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- EMDB-9892: Tel1 kinase compact monomer -

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Basic information

Entry
Database: EMDB / ID: EMD-9892
TitleTel1 kinase compact monomer
Map data
Sample
  • Organelle or cellular component: Tel1 kinase compact monomer
    • Protein or peptide: Serine/threonine-protein kinase TEL1
Keywordskinase / responds to DNA double-strand breaks / TRANSFERASE
Function / homology
Function and homology information


Pexophagy / DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / 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 ...Pexophagy / DNA Damage/Telomere Stress Induced Senescence / Sensing of DNA Double Strand Breaks / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / 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 / phosphorylation / DNA repair / protein serine kinase activity / protein serine/threonine kinase activity / DNA damage response / mitochondrion / ATP binding / nucleus
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 / FATC domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. ...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 / FATC domain / FATC / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / 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 / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase TEL1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsXin J
Funding support China, 1 items
OrganizationGrant numberCountry
National Basic Research Program of China (973 Program) China
CitationJournal: 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
DepositionApr 23, 2019-
Header (metadata) releaseJul 3, 2019-
Map releaseJul 3, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6jxa
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9892.png

Downloads & links

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Map

FileDownload / File: emd_9892.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.035 / Movie #1: 0.035
Minimum - Maximum-0.06860553 - 0.13487564
Average (Standard dev.)0.0005073465 (±0.0070535154)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 345.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z345.600345.600345.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-100-100-99
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0690.1350.001

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Supplemental data

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Sample components

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Entire : Tel1 kinase compact monomer

EntireName: Tel1 kinase compact monomer
Components
  • Organelle or cellular component: Tel1 kinase compact monomer
    • Protein or peptide: Serine/threonine-protein kinase TEL1

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Supramolecule #1: Tel1 kinase compact monomer

SupramoleculeName: Tel1 kinase compact monomer / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Serine/threonine-protein kinase TEL1

MacromoleculeName: 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
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 321.888312 KDa
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: RANDOM CONICAL TILT
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 25708

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