+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-9893 | |||||||||
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Title | Tel1 kinase butterfly symmetric dimer | |||||||||
Map data | ||||||||||
Sample |
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Keywords | kinase / responds to DNA double-strand breaks / TRANSFERASE | |||||||||
Function / homology | Function and homology information DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / Pexophagy / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / phosphatidylinositol-4-phosphate binding / telomeric DNA binding / signal transduction in response to DNA damage / negative regulation of TORC1 signaling / telomere maintenance / DNA damage checkpoint signaling ...DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / Pexophagy / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / phosphatidylinositol-4-phosphate binding / telomeric DNA binding / signal transduction in response to DNA damage / negative regulation of TORC1 signaling / telomere maintenance / DNA damage checkpoint signaling / double-strand break repair / chromatin organization / chromosome, telomeric region / non-specific serine/threonine protein kinase / protein kinase activity / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / mitochondrion / ATP binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Xin J | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Res / Year: 2019 Title: Structural basis of allosteric regulation of Tel1/ATM kinase. Authors: Jiyu Xin / Zhu Xu / Xuejuan Wang / Yanhua Tian / Zhihui Zhang / Gang Cai / Abstract: ATM/Tel1 is an apical kinase that orchestrates the multifaceted DNA damage response. Mutations of ATM/Tel1 are associated with ataxia telangiectasia syndrome. Here, we report cryo-EM structures of ...ATM/Tel1 is an apical kinase that orchestrates the multifaceted DNA damage response. Mutations of ATM/Tel1 are associated with ataxia telangiectasia syndrome. Here, we report cryo-EM structures of symmetric dimer (4.1 Å) and asymmetric dimer (4.3 Å) of Saccharomyces cerevisiae Tel1. In the symmetric state, the side chains in Tel1 C-terminus (residues 1129-2787) are discernible and an atomic model is built. The substrate binding groove is completely embedded in the symmetric dimer by the intramolecular PRD and intermolecular LID domains. Point mutations in these domains sensitize the S. cerevisiae cells to DNA damage agents and hinder Tel1 activation due to reduced binding affinity for its activator Xrs2/Nbs1. In the asymmetric state, one monomer becomes more compact in two ways: the kinase N-lobe moves down and the Spiral of α-solenoid moves upwards, which resemble the conformational changes observed in active mTOR. The accessibility of the activation loop correlates with the synergistic conformational disorders in the TRD1-TRD2 linker, FATC and PRD domains, where critical post-translational modifications and activating mutations are coincidently condensed. This study reveals a tunable allosteric network in ATM/Tel1, which is important for substrate recognition, recruitment and efficient phosphorylation. | |||||||||
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_9893.map.gz | 60 MB | EMDB map data format | |
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Header (meta data) | emd-9893-v30.xml emd-9893.xml | 11.1 KB 11.1 KB | Display Display | EMDB header |
Images | emd_9893.png | 131.4 KB | ||
Filedesc metadata | emd-9893.cif.gz | 6.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-9893 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-9893 | HTTPS FTP |
-Related structure data
Related structure data | 6jxcMC 9892C 9894C 6jxaC 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_9893.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: 1.35 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 : Tel1 kinase butterfly dimer
Entire | Name: Tel1 kinase butterfly dimer |
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Components |
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-Supramolecule #1: Tel1 kinase butterfly dimer
Supramolecule | Name: Tel1 kinase butterfly dimer / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Macromolecule #1: Serine/threonine-protein kinase TEL1
Macromolecule | Name: Serine/threonine-protein kinase TEL1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 321.888312 KDa |
Sequence | String: MEDHGIVETL NFLSSTKIKE RNNALDELTT ILKEDPERIP TKALSTTAEA LVELLASEHT KYCDLLRNLT VSTTNKLSLS ENRLSTISY VLRLFVEKSC ERFKVKTLKL LLAVVPELMV KDGSKSLLDA VSVHLSFALD ALIKSDPFKL KFMIHQWISL V DKICEYFQ ...String: MEDHGIVETL NFLSSTKIKE RNNALDELTT ILKEDPERIP TKALSTTAEA LVELLASEHT KYCDLLRNLT VSTTNKLSLS ENRLSTISY VLRLFVEKSC ERFKVKTLKL LLAVVPELMV KDGSKSLLDA VSVHLSFALD ALIKSDPFKL KFMIHQWISL V DKICEYFQ SQMKLSMVDK TLTNFISILL NLLALDTVGI FQVTRTITWT VIDFLRLSKK ENGNTRLIMS LINQLILKCH CF SVIDTLM LIKEAWSYNL TIGCTSNELV QDQLSLFDVM SSELMNHKLP YMIGQENYVE ELRSESLVSL YREYILLRLS NYK PQLFTV NHVEFSYIRG SRDKNSWFAL PDFRLRDRGG RSVWLKILGI TKSLLTYFAL NRKNENYSLL FKRRKCDSDI PSIL RISDD MDTFLIHLLE ENSSHEFEVL GLQLCSFYGT LQDFTKSFAE QLKELLFSKF EKIQCFNWVC FSFIPLLSQK ECELS NGDM ARLFKVCLPL VKSNESCQLS CLLLANSIKF SKQLLSDEKT INQIYDLYEL SDILGPILVT NESFMLWGYL QYVGKD FQS MNGISSADRI FEWLKSKWNQ LRGTDAKQDQ FCNFISWLGN KYDPENPFND KKGEGANPVS LCWDESHKIW QHFQEQR EF LLGVKPEEKS ECFNTPFFNL PKVSLDLTRY NEILYRLLEN IESDAFSSPL QKFTWVAKLI QIVDNLCGDS TFSEFIAA Y KRTTLITIPQ LSFDSQNSYQ SFFEEVLSIR TINVDHLVLD KINMKEIVND FIRMQKNKSQ TGTSAINYFE ASSEDTTQN NSPYTIGGRF QKPLHSTIDK AVRAYLWSSR NKSISERLVA ILEFSDCVST DVFISYLGTV CQWLKQAIGE KSSYNKILEE FTEVLGEKL LCNHYSSSNQ AMLLLTSYIE AIRPQWLSYP EQPLNSDCND ILDWIISRFE DNSFTGVAPT VNLSMLLLSL L QNHDLSHG SIRGGKQRVF ATFIKCLQKL DSSNIINIMN SISSYMAQVS YKNQSIIFYE IKSLFGPPQQ SIEKSAFYSL AM SMLSLVS YPSLVFSLED MMTYSGFNHT RAFIQQALNK ITVAFRYQNL TELFEYCKFD LIMYWFNRTK VPTSKLEKEW DIS LFGFAD IHEFLGRYFV EISAIYFSQG FNQKWILDML HAITGNGDAY LVDNSYYLCI PLAFISGGVN ELIFDILPQI SGKT TVKYH KKYRLLMLKW IIRFTDLGSL TELRSTVEKL FPTSYLSPYL FENSSVSMRY QYPLHIPLAL GATLVQTQFA HEKNN THEF KLLFLSVITD LEKTSTYIGK LRCARELKYL FVLYENVLVK SSTLNFIIIR LSKFLIDTQI HDEVITIFSS LLNLAD KNT FEIEPSLPNL FCKIFIYLRE NKQLSPSFQQ AIKLLEHRDL IKIKTWKYCL DAIFGNIVQD DIYENTELLD ASDCGVD DV VLVSLLFSYA RRPVASKIGC SLSKAAAINI LKHHVPKEYL SKNFKLWFAA LSRRILQQEV QRERSTNFNN EVHLKNFE M VFRHPEQPHM IYQRISTFNK EAELYDSTEV FFISECILTY LVGYSIGNSE SEFCFRDNIM NENKDKVAPL DKDVLNAIY PLANNFGMES FICDTYLSVN EPYNCWLSKF ARSLIHQISF NIPPIVCLYP LCKGSTAFCE LVLTDLFFLS TTYDPKSCLN WSNRIFTQI AMLLHVKDSE IKLKMLFNVI KMIRMGSRCK ERNCLRIYSS LDLQEICQIS LKIKEFKFGY LLFEEMNMPN I REMNINTL QKIYECINDG DFLAGLPVPH SIEGVLNSIN RIDSDTWKRF LFNNADFDAN YTTSLEEEKE SLIKATEDSG FY GLTSLLE SRLSGSSDVY KWNLELGDWK LLTPKVVDSK AKGLYYAIKN LPQDVGFAEK SLEKSLLTIF DSRQHFISQT EWM DTLNAI IEFIKIAAIP QDVTSFPQTL MSIMKADKER LNTIDFYDHK TTLKSRHTLM NVLSRNSLDE NVKCSKYLRL GSII QLANY VQLAIANGAP QDALRNATLM SKTVKNIAKL YDDPSVVSQI EKLASFTSAN ALWESREYKA PVMIMRDLLA QNEKN ISES ILYDDFKLLI NVPMDQIKAR LVKWSSESRL EPAAAIYEKI IVNWDINVED HESCSDVFYT LGSFLDEQAQ KLRSNG EIE DREHRSYTGK STLKALELIY KNTKLPENER KDAKRHYNRV LLQYNRDSEV LKALLLQKEK FLWHALHFYL NTLVFSN RY DNDIIDKFCG LWFENDDNSK INQLLYKEIG TIPSWKFLPW VNQIASKISM EENEFQKPLQ LTMKRLLYKL PYDSLYSV M SILLYEKQSN KDTNISQKIQ AVKKILLELQ GYDRGAFAKK YLLPVQEFCE MSVELANLKF VQNTKTLRLA NLKIGQYWL KQLNMEKLPL PTSNFTVKSS ADGRKARPYI VSVNETVGIT TTGLSLPKIV TFNISDGTTQ KALMKGSNDD LRQDAIMEQV FQQVNKVLQ NDKVLRNLDL GIRTYKVVPL GPKAGIIEFV ANSTSLHQIL SKLHTNDKIT FDQARKGMKA VQTKSNEERL K AYLKITNE IKPQLRNFFF DSFPDPLDWF EAKKTYTKGV AASSIVGYIL GLGDRHLNNI LLDCSTGEPI HIDLGIAFDQ GK LLPIPEL VPFRLTRDIV DGFGVTGVDG LFRRSCERVY AVLRKDYVKV MCVLNILKWD PLYSWVMSPV KKYEHLFEEE HEI TNFDNV SKFISNNDRN ENQESYRALK GVEEKLMGNG LSVESSVQDL IQQATDPSNL SVIYMGWSPF Y UniProtKB: Serine/threonine-protein kinase TEL1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: RANDOM CONICAL TILT |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Number images used: 83185 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |