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Yorodumi- EMDB-9950: 4.27 Angstrom resolution cryo-EM structure of human dimeric ATM kinase -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9950 | |||||||||
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Title | 4.27 Angstrom resolution cryo-EM structure of human dimeric ATM kinase | |||||||||
Map data | ||||||||||
Sample |
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Keywords | DNA damage response / KInase / CELL CYCLE | |||||||||
Function / homology | Function and homology information positive regulation of DNA catabolic process / establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / positive regulation of DNA damage response, signal transduction by p53 class mediator / cellular response to nitrosative stress / establishment of protein-containing complex localization to telomere / negative regulation of telomere capping / Sensing of DNA Double Strand Breaks / positive regulation of telomere maintenance via telomere lengthening / regulation of microglial cell activation ...positive regulation of DNA catabolic process / establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / positive regulation of DNA damage response, signal transduction by p53 class mediator / cellular response to nitrosative stress / establishment of protein-containing complex localization to telomere / negative regulation of telomere capping / Sensing of DNA Double Strand Breaks / positive regulation of telomere maintenance via telomere lengthening / regulation of microglial cell activation / meiotic telomere clustering / pre-B cell allelic exclusion / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / male meiotic nuclear division / histone mRNA catabolic process / female meiotic nuclear division / pexophagy / cellular response to X-ray / regulation of telomere maintenance via telomerase / peptidyl-serine autophosphorylation / DNA double-strand break processing / lipoprotein catabolic process / V(D)J recombination / regulation of autophagosome assembly / oocyte development / Impaired BRCA2 binding to PALB2 / reciprocal meiotic recombination / DNA repair complex / 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 / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / 1-phosphatidylinositol-3-kinase activity / response to ionizing radiation / mitotic spindle assembly checkpoint signaling / TP53 Regulates Transcription of Caspase Activators and Caspases / negative regulation of B cell proliferation / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / peroxisomal matrix / positive regulation of cell adhesion / replicative senescence / Regulation of HSF1-mediated heat shock response / signal transduction in response to DNA damage / somitogenesis / regulation of cellular response to heat / cellular response to retinoic acid / ovarian follicle development / negative regulation of TORC1 signaling / positive regulation of telomere maintenance via telomerase / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / Pexophagy / telomere maintenance / post-embryonic development / thymus development / Meiotic recombination / DNA Damage/Telomere Stress Induced Senescence / regulation of signal transduction by p53 class mediator / DNA damage checkpoint signaling / regulation of autophagy / Nonhomologous End-Joining (NHEJ) / determination of adult lifespan / TP53 Regulates Transcription of DNA Repair Genes / Stabilization of p53 / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M DNA damage checkpoint / double-strand break repair via homologous recombination / cellular response to reactive oxygen species / brain development / multicellular organism growth / HDR through Homologous Recombination (HRR) / Regulation of TP53 Activity through Methylation / cellular senescence / cellular response to gamma radiation / spindle / double-strand break repair via nonhomologous end joining / Regulation of TP53 Degradation / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / double-strand break repair / Processing of DNA double-strand break ends / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / heart development / peptidyl-serine phosphorylation / site of double-strand break / cytoplasmic vesicle / Regulation of TP53 Activity through Phosphorylation / neuron apoptotic process / regulation of apoptotic process / protein autophosphorylation / response to hypoxia / regulation of cell cycle / non-specific serine/threonine protein kinase / positive regulation of cell migration Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.27 Å | |||||||||
Authors | Xiao J / Liu M | |||||||||
Citation | Journal: Cell Res / Year: 2019 Title: Structural insights into the activation of ATM kinase. Authors: Jianxiong Xiao / Mengjie Liu / Yilun Qi / Yuriy Chaban / Chao Gao / Beiqing Pan / Yuan Tian / Zishuo Yu / Jie Li / Peijun Zhang / Yanhui Xu / | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_9950.map.gz | 5.2 MB | EMDB map data format | |
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Header (meta data) | emd-9950-v30.xml emd-9950.xml | 12.5 KB 12.5 KB | Display Display | EMDB header |
Images | emd_9950.png | 39.5 KB | ||
Filedesc metadata | emd-9950.cif.gz | 6.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9950 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9950 | HTTPS FTP |
-Validation report
Summary document | emd_9950_validation.pdf.gz | 358.2 KB | Display | EMDB validaton report |
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Full document | emd_9950_full_validation.pdf.gz | 357.8 KB | Display | |
Data in XML | emd_9950_validation.xml.gz | 6.1 KB | Display | |
Data in CIF | emd_9950_validation.cif.gz | 6.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9950 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-9950 | HTTPS FTP |
-Related structure data
Related structure data | 6k9lMC 9949C 9951C 6k9kC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_9950.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.62 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Dimeric human ATM (Ataxia telangiectasia mutated) kinase
Entire | Name: Dimeric human ATM (Ataxia telangiectasia mutated) kinase |
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Components |
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-Supramolecule #1: Dimeric human ATM (Ataxia telangiectasia mutated) kinase
Supramolecule | Name: Dimeric human ATM (Ataxia telangiectasia mutated) kinase type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Serine-protein kinase ATM
Macromolecule | Name: Serine-protein kinase ATM / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 351.127688 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MSLVLNDLLI CCRQLEHDRA TERKKEVEKF KRLIRDPETI KHLDRHSDSK QGKYLNWDAV FRFLQKYIQK ETECLRIAKP NVSASTQAS RQKKMQEISS LVKYFIKCAN RRAPRLKCQE LLNYIMDTVK DSSNGAIYGA DCSNILLKDI LSVRKYWCEI S QQQWLELF ...String: MSLVLNDLLI CCRQLEHDRA TERKKEVEKF KRLIRDPETI KHLDRHSDSK QGKYLNWDAV FRFLQKYIQK ETECLRIAKP NVSASTQAS RQKKMQEISS LVKYFIKCAN RRAPRLKCQE LLNYIMDTVK DSSNGAIYGA DCSNILLKDI LSVRKYWCEI S QQQWLELF SVYFRLYLKP SQDVHRVLVA RIIHAVTKGC CSQTDGLNSK FLDFFSKAIQ CARQEKSSSG LNHILAALTI FL KTLAVNF RIRVCELGDE ILPTLLYIWT QHRLNDSLKE VIIELFQLQI YIHHPKGAKT QEKGAYESTK WRSILYNLYD LLV NEISHI GSRGKYSSGF RNIAVKENLI ELMADICHQV FNEDTRSLEI SQSYTTTQRE SSDYSVPCKR KKIELGWEVI KDHL QKSQN DFDLVPWLQI ATQLISKYPA SLPNCELSPL LMILSQLLPQ QRHGERTPYV LRCLTEVALC QDKRSNLESS QKSDL LKLW NKIWCITFRG ISSEQIQAEN FGLLGAIIQG SLVEVDREFW KLFTGSACRP SCPAVCCLTL ALTTSIVPGT VKMGIE QNM CEVNRSFSLK ESIMKWLLFY QLEGDLENST EVPPILHSNF PHLVLEKILV SLTMKNCKAA MNFFQSVPEC EHHQKDK EE LSFSEVEELF LQTTFDKMDF LTIVRECGIE KHQSSIGFSV HQNLKESLDR CLLGLSEQLL NNYSSEITNS ETLVRCSR L LVGVLGCYCY MGVIAEEEAY KSELFQKAKS LMQCAGESIT LFKNKTNEEF RIGSLRNMMQ LCTRCLSNCT KKSPNKIAS GFFLRLLTSK LMNDIADICK SLASFIKKPF DRGEVESMED DTNGNLMEVE DQSSMNLFND YPDSSVSDAN EPGESQSTIG AINPLAEEY LSKQDLLFLD MLKFLCLCVT TAQTNTVSFR AADIRRKLLM LIDSSTLEPT KSLHLHMYLM LLKELPGEEY P LPMEDVLE LLKPLSNVCS LYRRDQDVCK TILNHVLHVV KNLGQSNMDS ENTRDAQGQF LTVIGAFWHL TKERKYIFSV RM ALVNCLK TLLEADPYSK WAILNVMGKD FPVNEVFTQF LADNHHQVRM LAAESINRLF QDTKGDSSRL LKALPLKLQQ TAF ENAYLK AQEGMREMSH SAENPETLDE IYNRKSVLLT LIAVVLSCSP ICEKQALFAL CKSVKENGLE PHLVKKVLEK VSET FGYRR LEDFMASHLD YLVLEWLNLQ DTEYNLSSFP FILLNYTNIE DFYRSCYKVL IPHLVIRSHF DEVKSIANQI QEDWK SLLT DCFPKILVNI LPYFAYEGTR DSGMAQQRET ATKVYDMLKS ENLLGKQIDH LFISNLPEIV VELLMTLHEP ANSSAS QST DLCDFSGDLD PAPNPPHFPS HVIKATFAYI SNCHKTKLKS ILEILSKSPD SYQKILLAIC EQAAETNNVY KKHRILK IY HLFVSLLLKD IKSGLGGAWA FVLRDVIYTL IHYINQRPSC IMDVSLRSFS LCCDLLSQVC QTAVTYCKDA LENHLHVI V GTLIPLVYEQ VEVQKQVLDL LKYLVIDNKD NENLYITIKL LDPFPDHVVF KDLRITQQKI KYSRGPFSLL EEINHFLSV SVYDALPLTR LEGLKDLRRQ LELHKDQMVD IMRASQDNPQ DGIMVKLVVN LLQLSKMAIN HTGEKEVLEA VGSCLGEVGP IDFSTIAIQ HSKDASYTKA LKLFEDKELQ WTFIMLTYLN NTLVEDCVKV RSAAVTCLKN ILATKTGHSF WEIYKMTTDP M LAYLQPFR TSRKKFLEVP RFDKENPFEG LDDINLWIPL SENHDIWIKT LTCAFLDSGG TKCEILQLLK PMCEVKTDFC QT VLPYLIH DILLQDTNES WRNLLSTHVQ GFFTSCLRHF SQTSRSTTPA NLDSESEHFF RCCLDKKSQR TMLAVVDYMR RQK RPSSGT IFNDAFWLDL NYLEVAKVAQ SCAAHFTALL YAEIYADKKS MDDQEKRSLA FEEGSQSTTI SSLSEKSKEE TGIS LQDLL LEIYRSIGEP DSLYGCGGGK MLQPITRLRT YEHEAMWGKA LVTYDLETAI PSSTRQAGII QALQNLGLCH ILSVY LKGL DYENKDWCPE LEELHYQAAW RNMQWDHCTS VSKEVEGTSY HESLYNALQS LRDREFSTFY ESLKYARVKE VEEMCK RSL ESVYSLYPTL SRLQAIGELE SIGELFSRSV THRQLSEVYI KWQKHSQLLK DSDFSFQEPI MALRTVILEI LMEKEMD NS QRECIKDILT KHLVELSILA RTFKNTQLPE RAIFQIKQYN SVSCGVSEWQ LEEAQVFWAK KEQSLALSIL KQMIKKLD A SCAANNPSLK LTYTECLRVC GNWLAETCLE NPAVIMQTYL EKAVEVAGNY DGESSDELRN GKMKAFLSLA RFSDTQYQR IENYMKSSEF ENKQALLKRA KEEVGLLREH KIQTNRYTVK VQRELELDEL ALRALKEDRK RFLCKAVENY INCLLSGEEH DMWVFRLCS LWLENSGVSE VNGMMKRDGM KIPTYKFLPL MYQLAARMGT KMMGGLGFHE VLNNLISRIS MDHPHHTLFI I LALANANR DEFLTKPEVA RRSRITKNVP KQSSQLDEDR TEAANRIICT IRSRRPQMVR SVEALCDAYI ILANLDATQW KT QRKGINI PADQPITKLK NLEDVVVPTM EIKVDHTGEY GNLVTIQSFK AEFRLAGGVN LPKIIDCVGS DGKERRQLVK GRD DLRQDA VMQQVFQMCN TLLQRNTETR KRKLTICTYK VVPLSQRSGV LEWCTGTVPI GEFLVNNEDG AHKRYRPNDF SAFQ CQKKM MEVQKKSFEE KYEVFMDVCQ NFQPVFRYFC MEKFLDPAIW FEKRLAYTRS VATSSIVGYI LGLGDRHVQN ILINE QSAE LVHIDLGVAF EQGKILPTPE TVPFRLTRDI VDGMGITGVE GVFRRCCEKT MEVMRNSQET LLTIVEVLLY DPLFDW TMN PLKALYLQQR PEDETELHPT LNADDQECKR NLSDIDQSFN KVAERVLMRL QEKLKGVEEG TVLSVGGQVN LLIQQAI DP KNLSRLFPGW KAWV UniProtKB: Serine-protein kinase ATM |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 282 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | #0 - Image recording ID: 1 / #0 - Film or detector model: FEI FALCON III (4k x 4k) / #0 - Average electron dose: 32.0 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Average electron dose: 38.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |