[English] 日本語
Yorodumi
- PDB-3rui: Crystal structure of Atg7C-Atg8 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3rui
TitleCrystal structure of Atg7C-Atg8 complex
Components
  • Autophagy-related protein 8
  • Ubiquitin-like modifier-activating enzyme ATG7
KeywordsLIGASE / Autophagy / Autophagosome formation / non-canonical E1 / ATP binding / Ubl / Atg8 / Atg12 / Atg10 / Atg3 / Ubl activation / thiolation / Zinc Finger / GxGxxG motif ATP binding motif / E1-like protein / Zinc binding / Atg8 protein binding
Function / homology
Function and homology information


Cvt vesicle membrane / Atg12 activating enzyme activity / Atg8 activating enzyme activity / TBC/RABGAPs / Receptor Mediated Mitophagy / extrinsic component of phagophore assembly site membrane / regulation of membrane invagination / protein modification by small protein conjugation / C-terminal protein lipidation / vacuole-isolation membrane contact site ...Cvt vesicle membrane / Atg12 activating enzyme activity / Atg8 activating enzyme activity / TBC/RABGAPs / Receptor Mediated Mitophagy / extrinsic component of phagophore assembly site membrane / regulation of membrane invagination / protein modification by small protein conjugation / C-terminal protein lipidation / vacuole-isolation membrane contact site / protein targeting to vacuole involved in autophagy / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / autophagy of mitochondrion / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus / Antigen processing: Ubiquitination & Proteasome degradation / cellular response to nitrogen starvation / phosphatidylethanolamine binding / protein-containing complex localization / fungal-type vacuole membrane / phagophore assembly site / reticulophagy / autophagosome membrane / autophagosome maturation / autophagosome assembly / autophagosome / regulation of macroautophagy / endoplasmic reticulum to Golgi vesicle-mediated transport / Neutrophil degranulation / mitochondrial membrane / macroautophagy / autophagy / protein tag activity / membrane fusion / ubiquitin protein ligase binding / mitochondrion / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Ubiquitin-like modifier-activating enzyme Atg7 / Ubiquitin-like modifier-activating enzyme Atg7, N-terminal / Ubiquitin-like modifier-activating enzyme Atg7, N-terminal, subdomain 1 / Ubiquitin-like modifier-activating enzyme Atg7, N-terminal, subdomain 2 / Ubiquitin-like modifier-activating enzyme ATG7 N-terminus / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold ...Ubiquitin-like modifier-activating enzyme Atg7 / Ubiquitin-like modifier-activating enzyme Atg7, N-terminal / Ubiquitin-like modifier-activating enzyme Atg7, N-terminal, subdomain 1 / Ubiquitin-like modifier-activating enzyme Atg7, N-terminal, subdomain 2 / Ubiquitin-like modifier-activating enzyme ATG7 N-terminus / Autophagy protein Atg8 ubiquitin-like / Autophagy protein Atg8 ubiquitin like / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin-like (UB roll) / NAD(P)-binding Rossmann-like Domain / Ubiquitin-like domain superfamily / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Autophagy-related protein 8 / Ubiquitin-like modifier-activating enzyme ATG7
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.906 Å
AuthorsHong, S.B. / Kim, B.W. / Song, H.K.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: Insights into noncanonical E1 enzyme activation from the structure of autophagic E1 Atg7 with Atg8.
Authors: Hong, S.B. / Kim, B.W. / Lee, K.E. / Kim, S.W. / Jeon, H. / Kim, J. / Song, H.K.
History
DepositionMay 5, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin-like modifier-activating enzyme ATG7
B: Autophagy-related protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1443
Polymers52,0792
Non-polymers651
Water5,729318
1
A: Ubiquitin-like modifier-activating enzyme ATG7
B: Autophagy-related protein 8
hetero molecules

A: Ubiquitin-like modifier-activating enzyme ATG7
B: Autophagy-related protein 8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,2886
Polymers104,1574
Non-polymers1312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_646y+1,x-1,-z+11
Buried area13120 Å2
ΔGint-82 kcal/mol
Surface area35300 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-16 kcal/mol
Surface area20660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.326, 71.326, 220.916
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-188-

HOH

-
Components

#1: Protein Ubiquitin-like modifier-activating enzyme ATG7 / ATG12-activating enzyme E1 ATG7 / Autophagy-related protein 7 / Cytoplasm to vacuole targeting protein 2


Mass: 38442.773 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN (UNP RESIDUES 293-630) / Mutation: C507S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: ATG7, APG7, CVT2, YHR171W / Production host: Escherichia coli (E. coli) / References: UniProt: P38862
#2: Protein Autophagy-related protein 8 / Autophagy-related ubiquitin-like modifier ATG8 / Cytoplasm to vacuole targeting protein 5


Mass: 13635.747 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-116
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288c / Gene: ATG8, APG8, AUT7, CVT5, YBL078C, YBL0732 / Production host: Escherichia coli (E. coli) / References: UniProt: P38182
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 318 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.02M proline, 0.1M Hepes pH 7.5, 10~7% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 4A10.9796, 0.9799, 0.95
SYNCHROTRONPhoton Factory AR-NW12A21
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDJun 1, 2010
ADSC QUANTUM 2102CCDJun 28, 2010
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal monochromatorMADMx-ray1
2Numerical link type Si(111) double crystal monochromator, liquid nitrogen coolingSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97991
30.951
411
ReflectionResolution: 1.9→41.611 Å / Num. obs: 43347 / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 1.9→1.97 Å / % possible all: 99.3

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SOLVEphasing
PHENIX(phenix.refine: 1.7_650)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.906→41.6 Å / SU ML: 0.22 / σ(F): 3 / Phase error: 21.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 1924 4.44 %RANDOM
Rwork0.1921 ---
all0.1933 ---
obs0.1933 43347 95 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.027 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.1293 Å20 Å2-0 Å2
2--6.1293 Å2-0 Å2
3----12.2585 Å2
Refinement stepCycle: LAST / Resolution: 1.906→41.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3504 0 1 318 3823
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093576
X-RAY DIFFRACTIONf_angle_d1.1524839
X-RAY DIFFRACTIONf_dihedral_angle_d13.2241348
X-RAY DIFFRACTIONf_chiral_restr0.076552
X-RAY DIFFRACTIONf_plane_restr0.005617
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9059-1.95360.28211180.2287244181
1.9536-2.00640.2911230.2248273789
2.0064-2.06550.26191280.2057282192
2.0655-2.13210.24871370.209288695
2.1321-2.20830.26991350.2002287794
2.2083-2.29670.24591390.2026296296
2.2967-2.40120.23411350.1905291195
2.4012-2.52780.21931370.1862294795
2.5278-2.68620.19781400.1881298697
2.6862-2.89350.20831420.1943305598
2.8935-3.18460.21331400.1952306699
3.1846-3.64520.19541450.17963153100
3.6452-4.59170.20241490.17033203100
4.5917-41.6210.21391560.2049337899

+
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