[English] 日本語
Yorodumi
- PDB-4j2g: Atg13 HORMA domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4j2g
TitleAtg13 HORMA domain
ComponentsKLTH0A00704p
KeywordsUNKNOWN FUNCTION / Autophagy / HORMA / Atg13
Function / homology
Function and homology information


Atg1/ULK1 kinase complex / protein localization to phagophore assembly site / piecemeal microautophagy of the nucleus / phagophore assembly site / mitophagy / cytosol
Similarity search - Function
Autophagy-related protein 13, N-terminal / Autophagy-related protein 13 / Autophagy-related protein 13 / Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A / HORMA domain / HORMA domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Autophagy-related protein 13
Similarity search - Component
Biological speciesLachancea thermotolerans (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.29 Å
AuthorsJao, C. / Stanley, R.E. / Ragusa, M.J. / Hurley, J.H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: A HORMA domain in Atg13 mediates PI 3-kinase recruitment in autophagy.
Authors: Jao, C.C. / Ragusa, M.J. / Stanley, R.E. / Hurley, J.H.
History
DepositionFeb 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2Apr 17, 2013Group: Database references / Structure summary
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: KLTH0A00704p
B: KLTH0A00704p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,2064
Polymers61,0142
Non-polymers1922
Water1,63991
1
A: KLTH0A00704p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6032
Polymers30,5071
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: KLTH0A00704p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6032
Polymers30,5071
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-11 kcal/mol
Surface area21370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.650, 65.670, 85.760
Angle α, β, γ (deg.)90.00, 101.46, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein KLTH0A00704p


Mass: 30507.037 Da / Num. of mol.: 2 / Fragment: UNP residues 1-260 / Mutation: L123M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lachancea thermotolerans (fungus) / Strain: ATCC 56472 / CBS 6340 / NRRL Y-8284 / Gene: KLTH0A00704g / Production host: Escherichia coli (E. coli) / References: UniProt: C5DB94
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2mM ammonium sulfate, 0.1M MES pH6.5, 20% w/v PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 28, 2012
RadiationMonochromator: filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.29→84.05 Å / Num. all: 29497 / % possible obs: 99 % / Observed criterion σ(F): 2.6 / Observed criterion σ(I): 12.1

-
Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.29→57.25 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.59 / SU B: 6.927 / SU ML: 0.17 / Cross valid method: THROUGHOUT / ESU R: 0.234 / ESU R Free: 0.21
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26279 1489 5.1 %RANDOM
Rwork0.21445 ---
obs0.21689 27778 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.413 Å2
Baniso -1Baniso -2Baniso -3
1--2.66 Å20 Å2-1.4 Å2
2--6.8 Å20 Å2
3----3.56 Å2
Refinement stepCycle: LAST / Resolution: 2.29→57.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3146 0 10 91 3247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193207
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.0521.9954323
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6685378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.52923.383133
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.16715604
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.061526
X-RAY DIFFRACTIONr_chiral_restr0.1310.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212270
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.29→2.349 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 105 -
Rwork0.31 2099 -
obs--99.86 %

+
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