydrate.top

+
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