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Yorodumi- EMDB-14955: Cryo-EM structure of Ku 70/80 bound to inositol hexakisphosphate -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14955 | |||||||||
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Title | Cryo-EM structure of Ku 70/80 bound to inositol hexakisphosphate | |||||||||
Map data | ||||||||||
Sample |
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Keywords | DNA repair / NHEJ / Ku 70/80 / DNA-PK / cancer / double-strand break / DNA binding protein | |||||||||
Function / homology | Function and homology information Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / cellular response to X-ray / nonhomologous end joining complex / DNA ligation ...Ku70:Ku80 complex / negative regulation of t-circle formation / DNA end binding / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / cellular response to X-ray / nonhomologous end joining complex / DNA ligation / nuclear telomere cap complex / regulation of smooth muscle cell proliferation / Cytosolic sensors of pathogen-associated DNA / double-strand break repair via classical nonhomologous end joining / IRF3-mediated induction of type I IFN / recombinational repair / regulation of telomere maintenance / U3 snoRNA binding / positive regulation of neurogenesis / protein localization to chromosome, telomeric region / cellular response to fatty acid / hematopoietic stem cell proliferation / cellular hyperosmotic salinity response / telomeric DNA binding / positive regulation of catalytic activity / 2-LTR circle formation / site of DNA damage / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / enzyme activator activity / 5'-deoxyribose-5-phosphate lyase activity / hematopoietic stem cell differentiation / positive regulation of protein kinase activity / ATP-dependent activity, acting on DNA / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / DNA helicase activity / activation of innate immune response / telomere maintenance / cellular response to leukemia inhibitory factor / neurogenesis / cyclin binding / small-subunit processome / protein-DNA complex / Nonhomologous End-Joining (NHEJ) / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cellular response to gamma radiation / double-strand break repair via nonhomologous end joining / double-strand break repair / double-stranded DNA binding / scaffold protein binding / secretory granule lumen / DNA recombination / ficolin-1-rich granule lumen / transcription regulator complex / chromosome, telomeric region / damaged DNA binding / transcription cis-regulatory region binding / response to xenobiotic stimulus / ribonucleoprotein complex / innate immune response / negative regulation of DNA-templated transcription / DNA damage response / ubiquitin protein ligase binding / Neutrophil degranulation / protein-containing complex binding / nucleolus / positive regulation of DNA-templated transcription / ATP hydrolysis activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / extracellular region / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Kefala Stavridi A / Chaplin AK / Blundell TL | |||||||||
Funding support | United Kingdom, 1 items
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Citation | Journal: Nucleic Acids Res / Year: 2023 Title: Structural and functional basis of inositol hexaphosphate stimulation of NHEJ through stabilization of Ku-XLF interaction. Authors: Antonia Kefala Stavridi / Amandine Gontier / Vincent Morin / Philippe Frit / Virginie Ropars / Nadia Barboule / Carine Racca / Sagun Jonchhe / Michael J Morten / Jessica Andreani / Alexey ...Authors: Antonia Kefala Stavridi / Amandine Gontier / Vincent Morin / Philippe Frit / Virginie Ropars / Nadia Barboule / Carine Racca / Sagun Jonchhe / Michael J Morten / Jessica Andreani / Alexey Rak / Pierre Legrand / Alexa Bourand-Plantefol / Steven W Hardwick / Dimitri Y Chirgadze / Paul Davey / Taiana Maia De Oliveira / Eli Rothenberg / Sebastien Britton / Patrick Calsou / Tom L Blundell / Paloma F Varela / Amanda K Chaplin / Jean-Baptiste Charbonnier / Abstract: The classical Non-Homologous End Joining (c-NHEJ) pathway is the predominant process in mammals for repairing endogenous, accidental or programmed DNA Double-Strand Breaks. c-NHEJ is regulated by ...The classical Non-Homologous End Joining (c-NHEJ) pathway is the predominant process in mammals for repairing endogenous, accidental or programmed DNA Double-Strand Breaks. c-NHEJ is regulated by several accessory factors, post-translational modifications, endogenous chemical agents and metabolites. The metabolite inositol-hexaphosphate (IP6) stimulates c-NHEJ by interacting with the Ku70-Ku80 heterodimer (Ku). We report cryo-EM structures of apo- and DNA-bound Ku in complex with IP6, at 3.5 Å and 2.74 Å resolutions respectively, and an X-ray crystallography structure of a Ku in complex with DNA and IP6 at 3.7 Å. The Ku-IP6 interaction is mediated predominantly via salt bridges at the interface of the Ku70 and Ku80 subunits. This interaction is distant from the DNA, DNA-PKcs, APLF and PAXX binding sites and in close proximity to XLF binding site. Biophysical experiments show that IP6 binding increases the thermal stability of Ku by 2°C in a DNA-dependent manner, stabilizes Ku on DNA and enhances XLF affinity for Ku. In cells, selected mutagenesis of the IP6 binding pocket reduces both Ku accrual at damaged sites and XLF enrolment in the NHEJ complex, which translate into a lower end-joining efficiency. Thus, this study defines the molecular bases of the IP6 metabolite stimulatory effect on the c-NHEJ repair activity. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14955.map.gz | 51 MB | EMDB map data format | |
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Header (meta data) | emd-14955-v30.xml emd-14955.xml | 17 KB 17 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14955_fsc.xml | 13.8 KB | Display | FSC data file |
Images | emd_14955.png | 56.9 KB | ||
Filedesc metadata | emd-14955.cif.gz | 6.5 KB | ||
Others | emd_14955_half_map_1.map.gz emd_14955_half_map_2.map.gz | 95.5 MB 95.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14955 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14955 | HTTPS FTP |
-Related structure data
Related structure data | 7zt6MC 7z6oC 7zvtC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_14955.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.652 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_14955_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_14955_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of Ku 70/80 bound to inositol hexakisphosphate
Entire | Name: Cryo-EM structure of Ku 70/80 bound to inositol hexakisphosphate |
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Components |
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-Supramolecule #1: Cryo-EM structure of Ku 70/80 bound to inositol hexakisphosphate
Supramolecule | Name: Cryo-EM structure of Ku 70/80 bound to inositol hexakisphosphate type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: X-ray repair cross-complementing protein 6
Macromolecule | Name: X-ray repair cross-complementing protein 6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 73.890336 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MNTIHHHHHH NTSGSGGGGG RLVPRGSMSE NLYFQGSMSG WESYYKTEGD EEAEEEQEEN LEASGDYKYS GRDSLIFLVD ASKAMFESQ SEDELTPFDM SIQCIQSVYI SKIISSDRDL LAVVFYGTEK DKNSVNFKNI YVLQELDNPG AKRILELDQF K GQQGQKRF ...String: MNTIHHHHHH NTSGSGGGGG RLVPRGSMSE NLYFQGSMSG WESYYKTEGD EEAEEEQEEN LEASGDYKYS GRDSLIFLVD ASKAMFESQ SEDELTPFDM SIQCIQSVYI SKIISSDRDL LAVVFYGTEK DKNSVNFKNI YVLQELDNPG AKRILELDQF K GQQGQKRF QDMMGHGSDY SLSEVLWVCA NLFSDVQFKM SHKRIMLFTN EDNPHGNDSA KASRARTKAG DLRDTGIFLD LM HLKKPGG FDISLFYRDI ISIAEDEDLR VHFEESSKLE DLLRKVRAKE TRKRALSRLK LKLNKDIVIS VGIYNLVQKA LKP PPIKLY RETNEPVKTK TRTFNTSTGG LLLPSDTKRS QIYGSRQIIL EKEETEELKR FDDPGLMLMG FKPLVLLKKH HYLR PSLFV YPEESLVIGS STLFSALLIK CLEKEVAALC RYTPRRNIPP YFVALVPQEE ELDDQKIQVT PPGFQLVFLP FADDK RKMP FTEKIMATPE QVGKMKAIVE KLRFTYRSDS FENPVLQQHF RNLEALALDL MEPEQAVDLT LPKVEAMNKR LGSLVD EFK ELVYPPDYNP EGKVTKRKHD NEGSGSKRPK VEYSEEELKT HISKGTLGKF TVPMLKEACR AYGLKSGLKK QELLEAL TK HFQD UniProtKB: X-ray repair cross-complementing protein 6 |
-Macromolecule #2: X-ray repair cross-complementing protein 5
Macromolecule | Name: X-ray repair cross-complementing protein 5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO EC number: Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 82.812438 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MVRSGNKAAV VLCMDVGFTM SNSIPGIESP FEQAKKVITM FVQRQVFAEN KDEIALVLFG TDGTDNPLSG GDQYQNITVH RHLMLPDFD LLEDIESKIQ PGSQQADFLD ALIVSMDVIQ HETIGKKFEK RHIEIFTDLS SRFSKSQLDI IIHSLKKCDI S LQFFLPFS ...String: MVRSGNKAAV VLCMDVGFTM SNSIPGIESP FEQAKKVITM FVQRQVFAEN KDEIALVLFG TDGTDNPLSG GDQYQNITVH RHLMLPDFD LLEDIESKIQ PGSQQADFLD ALIVSMDVIQ HETIGKKFEK RHIEIFTDLS SRFSKSQLDI IIHSLKKCDI S LQFFLPFS LGKEDGSGDR GDGPFRLGGH GPSFPLKGIT EQQKEGLEIV KMVMISLEGE DGLDEIYSFS ESLRKLCVFK KI ERHSIHW PCRLTIGSNL SIRIAAYKSI LQERVKKTWT VVDAKTLKKE DIQKETVYCL NDDDETEVLK EDIIQGFRYG SDI VPFSKV DEEQMKYKSE GKCFSVLGFC KSSQVQRRFF MGNQVLKVFA ARDDEAAAVA LSSLIHALDD LDMVAIVRYA YDKR ANPQV GVAFPHIKHN YECLVYVQLP FMEDLRQYMF SSLKNSKKYA PTEAQLNAVD ALIDSMSLAK KDEKTDTLED LFPTT KIPN PRFQRLFQCL LHRALHPREP LPPIQQHIWN MLNPPAEVTT KSQIPLSKIK TLFPLIEAKK KDQVTAQEIF QDNHED GPT AKKLKTEQGG AHFSVSSLAE GSVTSVGSVN PAENFRVLVK QKKASFEEAS NQLINHIEQF LDTNETPYFM KSIDCIR AF REEAIKFSEE QRFNNFLKAL QEKVEIKQLN HFWEIVVQDG ITLITKEEAS GSSVTAEEAK KFLAPKDKPS GDTAAVFE E GGDVDDLLDM I UniProtKB: X-ray repair cross-complementing protein 5 |
-Macromolecule #3: INOSITOL HEXAKISPHOSPHATE
Macromolecule | Name: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: IHP |
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Molecular weight | Theoretical: 660.035 Da |
Chemical component information | ChemComp-IHP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.7 µm / Nominal defocus min: 0.9 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 49.43 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |