[English] 日本語
Yorodumi
- PDB-6hka: The solution structure of the micelle-associated FATC domain of t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6hka
TitleThe solution structure of the micelle-associated FATC domain of the human protein kinase ataxia telangiectasia mutated (ATM)
ComponentsImmunoglobulin G-binding protein G,Serine-protein kinase ATM
KeywordsTRANSFERASE / Ataxia telangiectasia mutated (ATM) / FATC domain / phosphatidylinositol-3-kinase-related kinase (PIKKs) / ser/thr kinase / membrane binding
Function / homology
Function and homology information


cellular response to nitrosative stress / negative regulation of telomere capping / peptidyl-serine autophosphorylation / establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / Sensing of DNA Double Strand Breaks / establishment of protein-containing complex localization to telomere / positive regulation of telomere maintenance via telomere lengthening / negative regulation of B cell proliferation / regulation of telomere maintenance via telomerase ...cellular response to nitrosative stress / negative regulation of telomere capping / peptidyl-serine autophosphorylation / establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / Sensing of DNA Double Strand Breaks / establishment of protein-containing complex localization to telomere / positive regulation of telomere maintenance via telomere lengthening / negative regulation of B cell proliferation / regulation of telomere maintenance via telomerase / extrinsic component of synaptic vesicle membrane / DNA-dependent protein kinase activity / histone mRNA catabolic process / pre-B cell allelic exclusion / histone H2AXS139 kinase activity / DNA double-strand break processing / cellular response to X-ray / regulation of autophagosome assembly / pexophagy / positive regulation of autophagosome assembly / Impaired BRCA2 binding to PALB2 / DNA repair complex / reciprocal meiotic recombination / cellular response to stress / 1-phosphatidylinositol-3-kinase activity / mitotic spindle assembly checkpoint signaling / TP53 Regulates Transcription of Caspase Activators and Caspases / response to ionizing radiation / response to starvation / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / HDR through Single Strand Annealing (SSA) / mitotic G2 DNA damage checkpoint signaling / Resolution of D-loop Structures through Holliday Junction Intermediates / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / peroxisomal matrix / positive regulation of double-strand break repair / Impaired BRCA2 binding to RAD51 / replicative senescence / positive regulation of DNA damage response, signal transduction by p53 class mediator / Regulation of HSF1-mediated heat shock response / Presynaptic phase of homologous DNA pairing and strand exchange / cellular response to retinoic acid / DNA damage checkpoint signaling / positive regulation of double-strand break repair via homologous recombination / regulation of cellular response to heat / signal transduction in response to DNA damage / positive regulation of telomere maintenance via telomerase / positive regulation of cell adhesion / negative regulation of TORC1 signaling / regulation of signal transduction by p53 class mediator / Pexophagy / DNA damage response, signal transduction by p53 class mediator / intrinsic apoptotic signaling pathway in response to DNA damage / TP53 Regulates Transcription of DNA Repair Genes / cellular response to reactive oxygen species / Nonhomologous End-Joining (NHEJ) / Stabilization of p53 / double-strand break repair via homologous recombination / cellular response to gamma radiation / regulation of autophagy / Autodegradation of the E3 ubiquitin ligase COP1 / double-strand break repair via nonhomologous end joining / G2/M DNA damage checkpoint / Regulation of TP53 Activity through Methylation / cellular senescence / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / spindle / HDR through Homologous Recombination (HRR) / double-strand break repair / Regulation of TP53 Degradation / protein autophosphorylation / site of double-strand break / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / response to oxidative stress / cytoplasmic vesicle / Regulation of TP53 Activity through Phosphorylation / regulation of apoptotic process / regulation of cell cycle / non-specific serine/threonine protein kinase / protein stabilization / positive regulation of cell migration / positive regulation of apoptotic process / chromosome / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / positive regulation of gene expression / DNA damage response / nucleolus / protein-containing complex binding / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding
Similarity search - Function
Telomere-length maintenance and DNA damage repair / Serine/threonine-protein kinase ATM, plant / ATM, catalytic domain / Telomere-length maintenance and DNA damage repair / Telomere-length maintenance and DNA damage repair / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain ...Telomere-length maintenance and DNA damage repair / Serine/threonine-protein kinase ATM, plant / ATM, catalytic domain / Telomere-length maintenance and DNA damage repair / Telomere-length maintenance and DNA damage repair / IgG-binding B / B domain / M protein-type anchor domain / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / FATC domain / PIK-related kinase, FAT / FAT domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Immunoglobulin G-binding protein G / Serine-protein kinase ATM
Similarity search - Component
Biological speciesStreptococcus sp. group G (bacteria)
Homo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsAbd Rahim, M.S. / Dames, S.A.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationDA1183/3-1, DA1183/3-2 Germany
Citation
Journal: J.Biol.Chem. / Year: 2019
Title: NMR- and MD simulation-based structural characterization of the membrane-associating FATC domain of ataxia telangiectasia mutated.
Authors: Abd Rahim, M.S. / Cherniavskyi, Y.K. / Tieleman, D.P. / Dames, S.A.
#1: Journal: Biomol NMR Assign. / Year: 2018
Title: 1H, 15N and 13C chemical shift assignments of the micelle immersed FAT C-terminal (FATC) domains of the human protein kinases ataxia-telangiectasia mutated (ATM) and DNA-dependent protein ...Title: 1H, 15N and 13C chemical shift assignments of the micelle immersed FAT C-terminal (FATC) domains of the human protein kinases ataxia-telangiectasia mutated (ATM) and DNA-dependent protein kinase catalytic subunit (DNA-PKcs)fused to the B1 domain of streptococcal protein G (GB1)
Authors: Abd Rahim, M.S. / Sommer, L.A.M. / Wacker, A. / Schaad, M. / Dames, S.A.
History
DepositionSep 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1May 8, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc / pdbx_nmr_software
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_nmr_software.name
Revision 1.2Jul 17, 2019Group: Data collection / Category: pdbx_nmr_spectrometer / Item: _pdbx_nmr_spectrometer.model
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Immunoglobulin G-binding protein G,Serine-protein kinase ATM


Theoretical massNumber of molelcules
Total (without water)11,0211
Polymers11,0211
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area3300 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Antibody Immunoglobulin G-binding protein G,Serine-protein kinase ATM / IgG-binding protein G / Ataxia telangiectasia mutated / A-T mutated


Mass: 11021.240 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminally GB1-tagged (1-56), linker: thrombin and enterokinase sites (57-67), FATC domain of ATM (68-100),N-terminally GB1-tagged (1-56), linker: thrombin and enterokinase sites (57-67), ...Details: N-terminally GB1-tagged (1-56), linker: thrombin and enterokinase sites (57-67), FATC domain of ATM (68-100),N-terminally GB1-tagged (1-56), linker: thrombin and enterokinase sites (57-67), FATC domain of ATM (68-100)
Source: (gene. exp.) Streptococcus sp. group G (bacteria), (gene. exp.) Homo sapiens (human)
Gene: spg, ATM / Plasmid: pGEV2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P19909, UniProt: Q13315, non-specific serine/threonine protein kinase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
114isotropic12D 1H-15N HSQC
122isotropic32D 1H-15N HSQC
132isotropic32D 1H-13C HSQC aliphatic
142isotropic32D 1H-13C HSQC aromatic
153isotropic12D 1H-13C HSQC
162isotropic23D HNCA
172isotropic13D HN(CA)CB
182isotropic23D (H)CCH-TOCSY
192isotropic23D C(CO)NH
1102isotropic13D HNHA
1112isotropic13D HNHB
1122isotropic13D 1H-15N NOESY
1132isotropic33D 1H-13C NOESY aliphatic
1142isotropic33D 1H-13C NOESY aromatic
1154isotropic115N-T1
1164isotropic115N-T2
1174isotropic11H-15N NOE

-
Sample preparation

Details
TypeSolution-IDContentsDetails (eV)LabelSolvent system
solution2100 mM sodium chloride, 50 mM TRIS, 150 mM [U-100% 2H] DPC, 0.4 mM [U-100% 13C; U-100% 15N] 13C-15N-hATMfatc, 95% H2O/5% D2OGB1-tagged human ATM FATC in micelle-immersed form (150 mM d38-DPC)13C-15N-hATMfatc-gb1ent95% H2O/5% D2O
solution4100 mM sodium chloride, 50 mM TRIS, 150 mM [U-100% 2H] DPC, 0.5 mM [U-100% 15N] 15N-hATMfatc, 95% H2O/5% D2OGB1-tagged human ATM FATC in micelle-immersed form (150 mM d38-DPC)15N-hATMfatc-gb1ent95% H2O/5% D2O
solution3100 mM sodium chloride, 50 mM TRIS, 150 mM [U-100% 2H] DPC, 0.4 mM [U-10% 13C] 13C-hATMfatc, 95% H2O/5% D2OGB1-tagged human ATM FATC in micelle-immersed form (150 mM d38-DPC)10 % 13C-hATMfatc-gb1ent95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
100 mMsodium chloridenatural abundance2
50 mMTRISnatural abundance2
150 mMDPC[U-100% 2H]2
0.4 mM13C-15N-hATMfatc[U-100% 13C; U-100% 15N]2
100 mMsodium chloridenatural abundance4
50 mMTRISnatural abundance4
150 mMDPC[U-100% 2H]4
0.5 mM15N-hATMfatc[U-100% 15N]4
100 mMsodium chloridenatural abundance3
50 mMTRISnatural abundance3
150 mMDPC[U-100% 2H]3
0.4 mM13C-hATMfatc[U-10% 13C]3
Sample conditionsDetails: 50 mM Tris, 100 mM NaCl, 150 mM DPC (usually deuterated d38-DPC)
Ionic strength: 100 mM / Label: condition_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-IDDetails (eV)
Bruker AVANCE IIIBrukerAVANCE III5001with cryogenic probe
Bruker AVANCE IIIBrukerAVANCE III6002
Bruker AVANCE IIIBrukerAVANCE III9003with cryogenic probe

-
Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Xplor-NIHSchwieters, Kuszewski, Tjandra and Clorestructure calculation
RefinementMethod: simulated annealing / Software ordinal: 4
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / 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