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- EMDB-17265: ATM(Q2971A) activated by oxidative stress in complex with Mg AMP-... -

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Basic information

Entry
Database: EMDB / ID: EMD-17265
TitleATM(Q2971A) activated by oxidative stress in complex with Mg AMP-PNP and p53 peptide
Map dataUnsharpened map
Sample
  • Complex: ATM(Q2971A) dimer activated by H2O2 and bound to Mg AMP-PNP and p53 substrate peptide
    • Protein or peptide: Cellular tumor antigen p53
    • Protein or peptide: Serine-protein kinase ATM
  • Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
  • Ligand: MAGNESIUM ION
  • Ligand: ZINC ION
KeywordsAtaxia-Telangiectasia Mutated / ATM / kinase / oxidative stress / SIGNALING PROTEIN
Function / homology
Function and homology information


establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / cellular response to nitrosative stress / negative regulation of telomere capping / peptidyl-serine autophosphorylation / Sensing of DNA Double Strand Breaks / establishment of protein-containing complex localization to telomere / positive regulation of telomere maintenance via telomere lengthening / DNA-dependent protein kinase activity / extrinsic component of synaptic vesicle membrane ...establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / cellular response to nitrosative stress / negative regulation of telomere capping / peptidyl-serine autophosphorylation / Sensing of DNA Double Strand Breaks / establishment of protein-containing complex localization to telomere / positive regulation of telomere maintenance via telomere lengthening / DNA-dependent protein kinase activity / extrinsic component of synaptic vesicle membrane / histone mRNA catabolic process / regulation of telomere maintenance via telomerase / pre-B cell allelic exclusion / histone H2AXS139 kinase activity / DNA repair complex / cellular response to X-ray / DNA double-strand break processing / regulation of autophagosome assembly / pexophagy / negative regulation of helicase activity / signal transduction by p53 class mediator / negative regulation of glucose catabolic process to lactate via pyruvate / regulation of fibroblast apoptotic process / Loss of function of TP53 in cancer due to loss of tetramerization ability / Regulation of TP53 Expression / regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Impaired BRCA2 binding to PALB2 / negative regulation of miRNA processing / regulation of cell cycle G2/M phase transition / negative regulation of G1 to G0 transition / Transcriptional activation of cell cycle inhibitor p21 / intrinsic apoptotic signaling pathway in response to hypoxia / : / negative regulation of pentose-phosphate shunt / Activation of NOXA and translocation to mitochondria / germ cell nucleus / regulation of tissue remodeling / ATP-dependent DNA/DNA annealing activity / thymocyte apoptotic process / oligodendrocyte apoptotic process / oxidative stress-induced premature senescence / bone marrow development / positive regulation of thymocyte apoptotic process / positive regulation of mitochondrial membrane permeability / cellular response to actinomycin D / regulation of mitochondrial membrane permeability involved in apoptotic process / histone deacetylase regulator activity / circadian behavior / negative regulation of stem cell proliferation / positive regulation of programmed necrotic cell death / T cell proliferation involved in immune response / T cell lineage commitment / RUNX3 regulates CDKN1A transcription / B cell lineage commitment / TP53 Regulates Transcription of Death Receptors and Ligands / Activation of PUMA and translocation to mitochondria / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / mRNA transcription / reciprocal meiotic recombination / negative regulation of glial cell proliferation / negative regulation of neuroblast proliferation / regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of B cell proliferation / Regulation of TP53 Activity through Association with Co-factors / cellular response to stress / positive regulation of DNA damage response, signal transduction by p53 class mediator / ER overload response / mitochondrial DNA repair / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / neuroblast proliferation / 1-phosphatidylinositol-3-kinase activity / mitotic spindle assembly checkpoint signaling / cardiac septum morphogenesis / necroptotic process / TP53 Regulates Transcription of Caspase Activators and Caspases / response to ionizing radiation / HDR through Single Strand Annealing (SSA) / entrainment of circadian clock by photoperiod / stem cell proliferation / hematopoietic stem cell differentiation / negative regulation of DNA replication / 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) / negative regulation of mitophagy / somitogenesis / Zygotic genome activation (ZGA) / mitotic G2 DNA damage checkpoint signaling / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / Resolution of D-loop Structures through Holliday Junction Intermediates / PI5P Regulates TP53 Acetylation / positive regulation of release of cytochrome c from mitochondria / Association of TriC/CCT with target proteins during biosynthesis / fibroblast proliferation / intrinsic apoptotic signaling pathway by p53 class mediator / negative regulation of telomere maintenance via telomerase / SUMOylation of transcription factors / TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain
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 / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / 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 / Cellular tumor antigen p53, transactivation domain 2 / Transactivation domain 2 / p53 transactivation domain / P53 transactivation motif / FATC domain / : / p53 family signature. / p53, tetramerisation domain / P53 tetramerisation motif / p53, DNA-binding domain / P53 DNA-binding domain / p53 tumour suppressor family / PIK-related kinase, FAT / FAT domain / FATC / p53-like tetramerisation domain superfamily / p53/RUNT-type transcription factor, DNA-binding domain superfamily / FATC domain / PIK-related kinase / FAT domain profile. / FATC domain profile. / p53-like transcription factor, DNA-binding / 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
Cellular tumor antigen p53 / Serine-protein kinase ATM
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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_17265.png

Downloads & links

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Map

FileDownload / File: emd_17265.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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.25253838 - 0.5368221
Average (Standard dev.)0.0011033126 (±0.019360509)
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_17265_msk_1.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Additional map: Sharpened map

Fileemd_17265_additional_1.map
AnnotationSharpened map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: Half Map A

Fileemd_17265_half_map_1.map
AnnotationHalf Map A
Projections & Slices
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Half map: Half Map B

Fileemd_17265_half_map_2.map
AnnotationHalf Map B
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Sample components

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Entire : ATM(Q2971A) dimer activated by H2O2 and bound to Mg AMP-PNP and p...

EntireName: ATM(Q2971A) dimer activated by H2O2 and bound to Mg AMP-PNP and p53 substrate peptide
Components
  • Complex: ATM(Q2971A) dimer activated by H2O2 and bound to Mg AMP-PNP and p53 substrate peptide
    • Protein or peptide: Cellular tumor antigen p53
    • 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) dimer activated by H2O2 and bound to Mg AMP-PNP and p...

SupramoleculeName: ATM(Q2971A) dimer activated by H2O2 and bound to Mg AMP-PNP and p53 substrate peptide
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Cellular tumor antigen p53

MacromoleculeName: Cellular tumor antigen p53 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.362438 KDa
SequenceString:
EPPLSQETFS DL

UniProtKB: Cellular tumor antigen p53

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Macromolecule #2: Serine-protein kinase ATM

MacromoleculeName: Serine-protein kinase ATM / type: protein_or_peptide / ID: 2 / 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 #3: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

MacromoleculeName: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / 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 #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 5 / 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 reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF
Software: (Name: RELION (ver. 3.1), RELION (ver. 4.0), cryoSPARC (ver. 4))
Number images used: 30707
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-8oxm:
ATM(Q2971A) activated by oxidative stress in complex with Mg AMP-PNP and p53 peptide

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