+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-25141 | |||||||||
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Title | Human ATM Dimer Bound to Nbs1 | |||||||||
Map data | Nc28 consensus dimer | |||||||||
Sample |
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Keywords | Kinase / SIGNALING PROTEIN | |||||||||
Function / homology | Function and homology information telomere maintenance via telomere trimming / chromosomal region / telomeric 3' overhang formation / Mre11 complex / positive regulation of DNA catabolic process / establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / blastocyst growth / positive regulation of DNA damage response, signal transduction by p53 class mediator / cellular response to nitrosative stress ...telomere maintenance via telomere trimming / chromosomal region / telomeric 3' overhang formation / Mre11 complex / positive regulation of DNA catabolic process / establishment of RNA localization to telomere / positive regulation of telomerase catalytic core complex assembly / blastocyst growth / positive regulation of DNA damage response, signal transduction by p53 class mediator / cellular response to nitrosative stress / establishment of protein-containing complex localization to telomere / regulation of microglial cell activation / negative regulation of telomere capping / protection from non-homologous end joining at telomere / Sensing of DNA Double Strand Breaks / BRCA1-C complex / positive regulation of telomere maintenance via telomere lengthening / telomere maintenance in response to DNA damage / R-loop processing / meiotic telomere clustering / phosphorylation-dependent protein binding / t-circle formation / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / male meiotic nuclear division / histone mRNA catabolic process / pre-B cell allelic exclusion / female meiotic nuclear division / chromatin-protein adaptor activity / pexophagy / DNA strand resection involved in replication fork processing / DNA double-strand break processing / cellular response to X-ray / regulation of telomere maintenance via telomerase / homologous recombination / nuclear inclusion body / peptidyl-serine autophosphorylation / lipoprotein catabolic process / V(D)J recombination / positive regulation of telomere maintenance / oocyte development / isotype switching / Impaired BRCA2 binding to PALB2 / protein localization to site of double-strand break / HDR through MMEJ (alt-NHEJ) / mitotic G2/M transition checkpoint / positive regulation of kinase activity / reciprocal meiotic recombination / DNA repair complex / 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 / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / regulation of DNA-templated DNA replication initiation / DNA duplex unwinding / 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 / double-strand break repair via alternative nonhomologous end joining / TP53 Regulates Transcription of Caspase Activators and Caspases / negative regulation of B cell proliferation / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / TP53 Regulates Transcription of Genes Involved in Cytochrome C Release / peroxisomal matrix / protein K63-linked ubiquitination / neuromuscular process controlling balance / positive regulation of cell adhesion / positive regulation of double-strand break repair via homologous recombination / DNA damage response, signal transduction by p53 class mediator / replicative senescence / Regulation of HSF1-mediated heat shock response / neuroblast proliferation / signal transduction in response to DNA damage / somitogenesis / regulation of cellular response to heat / cellular response to retinoic acid / ovarian follicle development / positive regulation of protein autophosphorylation / 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 / Pexophagy / telomere maintenance / protein serine/threonine kinase activator activity / intrinsic apoptotic signaling pathway / post-embryonic development / thymus development / meiotic cell cycle / regulation of signal transduction by p53 class mediator / replication fork / DNA damage checkpoint signaling / regulation of autophagy / determination of adult lifespan / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.53 Å | |||||||||
Authors | Warren C / Pavletich NP | |||||||||
Funding support | United States, 2 items
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Citation | Journal: Elife / Year: 2022 Title: Structure of the human ATM kinase and mechanism of Nbs1 binding. Authors: Christopher Warren / Nikola P Pavletich / Abstract: DNA double-strand breaks (DSBs) can lead to mutations, chromosomal rearrangements, genome instability, and cancer. Central to the sensing of DSBs is the ATM (Ataxia-telangiectasia mutated) kinase, ...DNA double-strand breaks (DSBs) can lead to mutations, chromosomal rearrangements, genome instability, and cancer. Central to the sensing of DSBs is the ATM (Ataxia-telangiectasia mutated) kinase, which belongs to the phosphatidylinositol 3-kinase-related protein kinase (PIKK) family. In response to DSBs, ATM is activated by the MRN (Mre11-Rad50-Nbs1) protein complex through a poorly understood process that also requires double-stranded DNA. Previous studies indicate that the FxF/Y motif of Nbs1 directly binds to ATM, and is required to retain active ATM at sites of DNA damage. Here, we report the 2.5 Å resolution cryo-EM structures of human ATM and its complex with the Nbs1 FxF/Y motif. In keeping with previous structures of ATM and its yeast homolog Tel1, the dimeric human ATM kinase adopts a symmetric, butterfly-shaped structure. The conformation of the ATM kinase domain is most similar to the inactive states of other PIKKs, suggesting that activation may involve an analogous realigning of the N and C lobes along with relieving the blockage of the substrate-binding site. We also show that the Nbs1 FxF/Y motif binds to a conserved hydrophobic cleft within the Spiral domain of ATM, suggesting an allosteric mechanism of activation. We evaluate the importance of these structural findings with mutagenesis and biochemical assays. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_25141.map.gz | 10.7 MB | EMDB map data format | |
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Header (meta data) | emd-25141-v30.xml emd-25141.xml | 24.3 KB 24.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_25141_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_25141.png | 59 KB | ||
Filedesc metadata | emd-25141.cif.gz | 7.6 KB | ||
Others | emd_25141_additional_1.map.gz emd_25141_additional_2.map.gz emd_25141_additional_3.map.gz emd_25141_additional_4.map.gz emd_25141_additional_5.map.gz | 95 MB 95 MB 93.6 MB 95.9 MB 25.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-25141 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-25141 | HTTPS FTP |
-Validation report
Summary document | emd_25141_validation.pdf.gz | 440.1 KB | Display | EMDB validaton report |
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Full document | emd_25141_full_validation.pdf.gz | 439.6 KB | Display | |
Data in XML | emd_25141_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | emd_25141_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25141 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-25141 | HTTPS FTP |
-Related structure data
Related structure data | 7sidMC 7sicC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_25141.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Nc28 consensus dimer | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.078 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Nc28 symmetry expanded protomer
File | emd_25141_additional_1.map | ||||||||||||
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Annotation | Nc28 symmetry expanded protomer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Nc28 symmetry expanded protomer FATKD focused
File | emd_25141_additional_2.map | ||||||||||||
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Annotation | Nc28 symmetry expanded protomer FATKD focused | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Nc28 symmetry expanded protomer HEAT focused
File | emd_25141_additional_3.map | ||||||||||||
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Annotation | Nc28 symmetry expanded protomer HEAT focused | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Nc28 symmetry expanded protomer composite map
File | emd_25141_additional_4.map | ||||||||||||
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Annotation | Nc28 symmetry expanded protomer composite map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Nc28 dimer composite map
File | emd_25141_additional_5.map | ||||||||||||
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Annotation | Nc28 dimer composite map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Human ATM Dimer Bound to Nbs1
Entire | Name: Human ATM Dimer Bound to Nbs1 |
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Components |
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-Supramolecule #1: Human ATM Dimer Bound to Nbs1
Supramolecule | Name: Human ATM Dimer Bound to Nbs1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Serine-protein kinase ATM
Macromolecule | Name: Serine-protein kinase ATM / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 351.127688 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MSLVLNDLLI CCRQLEHDRA TERKKEVEKF KRLIRDPETI KHLDRHSDSK QGKYLNWDAV FRFLQKYIQK ETECLRIAKP NVSASTQAS RQKKMQEISS LVKYFIKCAN RRAPRLKCQE LLNYIMDTVK DSSNGAIYGA DCSNILLKDI LSVRKYWCEI S QQQWLELF ...String: MSLVLNDLLI CCRQLEHDRA TERKKEVEKF KRLIRDPETI KHLDRHSDSK QGKYLNWDAV FRFLQKYIQK ETECLRIAKP NVSASTQAS RQKKMQEISS LVKYFIKCAN RRAPRLKCQE LLNYIMDTVK DSSNGAIYGA DCSNILLKDI LSVRKYWCEI S QQQWLELF SVYFRLYLKP SQDVHRVLVA RIIHAVTKGC CSQTDGLNSK FLDFFSKAIQ CARQEKSSSG LNHILAALTI FL KTLAVNF RIRVCELGDE ILPTLLYIWT QHRLNDSLKE VIIELFQLQI YIHHPKGAKT QEKGAYESTK WRSILYNLYD LLV NEISHI GSRGKYSSGF RNIAVKENLI ELMADICHQV FNEDTRSLEI SQSYTTTQRE SSDYSVPCKR KKIELGWEVI KDHL QKSQN DFDLVPWLQI ATQLISKYPA SLPNCELSPL LMILSQLLPQ QRHGERTPYV LRCLTEVALC QDKRSNLESS QKSDL LKLW NKIWCITFRG ISSEQIQAEN FGLLGAIIQG SLVEVDREFW KLFTGSACRP SCPAVCCLTL ALTTSIVPGT VKMGIE QNM CEVNRSFSLK ESIMKWLLFY QLEGDLENST EVPPILHSNF PHLVLEKILV SLTMKNCKAA MNFFQSVPEC EHHQKDK EE LSFSEVEELF LQTTFDKMDF LTIVRECGIE KHQSSIGFSV HQNLKESLDR CLLGLSEQLL NNYSSEITNS ETLVRCSR L LVGVLGCYCY MGVIAEEEAY KSELFQKAKS LMQCAGESIT LFKNKTNEEF RIGSLRNMMQ LCTRCLSNCT KKSPNKIAS GFFLRLLTSK LMNDIADICK SLASFIKKPF DRGEVESMED DTNGNLMEVE DQSSMNLFND YPDSSVSDAN EPGESQSTIG AINPLAEEY LSKQDLLFLD MLKFLCLCVT TAQTNTVSFR AADIRRKLLM LIDSSTLEPT KSLHLHMYLM LLKELPGEEY P LPMEDVLE LLKPLSNVCS LYRRDQDVCK TILNHVLHVV KNLGQSNMDS ENTRDAQGQF LTVIGAFWHL TKERKYIFSV RM ALVNCLK TLLEADPYSK WAILNVMGKD FPVNEVFTQF LADNHHQVRM LAAESINRLF QDTKGDSSRL LKALPLKLQQ TAF ENAYLK AQEGMREMSH SAENPETLDE IYNRKSVLLT LIAVVLSCSP ICEKQALFAL CKSVKENGLE PHLVKKVLEK VSET FGYRR LEDFMASHLD YLVLEWLNLQ DTEYNLSSFP FILLNYTNIE DFYRSCYKVL IPHLVIRSHF DEVKSIANQI QEDWK SLLT DCFPKILVNI LPYFAYEGTR DSGMAQQRET ATKVYDMLKS ENLLGKQIDH LFISNLPEIV VELLMTLHEP ANSSAS QST DLCDFSGDLD PAPNPPHFPS HVIKATFAYI SNCHKTKLKS ILEILSKSPD SYQKILLAIC EQAAETNNVY KKHRILK IY HLFVSLLLKD IKSGLGGAWA FVLRDVIYTL IHYINQRPSC IMDVSLRSFS LCCDLLSQVC QTAVTYCKDA LENHLHVI V GTLIPLVYEQ VEVQKQVLDL LKYLVIDNKD NENLYITIKL LDPFPDHVVF KDLRITQQKI KYSRGPFSLL EEINHFLSV SVYDALPLTR LEGLKDLRRQ LELHKDQMVD IMRASQDNPQ DGIMVKLVVN LLQLSKMAIN HTGEKEVLEA VGSCLGEVGP IDFSTIAIQ HSKDASYTKA LKLFEDKELQ WTFIMLTYLN NTLVEDCVKV RSAAVTCLKN ILATKTGHSF WEIYKMTTDP M LAYLQPFR TSRKKFLEVP RFDKENPFEG LDDINLWIPL SENHDIWIKT LTCAFLDSGG TKCEILQLLK PMCEVKTDFC QT VLPYLIH DILLQDTNES WRNLLSTHVQ GFFTSCLRHF SQTSRSTTPA NLDSESEHFF RCCLDKKSQR TMLAVVDYMR RQK RPSSGT IFNDAFWLDL NYLEVAKVAQ SCAAHFTALL YAEIYADKKS MDDQEKRSLA FEEGSQSTTI SSLSEKSKEE TGIS LQDLL LEIYRSIGEP DSLYGCGGGK MLQPITRLRT YEHEAMWGKA LVTYDLETAI PSSTRQAGII QALQNLGLCH ILSVY LKGL DYENKDWCPE LEELHYQAAW RNMQWDHCTS VSKEVEGTSY HESLYNALQS LRDREFSTFY ESLKYARVKE VEEMCK RSL ESVYSLYPTL SRLQAIGELE SIGELFSRSV THRQLSEVYI KWQKHSQLLK DSDFSFQEPI MALRTVILEI LMEKEMD NS QRECIKDILT KHLVELSILA RTFKNTQLPE RAIFQIKQYN SVSCGVSEWQ LEEAQVFWAK KEQSLALSIL KQMIKKLD A SCAANNPSLK LTYTECLRVC GNWLAETCLE NPAVIMQTYL EKAVEVAGNY DGESSDELRN GKMKAFLSLA RFSDTQYQR IENYMKSSEF ENKQALLKRA KEEVGLLREH KIQTNRYTVK VQRELELDEL ALRALKEDRK RFLCKAVENY INCLLSGEEH DMWVFRLCS LWLENSGVSE VNGMMKRDGM KIPTYKFLPL MYQLAARMGT KMMGGLGFHE VLNNLISRIS MDHPHHTLFI I LALANANR DEFLTKPEVA RRSRITKNVP KQSSQLDEDR TEAANRIICT IRSRRPQMVR SVEALCDAYI ILANLDATQW KT QRKGINI PADQPITKLK NLEDVVVPTM EIKVDHTGEY GNLVTIQSFK AEFRLAGGVN LPKIIDCVGS DGKERRQLVK GRD DLRQDA VMQQVFQMCN TLLQRNTETR KRKLTICTYK VVPLSQRSGV LEWCTGTVPI GEFLVNNEDG AHKRYRPNDF SAFQ CQKKM MEVQKKSFEE KYEVFMDVCQ NFQPVFRYFC MEKFLDPAIW FEKRLAYTRS VATSSIVGYI LGLGDRHVQN ILINE QSAE LVHIDLGVAF EQGKILPTPE TVPFRLTRDI VDGMGITGVE GVFRRCCEKT MEVMRNSQET LLTIVEVLLY DPLFDW TMN PLKALYLQQR PEDETELHPT LNADDQECKR NLSDIDQSFN KVAERVLMRL QEKLKGVEEG TVLSVGGQVN LLIQQAI DP KNLSRLFPGW KAWV UniProtKB: Serine-protein kinase ATM |
-Macromolecule #2: Nibrin
Macromolecule | Name: Nibrin / type: protein_or_peptide / ID: 2 / Details: C-terminal 28aa of Human Nbs1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 3.514947 KDa |
Sequence | String: MEVQNQHAKE ESLADDLFRY NPYLKRRR UniProtKB: Nibrin |
-Macromolecule #3: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: ANP |
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Molecular weight | Theoretical: 506.196 Da |
Chemical component information | ChemComp-ANP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.42 mg/mL |
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Buffer | pH: 8 |
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 51.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |