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- EMDB-6803: Cryo-EM structure of Human DNA-PK Holoenzyme -

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Basic information

Entry
Database: EMDB / ID: EMD-6803
TitleCryo-EM structure of Human DNA-PK Holoenzyme
Map dataNone
Sample
  • Complex: PRKDC-Helix
    • Protein or peptide: X-ray repair cross-complementing protein 6
    • Protein or peptide: X-ray repair cross-complementing protein 5
    • Protein or peptide: PRKDC-Helix
    • DNA: DNA (34-MER)
    • DNA: DNA (36-MER)
    • Protein or peptide: DNA-dependent protein kinase catalytic subunit
KeywordsCryo-EM structure / DNA-PK / DNAPKcs / activation / NHEJ / DNA BINDING PROTEIN
Function / homology
Function and homology information


Ku70:Ku80 complex / negative regulation of t-circle formation / positive regulation of platelet formation / DNA end binding / T cell receptor V(D)J recombination / pro-B cell differentiation / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity ...Ku70:Ku80 complex / negative regulation of t-circle formation / positive regulation of platelet formation / DNA end binding / T cell receptor V(D)J recombination / pro-B cell differentiation / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase activity / histone H2AXS139 kinase activity / DNA-dependent protein kinase complex / immature B cell differentiation / DNA-dependent protein kinase-DNA ligase 4 complex / cellular response to X-ray / immunoglobulin V(D)J recombination / nonhomologous end joining complex / DNA ligation / nuclear telomere cap complex / regulation of smooth muscle cell proliferation / double-strand break repair via alternative nonhomologous end joining / Cytosolic sensors of pathogen-associated DNA / double-strand break repair via classical nonhomologous end joining / regulation of epithelial cell proliferation / IRF3-mediated induction of type I IFN / telomere capping / recombinational repair / regulation of telomere maintenance / U3 snoRNA binding / regulation of hematopoietic stem cell differentiation / positive regulation of neurogenesis / protein localization to chromosome, telomeric region / cellular response to fatty acid / hematopoietic stem cell proliferation / cellular hyperosmotic salinity response / maturation of 5.8S rRNA / negative regulation of cGAS/STING signaling pathway / T cell lineage commitment / telomeric DNA binding / positive regulation of catalytic activity / B cell lineage commitment / 2-LTR circle formation / positive regulation of double-strand break repair via nonhomologous end joining / site of DNA damage / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / enzyme activator activity / hematopoietic stem cell differentiation / ectopic germ cell programmed cell death / positive regulation of protein kinase activity / ATP-dependent activity, acting on DNA / somitogenesis / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / mitotic G1 DNA damage checkpoint signaling / DNA helicase activity / telomere maintenance / activation of innate immune response / neurogenesis / negative regulation of protein phosphorylation / positive regulation of erythrocyte differentiation / cellular response to leukemia inhibitory factor / small-subunit processome / cyclin binding / protein-DNA complex / positive regulation of translation / response to gamma radiation / Nonhomologous End-Joining (NHEJ) / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / brain development / peptidyl-threonine phosphorylation / protein modification process / protein destabilization / regulation of circadian rhythm / cellular response to gamma radiation / double-strand break repair via nonhomologous end joining / cellular response to insulin stimulus / rhythmic process / intrinsic apoptotic signaling pathway in response to DNA damage / double-strand break repair / E3 ubiquitin ligases ubiquitinate target proteins / T cell differentiation in thymus / heart development / double-stranded DNA binding / scaffold protein binding / peptidyl-serine phosphorylation / secretory granule lumen / DNA recombination / ficolin-1-rich granule lumen / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / chromosome, telomeric region / damaged DNA binding / transcription cis-regulatory region binding / non-specific serine/threonine protein kinase / protein kinase activity / response to xenobiotic stimulus / positive regulation of apoptotic process / ribonucleoprotein complex / protein domain specific binding / protein phosphorylation
Similarity search - Function
Ku70, bridge and pillars domain superfamily / : / Ku70 / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 beta-barrel domain ...Ku70, bridge and pillars domain superfamily / : / Ku70 / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 beta-barrel domain / Ku70/Ku80 C-terminal arm / Ku70/Ku80 N-terminal alpha/beta domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen / Ku70/Ku80 beta-barrel domain / DNA-dependent protein kinase catalytic subunit, CC3 / SPOC-like, C-terminal domain superfamily / DNA-dependent protein kinase catalytic subunit, catalytic domain / DNA-dependent protein kinase catalytic subunit, CC5 / DNA-dependent protein kinase catalytic subunit, CC1/2 / DNA-PKcs, N-terminal / DNA-dependent protein kinase catalytic subunit, CC3 / DNA-PKcs, CC5 / DNA-PKcs, N-terminal / DNA-dependent protein kinase catalytic subunit, CC1/2 / NUC194 / SAP domain superfamily / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / PIK-related kinase, FAT / FAT domain / FATC 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 / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Armadillo-like helical / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
X-ray repair cross-complementing protein 6 / X-ray repair cross-complementing protein 5 / DNA-dependent protein kinase catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.6 Å
AuthorsYin X / Liu M
Funding support China, 4 items
OrganizationGrant numberCountry
Ministry of Science and Technology of China2016YFA0500700 China
Strategic Priority Research Program of the Chinese Academy of SciencesXDB08000000 China
National Natural Science Foundation of ChinaU1432242,31425008,91419301 China
Program of Shanghai Subject Chief Scientist14XD1400500 China
CitationJournal: Cell Res / Year: 2017
Title: Cryo-EM structure of human DNA-PK holoenzyme.
Authors: Xiaotong Yin / Mengjie Liu / Yuan Tian / Jiawei Wang / Yanhui Xu /
Abstract: DNA-dependent protein kinase (DNA-PK) is a serine/threonine protein kinase complex composed of a catalytic subunit (DNA-PKcs) and KU70/80 heterodimer bound to DNA. DNA-PK holoenzyme plays a critical ...DNA-dependent protein kinase (DNA-PK) is a serine/threonine protein kinase complex composed of a catalytic subunit (DNA-PKcs) and KU70/80 heterodimer bound to DNA. DNA-PK holoenzyme plays a critical role in non-homologous end joining (NHEJ), the major DNA repair pathway. Here, we determined cryo-electron microscopy structure of human DNA-PK holoenzyme at 6.6 Å resolution. In the complex structure, DNA-PKcs, KU70, KU80 and DNA duplex form a 650-kDa heterotetramer with 1:1:1:1 stoichiometry. The N-terminal α-solenoid (∼2 800 residues) of DNA-PKcs adopts a double-ring fold and connects the catalytic core domain of DNA-PKcs and KU70/80-DNA. DNA-PKcs and KU70/80 together form a DNA-binding tunnel, which cradles ∼30-bp DNA and prevents sliding inward of DNA-PKcs along with DNA duplex, suggesting a mechanism by which the broken DNA end is protected from unnecessary processing. Structural and biochemical analyses indicate that KU70/80 and DNA coordinately induce conformational changes of DNA-PKcs and allosterically stimulate its kinase activity. We propose a model for activation of DNA-PKcs in which allosteric signals are generated upon DNA-PK holoenzyme formation and transmitted to the kinase domain through N-terminal HEAT repeats and FAT domain of DNA-PKcs. Our studies suggest a mechanism for recognition and protection of broken DNA ends and provide a structural basis for understanding the activation of DNA-PKcs and DNA-PK-mediated NHEJ pathway.
History
DepositionJul 29, 2017-
Header (metadata) releaseSep 6, 2017-
Map releaseSep 6, 2017-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / 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
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  • Surface view with fitted model
  • Atomic models: PDB-5y3r
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_6803.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Voxel sizeX=Y=Z: 1.3 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.052921083 - 0.13899168
Average (Standard dev.)0.0004368765 (±0.00405337)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 390.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z390.000390.000390.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0530.1390.000

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Supplemental data

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Sample components

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Entire : PRKDC-Helix

EntireName: PRKDC-Helix
Components
  • Complex: PRKDC-Helix
    • Protein or peptide: X-ray repair cross-complementing protein 6
    • Protein or peptide: X-ray repair cross-complementing protein 5
    • Protein or peptide: PRKDC-Helix
    • DNA: DNA (34-MER)
    • DNA: DNA (36-MER)
    • Protein or peptide: DNA-dependent protein kinase catalytic subunit

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Supramolecule #1: PRKDC-Helix

SupramoleculeName: PRKDC-Helix / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: X-ray repair cross-complementing protein 6

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.619352 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GRDSLIFLVD ASKAMFESQS EDELTPFDMS IQCIQSVYIS KIISSDRDLL AVVFYGTEKD KNSVNFKNIY VLQELDNPGA KRILELDQF KGQQGQKRFQ DMMGHGSDYS LSEVLWVCAN LFSDVQFKMS HKRIMLFTNE DNPHGNDSAK ASRARTKAGD L RDTGIFLD ...String:
GRDSLIFLVD ASKAMFESQS EDELTPFDMS IQCIQSVYIS KIISSDRDLL AVVFYGTEKD KNSVNFKNIY VLQELDNPGA KRILELDQF KGQQGQKRFQ DMMGHGSDYS LSEVLWVCAN LFSDVQFKMS HKRIMLFTNE DNPHGNDSAK ASRARTKAGD L RDTGIFLD LMHLKKPGGF DISLFYRDII SIAEDEDLRV HFEESSKLED LLRKVRAKET RKRALSRLKL KLNKDIVISV GI YNLVQKA LKPPPIKLYR ETNEPVKTKT RTFNTSTGGL LLPSDTKRSQ IYGSRQIILE KEETEELKRF DDPGLMLMGF KPL VLLKKH HYLRPSLFVY PEESLVIGSS TLFSALLIKC LEKEVAALCR YTPRRNIPPY FVALVPQEEE LDDQKIQVTP PGFQ LVFLP FADDKRKMPF TEKIMATPEQ VGKMKAIVEK LRFTYRSDSF ENPVLQQHFR NLEALALDLM EPEQAVDLTL PKVEA MNKR LGSLVDEFKE LVYPPDY

UniProtKB: X-ray repair cross-complementing protein 6

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Macromolecule #2: X-ray repair cross-complementing protein 5

MacromoleculeName: 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
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 60.972969 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NKAAVVLCMD VGFTMSNSIP GIESPFEQAK KVITMFVQRQ VFAENKDEIA LVLFGTDGTD NPLSGGDQYQ NITVHRHLML PDFDLLEDI ESKIQPGSQQ ADFLDALIVS MDVIQHETIG KKFEKRHIEI FTDLSSRFSK SQLDIIIHSL KKCDISLQFF L PFSLGKED ...String:
NKAAVVLCMD VGFTMSNSIP GIESPFEQAK KVITMFVQRQ VFAENKDEIA LVLFGTDGTD NPLSGGDQYQ NITVHRHLML PDFDLLEDI ESKIQPGSQQ ADFLDALIVS MDVIQHETIG KKFEKRHIEI FTDLSSRFSK SQLDIIIHSL KKCDISLQFF L PFSLGKED GSGDRGDGPF RLGGHGPSFP LKGITEQQKE GLEIVKMVMI SLEGEDGLDE IYSFSESLRK LCVFKKIERH SI HWPCRLT IGSNLSIRIA AYKSILQERV KKTWTVVDAK TLKKEDIQKE TVYCLNDDDE TEVLKEDIIQ GFRYGSDIVP FSK VDEEQM KYKSEGKCFS VLGFCKSSQV QRRFFMGNQV LKVFAARDDE AAAVALSSLI HALDDLDMVA IVRYAYDKRA NPQV GVAFP HIKHNYECLV YVQLPFMEDL RQYMFSSLKN SKKYAPTEAQ LNAVDALIDS MSLAKKDEKT DTLEDLFPTT KIPNP RFQR LFQCLLHRAL HPREPLPPIQ QHIWNMLNPP AEVTTKSQIP LSKIKTLFPL IE

UniProtKB: X-ray repair cross-complementing protein 5

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Macromolecule #3: PRKDC-Helix

MacromoleculeName: PRKDC-Helix / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.084182 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AAAAAAAAAA AAAAA

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Macromolecule #6: DNA-dependent protein kinase catalytic subunit

MacromoleculeName: DNA-dependent protein kinase catalytic subunit / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 468.885344 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: CSLLRLQETL SAADRCGAAL AGHQLIRGLG QECVLSSSPA VLALQTSLVF SRDFGLLVFV RKSLNSIEFR ECREEILKFL CIFLEKMGQ KIAPYSVEIK NTCTSVYTKD RAAKCKIPAL DLLIKLLQTF RSSRLMDEFK IGELFSKFYG ELALKKKIPD T VLEKVYEL ...String:
CSLLRLQETL SAADRCGAAL AGHQLIRGLG QECVLSSSPA VLALQTSLVF SRDFGLLVFV RKSLNSIEFR ECREEILKFL CIFLEKMGQ KIAPYSVEIK NTCTSVYTKD RAAKCKIPAL DLLIKLLQTF RSSRLMDEFK IGELFSKFYG ELALKKKIPD T VLEKVYEL LGLLGEVHPS EMINNAENLF RAFLGELKTQ MTSAVREPKL PVLAGCLKGL SSLLCNFTKS MEEDPQTSRE IF NFVLKAI RPQIDLKRYA VPSAGLRLFA LHASQFSTCL LDNYVSLFEV LLKWCAHTNV ELKKAALSAL ESFLKQVSNM VAK NAEMHK NKLQYFMEQF YGIIRNVDSN NKELSIAIRG YGLFAGPCKV INAKDVDFMY VELIQRCKQM FLTQTDTGDD RVYQ MPSFL QSVASVLLYL DTVPEVYTPV LEHLVVMQID SFPQYSPKMQ LVCCRAIVKV FLALAAKGPV LRNCISTVVH QGLIR ICSK PVVLPKGPES ESEDHRASGE VRTGKWKVPT YKDYVDLFRH LLSSDQMMDS ILADEAFFSV NSSSESLNHL LYDEFV KSV LKIVEKLDLT LEIQTVGEQE NGDEAPGVWM IPTSDPAANL HPAKPKDFSA FINLVEFCRE ILPEKQAEFF EPWVYSF SY ELILQSTRLP LISGFYKLLS ITVRNAKKIK YFEGVSPKSL KHSPEDPEKY SCFALFVKFG KEVAVKMKQY KDELLASC L TFLLSLPHNI IELDVRAYVP ALQMAFKLGL SYTPLAEVGL NALEEWSIYI DRHVMQPYYK DILPCLDGYL KTSALSDET KNNWEVSALS RAAQKGFNKV VLKHLKKTKN LSSNEAISLE EIRIRVVQML GSLGGQINKN LLTVTSSDEM MKSYVAWDRE KRLSFAVPF REMKPVIFLD VFLPRVTELA LTASDRQTKV AACELLHSMV MFMLGKATQM PEGGQGAPPM YQLYKRTFPV L LRLACDVD QVTRQLYEPL VMQLIHWFTN NKKFESQDTV ALLEAILDGI VDPVDSTLRD FCGRCIREFL KWSIKQITPQ QQ EKSPVNT KSLFKRLYSL ALHPNAFKRL GASLAFNNIY REFREEESLV EQFVFEALVI YMESLALAHA DEKSLGTIQQ CCD AIDHLC RIIEKKHVSL NKAKKRRLPR GFPPSASLCL LDLVKWLLAH CGRPQTECRH KSIELFYKFV PLLPGNRSPN LWLK DVLKE EGVSFLINTF EGGGCGQPSG ILAQPTLLYL RGPFSLQATL CWLDLLLAAL ECYNTFIGER TVGALQVLGT EAQSS LLKA VAFFLESIAM HDIIAAEKCF GTGAAGNRTS PQEGERYNYS KCTVVVRIME FTTTLLNTSP EGWKLLKKDL CNTHLM RVL VQTLCEPASI GFNIGDVQVM AHLPDVCVNL MKALKMSPYK DILETHLREK ITAQSIEELC AVNLYGPDAQ VDRSRLA AV VSACKQLHRA GLLHNILPSQ STDLHHSVGT ELLSLVYKGI APGDERQCLP SLDLSCKQLA SGLLELAFAF GGLCERLV S LLLNPAVLST ASLGSSQGSV IHFSHGEYFY SLFSETINTE LLKNLDLAVL ELMQSSVDNT KMVSAVLNGM LDQSFRERA NQKHQGLKLA TTILQHWKKC DSWWAKDSPL ETKMAVLALL AKILQIDSSV SFNTSHGSFP EVFTTYISLL ADTKLDLHLK GQAVTLLPF FTSLTGGSLE ELRRVLEQLI VAHFPMQSRE FPPGTPRFNN YVDCMKKFLD ALELSQSPML LELMTEVLCR E QQHVMEEL FQSSFRRIAR RGSCVTQVGL LESVYEMFRK DDPRLSFTRQ SFVDRSLLTL LWHCSLDALR EFFSTIVVDA ID VLKSRFT KLNESTFDTQ ITKKMGYYKI LDVMYSRLPK DDVHAKESKI NQVFHGSCIT EGNELTKTLI KLCYDAFTEN MAG ENQLLE RRRLYHCAAY NCAISVICCV FNELKFYQGF LFSEKPEKNL LIFENLIDLK RRYNFPVEVE VPMERKKKYI EIRK EAREA ANGDSDGPSY MSSLSYLADS TLSEEMSQFD FSTGVQSYSY SSQDPRPATG RFRRREQRDP TVHDDVLELE MDELN RHEC MAPLTALVKH MHRSLGPPQG EEDSVPRDLP SWMKFLHGKL GNPIVPLNIR LFLAKLVINT EEVFRPYAKH WLSPLL QLA ASENNGGEGI HYMVVEIVAT ILSWTGLATP TGVPKDEVLA NRLLNFLMKH VFHPKRAVFR HNLEIIKTLV ECWKDCL SI PYRLIFEKFS GKDPNSKDNS VGIQLLGIVM ANDLPPYDPQ CGIQSSEYFQ ALVNNMSFVR YKEVYAAAAE VLGLILRY V MERKNILEES LCELVAKQLK QHQNTMEDKF IVCLNKVTKS FPPLADRFMN AVFFLLPKFH GVLKTLCLEV VLCRVEGMT ELYFQLKSKD FVQVMRHRDD ERQKVCLDII YKMMPKLKPV ELRELLNPVV EFVSHPSTTC REQMYNILMW IHDNYRDPES ETDNDSQEI FKLAKDVLIQ GLIDENPGLQ LIIRNFWSHE TRLPSNTLDR LLALNSLYSP KIEVHFLSLA TNFLLEMTSM S PDYPNPMF EHPLSECEFQ EYTIDSDWRF RSTVLTPMFV ETQASQGTLQ TRTQEGSLSA RWPVAGQIRA TQQQHDFTLT QT ADGRSSF DWLTGSSTDP LVDHTSPSSD SLLFAHKRSE RLQRAPLKSV GPDFGKKRLG LPGDEVDNKV KGAAGRTDLL RLR RRFMRD QEKLSLMYAR KGVAEQKREK EIKSELKMKQ DAQVVLYRSY RHGDLPDIQI KHSSLITPLQ AVAQRDPIIA KQLF SSLFS GILKEMDKFK TLSEKNNITQ KLLQDFNRFL NTTFSFFPPF VSCIQDISCQ HAALLSLDPA AVSAGCLASL QQPVG IRLL EEALLRLLPA ELPAKRVRGK ARLPPDVLRW VELAKLYRSI GEYDVLRGIF TSEIGTKQIT QSALLAEARS DYSEAA KQY DEALNKQDWV DGEPTEAEKD FWELASLDCY NHLAEWKSLE YCSTASIDSE NPPDLNKIWS EPFYQETYLP YMIRSKL KL LLQGEADQSL LTFIDKAMHG ELQKAILELH YSQELSLLYL LQDDVDRAKY YIQNGIQSFM QNYSSIDVLL HQSRLTKL Q SVQALTEIQE FISFISKQGN LSSQVPLKRL LNTWTNRYPD AKMDPMNIWD DIITNRCFFL SKIEEKLTPL PEDNSMNVD QDGDPSDRME VQEQEEDISS LIRSCKFSMK MKMIDSARKQ NNFSLAMKLL KELHKESKTR DDWLVSWVQS YCRLSHCRSR SQGCSEQVL TVLKTVSLLD ENNVSSYLSK NILAFRDQNI LLGTTYRIIA NALSSEPACL AEIEEDKARR ILELSGSSSE D SEKVIAGL YQRAFQHLSE AVQAAEEEAQ PPSWSCGPAA GVIDAYMTLA DFCDQQLRKE EENASVIDSA ELQAYPALVV EK MLKALKL NSNEARLKFP RLLQIIERYP EETLSLMTKE ISSVPCWQFI SWISHMVALL DKDQAVAVQH SVEEITDNYP QAI VYPFII SSESYSFKDT STGHKNKEFV ARIKSKLDQG GVIQDFINAL DQLSNPELLF KDWSNDVRAE LAKTPVNKKN IEKM YERMY AALGDPKAPG LGAFRRKFIQ TFGKEFDKHF GKGGSKLLRM KLSDFNDITN MLLLKMNKDS KPPGNLKECS PWMSD FKVE FLRNELEIPG QYDGRGKPLP EYHVRIAGFD ERVTVMASLR RPKRIIIRGH DEREHPFLVK GGEDLRQDQR VEQLFQ VMN GILAQDSACS QRALQLRTYS VVPMTSRLGL IEWLENTVTL KDLLLNTMSQ EEKAAYLSDP RAPPCEYKDW LTKMSGK HD VGAYMLMYKG ANRTETVTSF RKRESKVPAD LLKRAFVRMS TSPEAFLALR SHFASSHALI CISHWILGIG DRHLNNFM V AMETGGVIGI DFGHAFGSAT QFLPVPELMP FRLTRQFINL MLPMKETGLM YSIMVHALRA FRSDPGLLTN TMDVFVKEP SFDWKNFEQK MLKKGGSWIQ EINVAEKNWY PRQKICYAKR KLAGANPAVI TCDELLLGHE KAPAFRDYVA VARGSKDHNI RAQEPESGL SEETQVKCLM DQATDPNILG RTWEGWEPWM

UniProtKB: DNA-dependent protein kinase catalytic subunit

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Macromolecule #4: DNA (34-MER)

MacromoleculeName: DNA (34-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 10.502785 KDa
SequenceString:
(DT)(DA)(DA)(DA)(DA)(DA)(DC)(DT)(DA)(DT) (DT)(DA)(DT)(DT)(DA)(DT)(DG)(DG)(DT)(DA) (DT)(DT)(DA)(DT)(DG)(DG)(DC)(DC)(DT) (DT)(DG)(DG)(DG)(DC)

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Macromolecule #5: DNA (36-MER)

MacromoleculeName: DNA (36-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.042164 KDa
SequenceString:
(DC)(DA)(DG)(DC)(DT)(DA)(DA)(DT)(DG)(DG) (DC)(DC)(DA)(DT)(DA)(DA)(DT)(DA)(DC)(DC) (DA)(DT)(DA)(DA)(DT)(DA)(DA)(DT)(DA) (DG)(DT)(DT)(DT)(DT)(DT)(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

Concentration0.6 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.7 µm / Nominal defocus min: 1.7 µm / Nominal magnification: 18000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-32 / Number real images: 3496 / Average exposure time: 8.0 sec. / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0)
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 53451
FSC plot (resolution estimation)

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