[English] 日本語
Yorodumi
- PDB-4gsk: Crystal structure of an Atg7-Atg10 crosslinked complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4gsk
TitleCrystal structure of an Atg7-Atg10 crosslinked complex
Components
  • Ubiquitin-like modifier-activating enzyme ATG7
  • Ubiquitin-like-conjugating enzyme ATG10
KeywordsPROTEIN TRANSPORT/LIGASE / Ubiquitin-like protein activation enzyme / Ubiquitin-like protein transfer enzyme / PROTEIN TRANSPORT-LIGASE complex
Function / homology
Function and homology information


Atg12 transferase activity / Atg12 activating enzyme activity / Atg8 activating enzyme activity / protein modification by small protein conjugation / extrinsic component of phagophore assembly site membrane / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / phagophore assembly site membrane / autophagy of mitochondrion ...Atg12 transferase activity / Atg12 activating enzyme activity / Atg8 activating enzyme activity / protein modification by small protein conjugation / extrinsic component of phagophore assembly site membrane / Macroautophagy / cytoplasm to vacuole targeting by the Cvt pathway / nucleophagy / phagophore assembly site membrane / autophagy of mitochondrion / piecemeal microautophagy of the nucleus / phagophore assembly site / Transferases; Acyltransferases; Aminoacyltransferases / cellular response to nitrogen starvation / Antigen processing: Ubiquitination & Proteasome degradation / autophagosome assembly / mitophagy / Neutrophil degranulation / macroautophagy / autophagy / mitochondrion / identical protein binding / membrane / cytoplasm / cytosol
Similarity search - Function
Ubiquitin-like-conjugating enzyme Atg10 / Ubiquitin-like-conjugating enzyme Atg3/Atg10 / Autophagocytosis associated protein, active-site domain / 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 / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold ...Ubiquitin-like-conjugating enzyme Atg10 / Ubiquitin-like-conjugating enzyme Atg3/Atg10 / Autophagocytosis associated protein, active-site domain / 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 / ThiF/MoeB/HesA family / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin-like modifier-activating enzyme ATG7 / Ubiquitin-like-conjugating enzyme ATG10
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKaiser, S.E. / Mao, K. / Taherbhoy, A.M. / Yu, S. / Olszewski, J.L. / Duda, D.M. / Kurinov, I. / Deng, A. / Fenn, T.D. / Klionsky, D.J. / Schulman, B.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Noncanonical E2 recruitment by the autophagy E1 revealed by Atg7-Atg3 and Atg7-Atg10 structures.
Authors: Kaiser, S.E. / Mao, K. / Taherbhoy, A.M. / Yu, S. / Olszewski, J.L. / Duda, D.M. / Kurinov, I. / Deng, A. / Fenn, T.D. / Klionsky, D.J. / Schulman, B.A.
History
DepositionAug 27, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references
Revision 1.2Dec 19, 2012Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ubiquitin-like modifier-activating enzyme ATG7
B: Ubiquitin-like modifier-activating enzyme ATG7
Y: Ubiquitin-like-conjugating enzyme ATG10
Z: Ubiquitin-like-conjugating enzyme ATG10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,6826
Polymers179,5524
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13090 Å2
ΔGint-73 kcal/mol
Surface area58380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.556, 146.186, 108.442
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
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: 69628.016 Da / Num. of mol.: 2 / Fragment: UNP residues 1-613 / Mutation: C39S, C195S, C375A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: APG7, ATG7, CVT2, YHR171W / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) GOLD / References: UniProt: P38862
#2: Protein Ubiquitin-like-conjugating enzyme ATG10 / Autophagy-related protein 10


Mass: 20147.807 Da / Num. of mol.: 2 / Mutation: C26S, C137S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: APG10, ATG10, YLL042C / Plasmid: pGEX-4T1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) RIL
References: UniProt: Q07879, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.78 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 76.5 mM sodium/potassium phosphate, pH 6.5, 9 mM Tris, pH 8.5, 153 mM sodium chloride, 100 mM glycine, 72 mM sodium/potassium tartrate, 19.125% PEG1000, 0.045% PEG5000 MME, 4.5% dioxane, ...Details: 76.5 mM sodium/potassium phosphate, pH 6.5, 9 mM Tris, pH 8.5, 153 mM sodium chloride, 100 mM glycine, 72 mM sodium/potassium tartrate, 19.125% PEG1000, 0.045% PEG5000 MME, 4.5% dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 29, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 43151 / Num. obs: 42754 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.134 / Χ2: 1.083 / Net I/σ(I): 9.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.9-33.30.76542260.838199.3
3-3.123.30.58442230.833199.3
3.12-3.273.20.42442290.88198.9
3.27-3.4430.29841800.941198.5
3.44-3.653.20.20642271.052199
3.65-3.943.30.14742551.137199.3
3.94-4.333.20.09942701.253199.1
4.33-4.963.10.07542771.253198.8
4.96-6.243.20.07743461.142199.6
6.24-5030.07245211.523198.9

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXdev_1000refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3T7E AND 3T7F

3t7e

3t7f


Resolution: 2.9→49.565 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.42 / σ(F): 0 / Phase error: 29.52 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2855 2154 5.04 %RANDOM
Rwork0.2362 ---
all0.2387 43201 --
obs0.2387 42709 98.9 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.665 Å2 / ksol: 0.369 e/Å3
Displacement parametersBiso max: 105.49 Å2 / Biso mean: 79.6706 Å2 / Biso min: 57.16 Å2
Baniso -1Baniso -2Baniso -3
1--27.8803 Å2-0 Å2-0 Å2
2---2.9421 Å2-0 Å2
3----30.4193 Å2
Refinement stepCycle: LAST / Resolution: 2.9→49.565 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11406 0 2 0 11408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00411680
X-RAY DIFFRACTIONf_angle_d0.84215832
X-RAY DIFFRACTIONf_chiral_restr0.0631796
X-RAY DIFFRACTIONf_plane_restr0.0041994
X-RAY DIFFRACTIONf_dihedral_angle_d13.8744323
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.96760.35651370.30992594273196
2.9676-3.04180.35631400.318926972837100
3.0418-3.1240.37831490.30472658280799
3.124-3.2160.34661400.29362665280599
3.216-3.31970.30851450.28022673281899
3.3197-3.43840.31481430.26432661280498
3.4384-3.5760.30841530.25172674282799
3.576-3.73870.31361490.22962678282799
3.7387-3.93570.27961460.23112675282199
3.9357-4.18220.24091280.21312744287299
4.1822-4.50490.24421520.19972691284398
4.5049-4.95790.2431170.19372738285599
4.9579-5.67440.25361490.219627442893100
5.6744-7.14570.34611450.27232767291299
7.1457-49.57220.24811610.20762896305799

+
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