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- PDB-6hka: The solution structure of the micelle-associated FATC domain of t... -

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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


establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / negative regulation of telomere capping / Sensing of DNA Double Strand Breaks / cellular response to nitrosative stress / peptidyl-serine autophosphorylation / establishment of protein-containing complex localization to telomere / meiotic telomere clustering / positive regulation of telomere maintenance via telomere lengthening / pre-B cell allelic exclusion ...establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / negative regulation of telomere capping / Sensing of DNA Double Strand Breaks / cellular response to nitrosative stress / peptidyl-serine autophosphorylation / establishment of protein-containing complex localization to telomere / meiotic telomere clustering / positive regulation of telomere maintenance via telomere lengthening / pre-B cell allelic exclusion / male meiotic nuclear division / histone mRNA catabolic process / extrinsic component of synaptic vesicle membrane / regulation of telomere maintenance via telomerase / female meiotic nuclear division / DNA double-strand break processing / lipoprotein catabolic process / regulation of autophagosome assembly / cellular response to X-ray / V(D)J recombination / oocyte development / pexophagy / Impaired BRCA2 binding to PALB2 / reciprocal meiotic recombination / DNA repair complex / positive regulation of DNA damage response, signal transduction by p53 class mediator / IgG binding / 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) / Resolution of D-loop Structures through Holliday Junction Intermediates / 1-phosphatidylinositol-3-kinase activity / HDR through Single Strand Annealing (SSA) / response to ionizing radiation / positive regulation of double-strand break repair / Impaired BRCA2 binding to RAD51 / mitotic spindle assembly checkpoint signaling / negative regulation of B cell proliferation / TP53 Regulates Transcription of Caspase Activators and Caspases / cellular response to stress / mitotic G2 DNA damage checkpoint signaling / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / peroxisomal matrix / Presynaptic phase of homologous DNA pairing and strand exchange / replicative senescence / signal transduction in response to DNA damage / Regulation of HSF1-mediated heat shock response / somitogenesis / regulation of cellular response to heat / ovarian follicle development / negative regulation of TORC1 signaling / cellular response to retinoic acid / positive regulation of telomere maintenance via telomerase / telomere maintenance / positive regulation of cell adhesion / Pexophagy / DNA damage checkpoint signaling / thymus development / regulation of signal transduction by p53 class mediator / post-embryonic development / determination of adult lifespan / cellular response to reactive oxygen species / TP53 Regulates Transcription of DNA Repair Genes / DNA damage response, signal transduction by p53 class mediator / Nonhomologous End-Joining (NHEJ) / Stabilization of p53 / Autodegradation of the E3 ubiquitin ligase COP1 / double-strand break repair via homologous recombination / cellular response to gamma radiation / G2/M DNA damage checkpoint / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / brain development / DNA Damage/Telomere Stress Induced Senescence / Regulation of TP53 Activity through Methylation / HDR through Homologous Recombination (HRR) / Meiotic recombination / double-strand break repair via nonhomologous end joining / spindle / multicellular organism growth / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / cellular senescence / Regulation of TP53 Degradation / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / chromosome / heart development / Processing of DNA double-strand break ends / protein autophosphorylation / regulation of apoptotic process / neuron apoptotic process / Regulation of TP53 Activity through Phosphorylation / non-specific serine/threonine protein kinase / regulation of cell cycle / regulation of autophagy / protein phosphorylation
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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

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Experimental details

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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

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Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent 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

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NMR measurement

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

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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

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