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- EMDB-3669: Closed dimer (C1) of human ATM (Ataxia telangiectasia mutated) -

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Basic information

Entry
Database: EMDB / ID: EMD-3669
TitleClosed dimer (C1) of human ATM (Ataxia telangiectasia mutated)
Map dataClosed dimer (C1) of human ATM (Ataxia telangiectasia mutated)
Sample
  • Organelle or cellular component: Dimeric human ATM (Ataxia telangiectasia mutated) kinase
    • Protein or peptide: Serine-protein kinase ATM
KeywordsPIKK / kinase / DNA-repair / HEAT-repeats / SIGNALING PROTEIN
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 / negative regulation of telomere capping / Sensing of DNA Double Strand Breaks / cellular response to nitrosative stress / establishment of protein-containing complex localization to telomere / regulation of microglial cell activation / meiotic telomere clustering / positive regulation of telomere maintenance via telomere lengthening ...positive regulation of DNA catabolic process / 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 / establishment of protein-containing complex localization to telomere / regulation of microglial cell activation / meiotic telomere clustering / positive regulation of telomere maintenance via telomere lengthening / pre-B cell allelic exclusion / male meiotic nuclear division / histone mRNA catabolic process / female meiotic nuclear division / extrinsic component of synaptic vesicle membrane / regulation of telomere maintenance via telomerase / cellular response to X-ray / peptidyl-serine autophosphorylation / DNA double-strand break processing / lipoprotein catabolic process / regulation of autophagosome assembly / V(D)J recombination / pexophagy / Impaired BRCA2 binding to PALB2 / oocyte development / reciprocal meiotic recombination / positive regulation of DNA damage response, signal transduction by p53 class mediator / DNA repair complex / 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) / positive regulation of double-strand break repair / response to ionizing radiation / Impaired BRCA2 binding to RAD51 / mitotic spindle assembly checkpoint signaling / negative regulation of B cell proliferation / cellular response to stress / TP53 Regulates Transcription of Caspase Activators and Caspases / 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 / cellular response to retinoic acid / negative regulation of TORC1 signaling / 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 / Nonhomologous End-Joining (NHEJ) / TP53 Regulates Transcription of DNA Repair Genes / Stabilization of p53 / Autodegradation of the E3 ubiquitin ligase COP1 / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / cellular response to gamma radiation / brain development / multicellular organism growth / DNA Damage/Telomere Stress Induced Senescence / Regulation of TP53 Activity through Methylation / Meiotic recombination / HDR through Homologous Recombination (HRR) / double-strand break repair via nonhomologous end joining / spindle / intrinsic apoptotic signaling pathway in response to DNA damage / cellular senescence / positive regulation of neuron apoptotic process / Regulation of TP53 Degradation / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / peptidyl-serine phosphorylation / site of double-strand break / chromosome / heart development / Processing of DNA double-strand break ends / protein autophosphorylation / neuron apoptotic process / regulation of apoptotic process / Regulation of TP53 Activity through Phosphorylation / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity
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 / PIK-related kinase, FAT / FAT domain / FATC / 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 / PIK-related kinase, FAT / FAT 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 / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine-protein kinase ATM
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.7 Å
AuthorsBaretic D / Pollard HK
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (United Kingdom)MC_U105184308 United Kingdom
LMB/AstraZenecaMC_A024-5PF9H United Kingdom
CitationJournal: Sci Adv / Year: 2017
Title: Structures of closed and open conformations of dimeric human ATM.
Authors: Domagoj Baretić / Hannah K Pollard / David I Fisher / Christopher M Johnson / Balaji Santhanam / Caroline M Truman / Tomas Kouba / Alan R Fersht / Christopher Phillips / Roger L Williams /
Abstract: ATM (ataxia-telangiectasia mutated) is a phosphatidylinositol 3-kinase-related protein kinase (PIKK) best known for its role in DNA damage response. ATM also functions in oxidative stress response, ...ATM (ataxia-telangiectasia mutated) is a phosphatidylinositol 3-kinase-related protein kinase (PIKK) best known for its role in DNA damage response. ATM also functions in oxidative stress response, insulin signaling, and neurogenesis. Our electron cryomicroscopy (cryo-EM) suggests that human ATM is in a dynamic equilibrium between closed and open dimers. In the closed state, the PIKK regulatory domain blocks the peptide substrate-binding site, suggesting that this conformation may represent an inactive or basally active enzyme. The active site is held in this closed conformation by interaction with a long helical hairpin in the TRD3 (tetratricopeptide repeats domain 3) domain of the symmetry-related molecule. The open dimer has two protomers with only a limited contact interface, and it lacks the intermolecular interactions that block the peptide-binding site in the closed dimer. This suggests that the open conformation may be more active. The ATM structure shows the detailed topology of the regulator-interacting N-terminal helical solenoid. The ATM conformational dynamics shown by the structures represent an important step in understanding the enzyme regulation.
History
DepositionApr 13, 2017-
Header (metadata) releaseApr 26, 2017-
Map releaseMay 17, 2017-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5np0
  • Surface level: 0.035
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3669.png

Downloads & links

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Map

FileDownload / File: emd_3669.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationClosed dimer (C1) of human ATM (Ataxia telangiectasia mutated)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.43 Å/pix.
x 300 pix.
= 429. Å		1.43 Å/pix.
x 300 pix.
= 429. Å		1.43 Å/pix.
x 300 pix.
= 429. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.43 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.028897868 - 0.09947639
Average (Standard dev.)-0.0000113511205 (±0.0042891996)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 428.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.431.431.43
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z429.000429.000429.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0290.099-0.000

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Supplemental data

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Sample components

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Entire : Dimeric human ATM (Ataxia telangiectasia mutated) kinase

EntireName: Dimeric human ATM (Ataxia telangiectasia mutated) kinase
Components
  • Organelle or cellular component: Dimeric human ATM (Ataxia telangiectasia mutated) kinase
    • Protein or peptide: Serine-protein kinase ATM

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Supramolecule #1: Dimeric human ATM (Ataxia telangiectasia mutated) kinase

SupramoleculeName: Dimeric human ATM (Ataxia telangiectasia mutated) kinase
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all / Details: homodimer
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 705 KDa

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Macromolecule #1: Serine-protein kinase ATM

MacromoleculeName: Serine-protein kinase ATM / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 352.393969 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKH MSLVLNDLLI CCRQLEHDRA TERKKEVEKF KRLIRDPETI KHLDRHSDSK QGKYLNWDAV FRFLQKYIQK ETECLRIAK PNVSASTQAS RQKKMQEISS LVKYFIKCAN RRAPRLKCQE LLNYIMDTVK DSSNGAIYGA DCSNILLKDI L SVRKYWCE ...String:
MDYKDDDDKH MSLVLNDLLI CCRQLEHDRA TERKKEVEKF KRLIRDPETI KHLDRHSDSK QGKYLNWDAV FRFLQKYIQK ETECLRIAK PNVSASTQAS RQKKMQEISS LVKYFIKCAN RRAPRLKCQE LLNYIMDTVK DSSNGAIYGA DCSNILLKDI L SVRKYWCE ISQQQWLELF SVYFRLYLKP SQDVHRVLVA RIIHAVTKGC CSQTDGLNSK FLDFFSKAIQ CARQEKSSSG LN HILAALT IFLKTLAVNF RIRVCELGDE ILPTLLYIWT QHRLNDSLKE VIIELFQLQI YIHHPKGAKT QEKGAYESTK WRS ILYNLY DLLVNEISHI GSRGKYSSGF RNIAVKENLI ELMADICHQV FNEDTRSLEI SQSYTTTQRE SSDYSVPCKR KKIE LGWEV IKDHLQKSQN DFDLVPWLQI ATQLISKYPA SLPNCELSPL LMILSQLLPQ QRHGERTPYV LRCLTEVALC QDKRS NLES SQKSDLLKLW NKIWCITFRG ISSEQIQAEN FGLLGAIIQG SLVEVDREFW KLFTGSACRP SCPAVCCLTL ALTTSI VPG TVKMGIEQNM CEVNRSFSLK ESIMKWLLFY QLEGDLENST EVPPILHSNF PHLVLEKILV SLTMKNCKAA MNFFQSV PE CEHHQKDKEE LSFSEVEELF LQTTFDKMDF LTIVRECGIE KHQSSIGFSV HQNLKESLDR CLLGLSEQLL NNYSSEIT N SETLVRCSRL LVGVLGCYCY MGVIAEEEAY KSELFQKAKS LMQCAGESIT LFKNKTNEEF RIGSLRNMMQ LCTRCLSNC TKKSPNKIAS GFFLRLLTSK LMNDIADICK SLASFIKKPF DRGEVESMED DTNGNLMEVE DQSSMNLFND YPDSSVSDAN EPGESQSTI GAINPLAEEY LSKQDLLFLD MLKFLCLCVT TAQTNTVSFR AADIRRKLLM LIDSSTLEPT KSLHLHMYLM L LKELPGEE YPLPMEDVLE LLKPLSNVCS LYRRDQDVCK TILNHVLHVV KNLGQSNMDS ENTRDAQGQF LTVIGAFWHL TK ERKYIFS VRMALVNCLK TLLEADPYSK WAILNVMGKD FPVNEVFTQF LADNHHQVRM LAAESINRLF QDTKGDSSRL LKA LPLKLQ QTAFENAYLK AQEGMREMSH SAENPETLDE IYNRKSVLLT LIAVVLSCSP ICEKQALFAL CKSVKENGLE PHLV KKVLE KVSETFGYRR LEDFMASHLD YLVLEWLNLQ DTEYNLSSFP FILLNYTNIE DFYRSCYKVL IPHLVIRSHF DEVKS IANQ IQEDWKSLLT DCFPKILVNI LPYFAYEGTR DSGMAQQRET ATKVYDMLKS ENLLGKQIDH LFISNLPEIV VELLMT LHE PANSSASQST DLCDFSGDLD PAPNPPHFPS HVIKATFAYI SNCHKTKLKS ILEILSKSPD SYQKILLAIC EQAAETN NV YKKHRILKIY HLFVSLLLKD IKSGLGGAWA FVLRDVIYTL IHYINQRPSC IMDVSLRSFS LCCDLLSQVC QTAVTYCK D ALENHLHVIV GTLIPLVYEQ VEVQKQVLDL LKYLVIDNKD NENLYITIKL LDPFPDHVVF KDLRITQQKI KYSRGPFSL LEEINHFLSV SVYDALPLTR LEGLKDLRRQ LELHKDQMVD IMRASQDNPQ DGIMVKLVVN LLQLSKMAIN HTGEKEVLEA VGSCLGEVG PIDFSTIAIQ HSKDASYTKA LKLFEDKELQ WTFIMLTYLN NTLVEDCVKV RSAAVTCLKN ILATKTGHSF W EIYKMTTD PMLAYLQPFR TSRKKFLEVP RFDKENPFEG LDDINLWIPL SENHDIWIKT LTCAFLDSGG TKCEILQLLK PM CEVKTDF CQTVLPYLIH DILLQDTNES WRNLLSTHVQ GFFTSCLRHF SQTSRSTTPA NLDSESEHFF RCCLDKKSQR TML AVVDYM RRQKRPSSGT IFNDAFWLDL NYLEVAKVAQ SCAAHFTALL YAEIYADKKS MDDQEKRSLA FEEGSQSTTI SSLS EKSKE ETGISLQDLL LEIYRSIGEP DSLYGCGGGK MLQPITRLRT YEHEAMWGKA LVTYDLETAI PSSTRQAGII QALQN LGLC HILSVYLKGL DYENKDWCPE LEELHYQAAW RNMQWDHCTS VSKEVEGTSY HESLYNALQS LRDREFSTFY ESLKYA RVK EVEEMCKRSL ESVYSLYPTL SRLQAIGELE SIGELFSRSV THRQLSEVYI KWQKHSQLLK DSDFSFQEPI MALRTVI LE ILMEKEMDNS QRECIKDILT KHLVELSILA RTFKNTQLPE RAIFQIKQYN SVSCGVSEWQ LEEAQVFWAK KEQSLALS I LKQMIKKLDA SCAANNPSLK LTYTECLRVC GNWLAETCLE NPAVIMQTYL EKAVEVAGNY DGESSDELRN GKMKAFLSL ARFSDTQYQR IENYMKSSEF ENKQALLKRA KEEVGLLREH KIQTNRYTVK VQRELELDEL ALRALKEDRK RFLCKAVENY INCLLSGEE HDMWVFRLCS LWLENSGVSE VNGMMKRDGM KIPTYKFLPL MYQLAARMGT KMMGGLGFHE VLNNLISRIS M DHPHHTLF IILALANANR DEFLTKPEVA RRSRITKNVP KQSSQLDEDR TEAANRIICT IRSRRPQMVR SVEALCDAYI IL ANLDATQ WKTQRKGINI PADQPITKLK NLEDVVVPTM EIKVDHTGEY GNLVTIQSFK AEFRLAGGVN LPKIIDCVGS DGK ERRQLV KGRDDLRQDA VMQQVFQMCN TLLQRNTETR KRKLTICTYK VVPLSQRSGV LEWCTGTVPI GEFLVNNEDG AHKR YRPND FSAFQCQKKM MEVQKKSFEE KYEVFMDVCQ NFQPVFRYFC MEKFLDPAIW FEKRLAYTRS VATSSIVGYI LGLGD RHVQ NILINEQSAE LVHIDLGVAF EQGKILPTPE TVPFRLTRDI VDGMGITGVE GVFRRCCEKT MEVMRNSQET LLTIVE VLL YDPLFDWTMN PLKALYLQQR PEDETELHPT LNADDQECKR NLSDIDQSFN KVAERVLMRL QEKLKGVEEG TVLSVGG QV NLLIQQAIDP KNLSRLFPGW KAWV

UniProtKB: Serine-protein kinase ATM

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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

Concentration0.6 mg/mL
BufferpH: 8
Component:
ConcentrationNameFormula
25.0 mMHEPES pH 7.5
25.0 mMTris pH 8.8
150.0 mMsodium chlorideNaCl
0.01 %Tween 20
2.0 mMTCEP
GridModel: Quantifoil, UltrAuFoil, R1.2/1.3 / Material: GOLD / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: HOMEMADE PLUNGER / Details: 3 uL of sample/grid blotted for 12 s.
DetailsN-terminally FLAG-tagged ATM kinase was purified by affinity chromatography (anti-FLAG), overnight dialysis and gel-filtration. The sample was flash-frozen in liquid nitrogen until used for cryo-EM.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 80.15 K
Specialist opticsEnergy filter - Name: GIF / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-20 / Number grids imaged: 4 / Number real images: 2720 / Average exposure time: 0.8 sec. / Average electron dose: 2.1 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 35714 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 2.5 µm / Nominal magnification: 97902
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 371671
Startup modelType of model: INSILICO MODEL
In silico model: Experimental images were used to generate the initial model in EMAN2.
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 25315
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 1.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4jsp


Chain - Source name: PDB / Chain - Initial model type: experimental model
Details: building de novo the structure of ATM N-solenoid and modelling of the ATM FATKIN (using mTOR FATKIN PDB:4JSP)
RefinementSpace: REAL
Output model

PDB-5np0:
Closed dimer of human ATM (Ataxia telangiectasia mutated)

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