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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


positive regulation of platelet formation / Ku70:Ku80 complex / negative regulation of t-circle formation / T cell receptor V(D)J recombination / DNA end binding / pro-B cell differentiation / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase activity / DNA-dependent protein kinase complex ...positive regulation of platelet formation / Ku70:Ku80 complex / negative regulation of t-circle formation / T cell receptor V(D)J recombination / DNA end binding / pro-B cell differentiation / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase activity / DNA-dependent protein kinase complex / histone H2AXS139 kinase activity / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / immature B cell differentiation / regulation of smooth muscle cell proliferation / cellular response to X-ray / nuclear telomere cap complex / double-strand break repair via alternative nonhomologous end joining / regulation of epithelial cell proliferation / double-strand break repair via classical nonhomologous end joining / telomere capping / Cytosolic sensors of pathogen-associated DNA / IRF3-mediated induction of type I IFN / positive regulation of neurogenesis / regulation of hematopoietic stem cell differentiation / recombinational repair / regulation of telomere maintenance / U3 snoRNA binding / protein localization to chromosome, telomeric region / maturation of 5.8S rRNA / T cell lineage commitment / cellular hyperosmotic salinity response / negative regulation of cGAS/STING signaling pathway / positive regulation of double-strand break repair via nonhomologous end joining / 2-LTR circle formation / B cell lineage commitment / telomeric DNA binding / hematopoietic stem cell proliferation / negative regulation of protein phosphorylation / positive regulation of protein kinase activity / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / site of DNA damage / peptidyl-threonine phosphorylation / 5'-deoxyribose-5-phosphate lyase activity / hematopoietic stem cell differentiation / ATP-dependent activity, acting on DNA / ectopic germ cell programmed cell death / somitogenesis / telomere maintenance via telomerase / mitotic G1 DNA damage checkpoint signaling / neurogenesis / telomere maintenance / activation of innate immune response / DNA helicase activity / cyclin binding / positive regulation of erythrocyte differentiation / positive regulation of translation / cellular response to leukemia inhibitory factor / response to gamma radiation / small-subunit processome / enzyme activator activity / Nonhomologous End-Joining (NHEJ) / cellular response to gamma radiation / protein-DNA complex / regulation of circadian rhythm / brain development / protein destabilization / peptidyl-serine phosphorylation / double-strand break repair via nonhomologous end joining / protein modification process / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cellular response to insulin stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / rhythmic process / T cell differentiation in thymus / double-strand break repair / E3 ubiquitin ligases ubiquitinate target proteins / heart development / double-stranded DNA binding / scaffold protein binding / secretory granule lumen / DNA recombination / transcription regulator complex / ficolin-1-rich granule lumen / damaged DNA binding / RNA polymerase II-specific DNA-binding transcription factor binding / chromosome, telomeric region / protein phosphorylation / non-specific serine/threonine protein kinase / protein kinase activity / transcription cis-regulatory region binding / positive regulation of apoptotic process / ribonucleoprotein complex / protein domain specific binding / innate immune response / protein serine kinase activity / negative regulation of DNA-templated transcription / protein serine/threonine kinase activity / ubiquitin protein ligase binding
Similarity search - Function
Ku70, bridge and pillars domain superfamily / : / DNA-dependent protein kinase catalytic subunit, CC3 / 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 ...Ku70, bridge and pillars domain superfamily / : / DNA-dependent protein kinase catalytic subunit, CC3 / 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 / Ku70 / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 N-terminal alpha/beta domain / Ku70/Ku80 beta-barrel domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen / Ku70/Ku80 beta-barrel domain / SPOC-like, C-terminal domain superfamily / SAP domain superfamily / SAP motif profile. / SAP domain / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / : / 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 / 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-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing 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
  • Imaged by UCSF Chimera
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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

emd_6803.png

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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 300 pix.
= 390. Å		1.3 Å/pix.
x 300 pix.
= 390. Å		1.3 Å/pix.
x 300 pix.
= 390. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
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
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND3 (ver. 3) / Type: NONE
Startup modelType of model: EMDB MAP
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
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0)
FSC plot (resolution estimation)

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