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- EMDB-10120: Structure of nucleotide-bound Tel1/ATM -

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Basic information

Entry
Database: EMDB / ID: EMD-10120
TitleStructure of nucleotide-bound Tel1/ATM
Map dataTel1 Whole Dimer
Sample
  • Complex: Tel1/ATM
    • Protein or peptide: Serine/threonine-protein kinase TEL1,Serine/threonine-protein kinase TEL1,Serine/threonine-protein kinase TEL1,Serine/threonine-protein kinase TEL1,Serine/threonine-protein kinase TEL1
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
KeywordsKinase / DNA Damage Response / CryoEM / Phosphatidylinositol-3-kinase-like kinase / HYDROLASE
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 / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / DNA damage response / mitochondrion / ATP binding / nucleus / cytoplasm
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 / FAT domain profile. / FATC domain profile. / FATC 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 / FATC domain / FATC / FAT domain profile. / FATC domain profile. / FATC domain / PIK-related kinase / Phosphatidylinositol 3- and 4-kinases signature 1. / Phosphatidylinositol 3- and 4-kinases signature 2. / Phosphatidylinositol 3/4-kinase, conserved site / Phosphatidylinositol 3-/4-kinase, catalytic domain superfamily / Phosphoinositide 3-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinases catalytic domain profile. / Phosphatidylinositol 3-/4-kinase, catalytic domain / Phosphatidylinositol 3- and 4-kinase / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase TEL1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsYates LA / Williams RM
Funding support United Kingdom, 1 items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Structure / Year: 2020
Title: Cryo-EM Structure of Nucleotide-Bound Tel1 Unravels the Molecular Basis of Inhibition and Structural Rationale for Disease-Associated Mutations.
Authors: Luke A Yates / Rhys M Williams / Sarem Hailemariam / Rafael Ayala / Peter Burgers / Xiaodong Zhang /
Abstract: Yeast Tel1 and its highly conserved human ortholog ataxia-telangiectasia mutated (ATM) are large protein kinases central to the maintenance of genome integrity. Mutations in ATM are found in ataxia- ...Yeast Tel1 and its highly conserved human ortholog ataxia-telangiectasia mutated (ATM) are large protein kinases central to the maintenance of genome integrity. Mutations in ATM are found in ataxia-telangiectasia (A-T) patients and ATM is one of the most frequently mutated genes in many cancers. Using cryoelectron microscopy, we present the structure of Tel1 in a nucleotide-bound state. Our structure reveals molecular details of key residues surrounding the nucleotide binding site and provides a structural and molecular basis for its intrinsically low basal activity. We show that the catalytic residues are in a productive conformation for catalysis, but the phosphatidylinositol 3-kinase-related kinase (PIKK) regulatory domain insert restricts peptide substrate access and the N-lobe is in an open conformation, thus explaining the requirement for Tel1 activation. Structural comparisons with other PIKKs suggest a conserved and common allosteric activation mechanism. Our work also provides a structural rationale for many mutations found in A-T and cancer.
History
DepositionJul 9, 2019-
Header (metadata) releaseOct 30, 2019-
Map releaseOct 30, 2019-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6s8f
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10120.png

Downloads & links

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Map

FileDownload / File: emd_10120.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTel1 Whole Dimer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 380 pix.
= 412.3 Å		1.09 Å/pix.
x 380 pix.
= 412.3 Å		1.09 Å/pix.
x 380 pix.
= 412.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.085 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.032512594 - 0.08536378
Average (Standard dev.)-0.00027760275 (±0.00329771)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions380380380
Spacing380380380
CellA=B=C: 412.30002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0851.0851.085
M x/y/z380380380
origin x/y/z0.0000.0000.000
length x/y/z412.300412.300412.300
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ307236
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS380380380
D min/max/mean-0.0330.085-0.000

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Supplemental data

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Additional map: Tel1 Kinase Core Dimer

Fileemd_10120_additional_1.map
AnnotationTel1 Kinase Core Dimer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Tel1 FATKIN Dimer

Fileemd_10120_additional_2.map
AnnotationTel1 FATKIN Dimer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tel1/ATM

EntireName: Tel1/ATM
Components
  • Complex: Tel1/ATM
    • Protein or peptide: Serine/threonine-protein kinase TEL1,Serine/threonine-protein kinase TEL1,Serine/threonine-protein kinase TEL1,Serine/threonine-protein kinase TEL1,Serine/threonine-protein kinase TEL1
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Tel1/ATM

SupramoleculeName: Tel1/ATM / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: Serine/threonine-protein kinase TEL1,Serine/threonine-protein kin...

MacromoleculeName: Serine/threonine-protein kinase TEL1,Serine/threonine-protein kinase TEL1,Serine/threonine-protein kinase TEL1,Serine/threonine-protein kinase TEL1,Serine/threonine-protein kinase TEL1
type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 292.579406 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) 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(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)GS IRGGKQRVFA TFIKCLQKLD SSNIINIMNS ISSYMAQV S YKNQSIIFYE IKSLFGPPQQ SIEKSAFYSL AMSMLSLVSY PSLVFSLEDM MTYSGFNHTR AFIQQALNKI TVAFRYQNL TELFEYCKFD LIMYWFNRTK VPTSKLEKEW DISLFGFADI HEFLGRYFVE ISAIYFSQGF NQKWILDMLH AITGNGDAYL VDNSYYLCI PLAFISGGVN ELIFDILPQI SGKTTVKYHK KYRLLMLKWI IRFTDLGSLT ELRSTVEKLF PTSYLSPYLF E NSSVSMRY QYPLHIPLAL GATLVQTQFA HEKNNTHEFK LLFLSVITDL EKTSTYIGKL RCARELKYLF VLYENVLVKS ST LNFIIIR LSKFLIDTQI HDEVITIFSS LLNLADKNTF EIEPSLPNLF CKIFIYLREN KQLSPSFQQA IKLLEHRDLI KIK TWKYCL DAIFGNIVQD DIYENTELLD ASDCGVDDVV LVSLLFSYAR RPVASKIGCS LSKAAAINIL KHHVPKEYLS KNFK LWFAA LSRRILQQEV QRERSTNFNN EVHLKNFEMV FRHPEQPHMI YQRISTFNKE AELYDSTEVF FISECILTYL VGYSI GNSE SEFCFRDNIM NENKDKVAPL DKDVLNAIYP LANNFGMESF ICDTYLSVNE PYNCWLSKFA RSLIHQISFN IPPIVC LYP LCKGSTAFCE LVLTDLFFLS TTYDPKSCLN WSNRIFTQIA MLLHVKDSEI KLKMLFNVIK MIRMGSRCKE RNCLRIY SS LDLQEICQIS LKIKEFKFGY LLFEEMNMPN IREMNINTLQ KIYECINDGD FLAGLPVPHS IEGVLNSINR IDSDTWKR F LFNNADFDAN YTTSLEEEKE SLIKATEDSG FYGLTSLLES RLSGSSDVYK WNLELGDWKL LTPKVVDSKA KGLYYAIKN LPQDVGFAEK SLEKSLLTIF DSRQHFISQT EWMDTLNAII EFIKIAAIPQ DVTSFPQTLM SIMKADKERL NTIDFYDHKT TLKSRHTLM NVLSRNSLDE NVKCSKYLRL GSIIQLANYV QLAIANGAPQ DALRNATLMS KTVKNIAKLY DDPSVVSQIE K LASFTSAN ALWESREYKA PVMIMRDLLA QNEKNISESI LYDDFKLLIN VPMDQIKARL VKWSSESRLE PAAAIYEKII VN WDINVED HESCSDVFYT LGSFLDEQAQ KLRSNGEIED REHRSYTGKS TLKALELIYK NTKLPENERK DAKRHYNRVL LQY NRDSEV LKALLLQKEK FLWHALHFYL NTLVFSNRYD NDIIDKFCGL WFENDDNSKI NQLLYKEIGT IPSWKFLPWV NQIA SKISM EENEFQKPLQ LTMKRLLYKL PYDSLYSVMS ILLYEKQSNK DTNISQKIQA VKKILLELQG YDRGAFAKKY LLPVQ EFCE MSVELANLKF VQNTKTLRLA NLKIGQYWLK QLNMEKLPLP TSNFTVKSSA DGRKARPYIV SVNETVGITT TGLSLP KIV TFNISDGTTQ KALMKGSNDD LRQDAIMEQV FQQVNKVLQN DKVLRNLDLG IRTYKVVPLG PKAGIIEFVA NSTSLHQ IL SKLHTNDKIT FDQARKGMKA VQTKSNEERL KAYLKITNEI KPQLRNFFFD SFPDPLDWFE AKKTYTKGVA ASSIVGYI L GLGDRHLNNI LLDCSTGEPI HIDLGIAFDQ GKLLPIPELV PFRLTRDIVD GFGVTGVDGL FRRSCERVYA VLRKDYVKV MCVLNILKWD PLYSWVMSPV KKYEHLFEEE HEITNFDNVS KFISNNDRNE NQESYRALKG VEEKLMGNGL SVESSVQDLI QQATDPSNL SVIYMGWSPF Y

UniProtKB: Serine/threonine-protein kinase TEL1

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Macromolecule #2: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 2 / Number of copies: 2 / Formula: ANP
Molecular weightTheoretical: 506.196 Da
Chemical component information

ChemComp-ANP:
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / AMP-PNP, energy-carrying molecule analogue*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 88.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

4097

Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 167596
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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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

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