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- EMDB-17268: ATM(Q2971A) dimeric C-terminal region in complex with Mg AMP-PNP -

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Basic information

Entry
Database: EMDB / ID: EMD-17268
TitleATM(Q2971A) dimeric C-terminal region in complex with Mg AMP-PNP
Map dataUnsharpened map
Sample
  • Complex: ATM(Q2971A) dimeric C-terminal region bound to Mg AMP-PNP
    • Protein or peptide: Serine-protein kinase ATM
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsAtaxia-Telangiectasia Mutated / ATM / kinase / 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 / positive regulation of DNA damage response, signal transduction by p53 class mediator / establishment of protein-containing complex localization to telomere / cellular response to nitrosative stress / 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 / establishment of protein-containing complex localization to telomere / cellular response to nitrosative stress / 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 / 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 / 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 / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / Presynaptic phase of homologous DNA pairing and strand exchange / peroxisomal matrix / replicative senescence / Regulation of HSF1-mediated heat shock response / signal transduction in response to DNA damage / 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 / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / telomere maintenance / positive regulation of cell adhesion / Pexophagy / post-embryonic development / thymus development / regulation of signal transduction by p53 class mediator / DNA damage checkpoint signaling / regulation of autophagy / determination of adult lifespan / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / Stabilization of p53 / double-strand break repair via homologous recombination / Autodegradation of the E3 ubiquitin ligase COP1 / G2/M DNA damage checkpoint / brain development / multicellular organism growth / DNA Damage/Telomere Stress Induced Senescence / HDR through Homologous Recombination (HRR) / cellular response to gamma radiation / Regulation of TP53 Activity through Methylation / Meiotic recombination / double-strand break repair via nonhomologous end joining / spindle / cellular response to reactive oxygen species / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of neuron apoptotic process / cellular senescence / Regulation of TP53 Degradation / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / heart development / site of double-strand break / Processing of DNA double-strand break ends / peptidyl-serine phosphorylation / cytoplasmic vesicle / regulation of apoptotic process / neuron apoptotic process / Regulation of TP53 Activity through Phosphorylation / protein autophosphorylation / response to hypoxia / regulation of cell cycle / non-specific serine/threonine protein kinase / positive regulation of cell migration
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: 2.5 Å
AuthorsHowes AC / Perisic O / Williams RL
Funding support United Kingdom, 3 items
OrganizationGrant numberCountry
Cancer Research UKC14801/A21211 United Kingdom
Cancer Research UKDRCPGM/100014 United Kingdom
Medical Research Council (MRC, United Kingdom)MC_U105184308 United Kingdom
CitationJournal: Sci Adv / Year: 2023
Title: Structural insights into the activation of ataxia-telangiectasia mutated by oxidative stress.
Authors: Anna C Howes / Olga Perisic / Roger L Williams /
Abstract: Ataxia-telangiectasia mutated (ATM) is a master kinase regulating DNA damage response that is activated by DNA double-strand breaks. However, ATM is also directly activated by reactive oxygen ...Ataxia-telangiectasia mutated (ATM) is a master kinase regulating DNA damage response that is activated by DNA double-strand breaks. However, ATM is also directly activated by reactive oxygen species, but how oxidative activation is achieved remains unknown. We determined the cryo-EM structure of an HO-activated ATM and showed that under oxidizing conditions, ATM formed an intramolecular disulfide bridge between two protomers that are rotated relative to each other when compared to the basal state. This rotation is accompanied by release of the substrate-blocking PRD region and twisting of the N-lobe relative to the C-lobe, which greatly optimizes catalysis. This active site remodeling enabled us to capture a substrate (p53) bound to the enzyme. This provides the first structural insights into how ATM is activated during oxidative stress.
History
DepositionMay 2, 2023-
Header (metadata) releaseSep 27, 2023-
Map releaseSep 27, 2023-
UpdateOct 11, 2023-
Current statusOct 11, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17268.png

Downloads & links

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Map

FileDownload / File: emd_17268.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 400 pix.
= 330.4 Å		0.83 Å/pix.
x 400 pix.
= 330.4 Å		0.83 Å/pix.
x 400 pix.
= 330.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.21919693 - 0.5428834
Average (Standard dev.)0.00060885935 (±0.014874373)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 330.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17268_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map

Fileemd_17268_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A

Fileemd_17268_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_17268_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : ATM(Q2971A) dimeric C-terminal region bound to Mg AMP-PNP

EntireName: ATM(Q2971A) dimeric C-terminal region bound to Mg AMP-PNP
Components
  • Complex: ATM(Q2971A) dimeric C-terminal region bound to Mg AMP-PNP
    • Protein or peptide: Serine-protein kinase ATM
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION

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Supramolecule #1: ATM(Q2971A) dimeric C-terminal region bound to Mg AMP-PNP

SupramoleculeName: ATM(Q2971A) dimeric C-terminal region bound to Mg AMP-PNP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: The map deposited is from local refinement on the C-terminal region of the ATM dimer to obtain higher resolution details. Please note the sample contains the whole ATM dimer itself and not ...Details: The map deposited is from local refinement on the C-terminal region of the ATM dimer to obtain higher resolution details. Please note the sample contains the whole ATM dimer itself and not just the C-terminal region.
Source (natural)Organism: Homo sapiens (human)

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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: 365.005562 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYKDDDDKH MGVQVETISP GDGRTFPKRG QTCVVHYTGM LEDGKKFDSS RDRNKPFKFM LGKQEVIRGW EEGVAQMSVG QRAKLTISP DYAYGATGHP GIIPPHATLV FDVELLKLEG GSAGSGSASM SLVLNDLLIC CRQLEHDRAT ERKKEVEKFK R LIRDPETI ...String:
MDYKDDDDKH MGVQVETISP GDGRTFPKRG QTCVVHYTGM LEDGKKFDSS RDRNKPFKFM LGKQEVIRGW EEGVAQMSVG QRAKLTISP DYAYGATGHP GIIPPHATLV FDVELLKLEG GSAGSGSASM SLVLNDLLIC CRQLEHDRAT ERKKEVEKFK R LIRDPETI KHLDRHSDSK QGKYLNWDAV FRFLQKYIQK ETECLRIAKP NVSASTQASR QKKMQEISSL VKYFIKCANR RA PRLKCQE LLNYIMDTVK DSSNGAIYGA DCSNILLKDI LSVRKYWCEI SQQQWLELFS VYFRLYLKPS QDVHRVLVAR IIH AVTKGC CSQTDGLNSK FLDFFSKAIQ CARQEKSSSG LNHILAALTI FLKTLAVNFR IRVCELGDEI LPTLLYIWTQ HRLN DSLKE VIIELFQLQI YIHHPKGAKT QEKGAYESTK WRSILYNLYD LLVNEISHIG SRGKYSSGFR NIAVKENLIE LMADI CHQV FNEDTRSLEI SQSYTTTQRE SSDYSVPCKR KKIELGWEVI KDHLQKSQND FDLVPWLQIA TQLISKYPAS LPNCEL SPL LMILSQLLPQ QRHGERTPYV LRCLTEVALC QDKRSNLESS QKSDLLKLWN KIWCITFRGI SSEQIQAENF GLLGAII QG SLVEVDREFW KLFTGSACRP SCPAVCCLTL ALTTSIVPGT VKMGIEQNMC EVNRSFSLKE SIMKWLLFYQ LEGDLENS T EVPPILHSNF PHLVLEKILV SLTMKNCKAA MNFFQSVPEC EHHQKDKEEL SFSEVEELFL QTTFDKMDFL TIVRECGIE KHQSSIGFSV HQNLKESLDR CLLGLSEQLL NNYSSEITNS ETLVRCSRLL VGVLGCYCYM GVIAEEEAYK SELFQKAKSL MQCAGESIT LFKNKTNEEF RIGSLRNMMQ LCTRCLSNCT KKSPNKIASG FFLRLLTSKL MNDIADICKS LASFIKKPFD R GEVESMED DTNGNLMEVE DQSSMNLFND YPDSSVSDAN EPGESQSTIG AINPLAEEYL SKQDLLFLDM LKFLCLCVTT AQ TNTVSFR AADIRRKLLM LIDSSTLEPT KSLHLHMYLM LLKELPGEEY PLPMEDVLEL LKPLSNVCSL YRRDQDVCKT ILN HVLHVV KNLGQSNMDS ENTRDAQGQF LTVIGAFWHL TKERKYIFSV RMALVNCLKT LLEADPYSKW AILNVMGKDF PVNE VFTQF LADNHHQVRM LAAESINRLF QDTKGDSSRL LKALPLKLQQ TAFENAYLKA QEGMREMSHS AENPETLDEI YNRKS VLLT LIAVVLSCSP ICEKQALFAL CKSVKENGLE PHLVKKVLEK VSETFGYRRL EDFMASHLDY LVLEWLNLQD TEYNLS SFP FILLNYTNIE DFYRSCYKVL IPHLVIRSHF DEVKSIANQI QEDWKSLLTD CFPKILVNIL PYFAYEGTRD SGMAQQR ET ATKVYDMLKS ENLLGKQIDH LFISNLPEIV VELLMTLHEP ANSSASQSTD LCDFSGDLDP APNPPHFPSH VIKATFAY I SNCHKTKLKS ILEILSKSPD SYQKILLAIC EQAAETNNVY KKHRILKIYH LFVSLLLKDI KSGLGGAWAF VLRDVIYTL IHYINQRPSC IMDVSLRSFS LCCDLLSQVC QTAVTYCKDA LENHLHVIVG TLIPLVYEQV EVQKQVLDLL KYLVIDNKDN ENLYITIKL LDPFPDHVVF KDLRITQQKI KYSRGPFSLL EEINHFLSVS VYDALPLTRL EGLKDLRRQL ELHKDQMVDI M RASQDNPQ DGIMVKLVVN LLQLSKMAIN HTGEKEVLEA VGSCLGEVGP IDFSTIAIQH SKDASYTKAL KLFEDKELQW TF IMLTYLN NTLVEDCVKV RSAAVTCLKN ILATKTGHSF WEIYKMTTDP MLAYLQPFRT SRKKFLEVPR FDKENPFEGL DDI NLWIPL SENHDIWIKT LTCAFLDSGG TKCEILQLLK PMCEVKTDFC QTVLPYLIHD ILLQDTNESW RNLLSTHVQG FFTS CLRHF SQTSRSTTPA NLDSESEHFF RCCLDKKSQR TMLAVVDYMR RQKRPSSGTI FNDAFWLDLN YLEVAKVAQS CAAHF TALL YAEIYADKKS MDDQEKRSLA FEEGSQSTTI SSLSEKSKEE TGISLQDLLL EIYRSIGEPD SLYGCGGGKM LQPITR LRT YEHEAMWGKA LVTYDLETAI PSSTRQAGII QALQNLGLCH ILSVYLKGLD YENKDWCPEL EELHYQAAWR NMQWDHC TS VSKEVEGTSY HESLYNALQS LRDREFSTFY ESLKYARVKE VEEMCKRSLE SVYSLYPTLS RLQAIGELES IGELFSRS V THRQLSEVYI KWQKHSQLLK DSDFSFQEPI MALRTVILEI LMEKEMDNSQ RECIKDILTK HLVELSILAR TFKNTQLPE RAIFQIKQYN SVSCGVSEWQ LEEAQVFWAK KEQSLALSIL KQMIKKLDAS CAANNPSLKL TYTECLRVCG NWLAETCLEN PAVIMQTYL EKAVEVAGNY DGESSDELRN GKMKAFLSLA RFSDTQYQRI ENYMKSSEFE NKQALLKRAK EEVGLLREHK I QTNRYTVK VQRELELDEL ALRALKEDRK RFLCKAVENY INCLLSGEEH DMWVFRLCSL WLENSGVSEV NGMMKRDGMK IP TYKFLPL MYQLAARMGT KMMGGLGFHE VLNNLISRIS MDHPHHTLFI ILALANANRD EFLTKPEVAR RSRITKNVPK QSS QLDEDR TEAANRIICT IRSRRPQMVR SVEALCDAYI ILANLDATQW KTQRKGINIP ADQPITKLKN LEDVVVPTME IKVD HTGEY GNLVTIQSFK AEFRLAGGVN LPKIIDCVGS DGKERRQLVK GRDDLRQDAV MQQVFQMCNT LLQRNTETRK RKLTI CTYK VVPLSQRSGV LEWCTGTVPI GEFLVNNEDG AHKRYRPNDF SAFQCQKKMM EVQKKSFEEK YEVFMDVCQN FQPVFR YFC MEKFLDPAIW FEKRLAYTRS VATSSIVGYI LGLGDRHVQN ILINEQSAEL VHIDLGVAFE QGKILPTPET VPFRLTR DI VDGMGITGVE GVFRRCCEKT MEVMRNSQET LLTIVEVLLY DPLFDWTMNP LKALYLAQRP EDETELHPTL NADDQECK R NLSDIDQSFN KVAERVLMRL QEKLKGVEEG TVLSVGGQVN LLIQQAIDPK NLSRLFPGWK AWV

UniProtKB: Serine-protein kinase ATM

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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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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 39.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7sic

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF
Software: (Name: RELION (ver. 3.1), RELION (ver. 4.0), cryoSPARC (ver. 4))
Number images used: 1207435
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

7sic


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-8oxq:
ATM(Q2971A) dimeric C-terminal region in complex with Mg AMP-PNP

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