[English] 日本語
Yorodumi
- PDB-2a0t: NMR structure of the FHA1 domain of Rad53 in complex with a biolo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2a0t
TitleNMR structure of the FHA1 domain of Rad53 in complex with a biological relevant phosphopeptide derived from Madt1
Components
  • Hypothetical 73.8 kDa protein in SAS3-SEC17 intergenic region, residues 301-310
  • Serine/threonine-protein kinase RAD53
KeywordsTRANSFERASE / FHA domain. Rad53 / Mdt1 / phosphothreonine / phosphoprotein
Function / homology
Function and homology information


deoxyribonucleoside triphosphate biosynthetic process / meiotic recombination checkpoint signaling / dual-specificity kinase / telomere maintenance in response to DNA damage / negative regulation of DNA damage checkpoint / DNA replication origin binding / DNA replication initiation / regulation of DNA repair / protein serine/threonine/tyrosine kinase activity / DNA damage checkpoint signaling ...deoxyribonucleoside triphosphate biosynthetic process / meiotic recombination checkpoint signaling / dual-specificity kinase / telomere maintenance in response to DNA damage / negative regulation of DNA damage checkpoint / DNA replication origin binding / DNA replication initiation / regulation of DNA repair / protein serine/threonine/tyrosine kinase activity / DNA damage checkpoint signaling / G2/M transition of mitotic cell cycle / intracellular protein localization / protein tyrosine kinase activity / protein kinase activity / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / mRNA binding / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
R3H domain, Cip2-type / Pin4-like, RNA recognition motif / Serine/threonine-protein kinase Rad53 / Tumour Suppressor Smad4 - #20 / : / Tumour Suppressor Smad4 / Aurora kinase / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain ...R3H domain, Cip2-type / Pin4-like, RNA recognition motif / Serine/threonine-protein kinase Rad53 / Tumour Suppressor Smad4 - #20 / : / Tumour Suppressor Smad4 / Aurora kinase / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Serine/threonine-protein kinase RAD53 / RNA-binding protein PIN4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsMahajan, A. / Yuan, C. / Pike, B.L. / Heierhorst, J. / Chang, C.-F. / Tsai, M.-D.
Citation
Journal: J.Am.Chem.Soc. / Year: 2005
Title: FHA Domain-Ligand Interactions: Importance of Integrating Chemical and Biological Approaches
Authors: Mahajan, A. / Yuan, C. / Pike, B.L. / Heierhorst, J. / Chang, C.-F. / Tsai, M.-D.
#1: Journal: J.Mol.Biol. / Year: 2001
Title: Solution structures of two FHA1-phosphothreonine peptide complexes provide insight into the structural basis of the ligand specificity of FHA1 from yeast Rad53
Authors: Yuan, C. / Yongkiettrakul, S. / Byeon, I.-J.L. / Zhou, S. / Tsai, M.-D.
History
DepositionJun 16, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Serine/threonine-protein kinase RAD53
B: Hypothetical 73.8 kDa protein in SAS3-SEC17 intergenic region, residues 301-310


Theoretical massNumber of molelcules
Total (without water)18,3402
Polymers18,3402
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 50structures with acceptable covalent geometry, structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #1closest to the average, lowest energy

-
Components

#1: Protein Serine/threonine-protein kinase RAD53 / Serine-protein kinase 1


Mass: 17093.490 Da / Num. of mol.: 1 / Fragment: N-terminal FHA domain (FHA1)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SPK1 or Rad53 / Plasmid: pGEX-4T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P22216, EC: 2.7.1.37
#2: Protein/peptide Hypothetical 73.8 kDa protein in SAS3-SEC17 intergenic region, residues 301-310


Mass: 1246.173 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in Saccharomyces cerevisiae (yeast)
References: UniProt: P34217
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-edited 13C/15N-filtered NOESY
1223D 13C/15N-filtered, 13C-edited NOESY
1323D 13C-separated NOESY
1412D 13C/15N-filtered NOESY
1522D 13C/15N-filtered TOCSY
1612D 13C/15N-filtered COSY

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5 mM FHA1 U-13C, 15N, ~0.8 mM peptide, 10 mM sodium phosphate buffer (pH 6.5), 1 mM DTT,1 mM EDTA, 90% H2O, 10% D2O90% H2O/10% D2O
20.5 mM FHA1 U-13C, 15N, ~0.8 mM peptide, 10 mM sodium phosphate buffer (pH 6.5), 1 mM DTT, 1 mM EDTA, 100% D2O100% D2O
Sample conditionsIonic strength: 10 mM sodium phosphate, 1 mM DTT, and 1 mM EDTA
pH: 6.5 / Pressure: ambient / Temperature: 293 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX8001
Bruker DMXBrukerDMX6002
Bruker AVANCEBrukerAVANCE8003
Bruker AVANCEBrukerAVANCE5004

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipeDelaglio, F.processing
NMRView5Johnson, B.data analysis
CNS1.1Brunger et al.structure solution
CNS1.1Brunger et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: The complex structures are generated using a total of 2524 NMR constraints including constraints in this PDB file and constraints of free FHA1 in PDB access code 1K3J
NMR representativeSelection criteria: closest to the average, lowest energy
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry, structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 20

+
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