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- EMDB-25113: DNA-PK complex of DNA end processing -

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Basic information

Entry
Database: EMDB / ID: EMD-25113
TitleDNA-PK complex of DNA end processing
Map data
Sample
  • Complex: Complex of DNA-PKcs, KU70, Ku80, Artemis and DNA
    • Protein or peptide: DNA-dependent protein kinase catalytic subunit
    • Protein or peptide: X-ray repair cross-complementing protein 6
    • Protein or peptide: X-ray repair cross-complementing protein 5
    • Protein or peptide: Protein artemis
    • DNA: Hairpin_1
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: ZINC ION
Keywordsendonuclease / Kinase / complex / DNA BINDING PROTEIN / TRANSFERASE / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


positive regulation of platelet formation / Ku70:Ku80 complex / T cell receptor V(D)J recombination / single-stranded DNA endodeoxyribonuclease activity / negative regulation of t-circle formation / pro-B cell differentiation / DNA end binding / DNA-dependent protein kinase activity / small-subunit processome assembly / positive regulation of lymphocyte differentiation ...positive regulation of platelet formation / Ku70:Ku80 complex / T cell receptor V(D)J recombination / single-stranded DNA endodeoxyribonuclease activity / negative regulation of t-circle formation / pro-B cell differentiation / DNA end binding / DNA-dependent protein kinase activity / small-subunit processome assembly / positive regulation of lymphocyte differentiation / histone H2AXS139 kinase activity / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / immunoglobulin V(D)J recombination / nonhomologous end joining complex / immature B cell differentiation / V(D)J recombination / regulation of smooth muscle cell proliferation / cellular response to X-ray / regulation of epithelial cell proliferation / double-strand break repair via alternative nonhomologous end joining / double-strand break repair via classical nonhomologous end joining / nuclear telomere cap complex / Cytosolic sensors of pathogen-associated DNA / telomere capping / IRF3-mediated induction of type I IFN / 5'-3' exonuclease activity / 5'-3' DNA exonuclease activity / regulation of hematopoietic stem cell differentiation / recombinational repair / regulation of telomere maintenance / positive regulation of neurogenesis / U3 snoRNA binding / protein localization to chromosome, telomeric region / T cell lineage commitment / maturation of 5.8S rRNA / cellular hyperosmotic salinity response / positive regulation of double-strand break repair via nonhomologous end joining / B cell lineage commitment / negative regulation of cGAS/STING signaling pathway / 2-LTR circle formation / response to ionizing radiation / hematopoietic stem cell proliferation / peptidyl-threonine phosphorylation / telomeric DNA binding / DNA 3'-5' helicase / negative regulation of protein phosphorylation / positive regulation of protein kinase activity / 5'-deoxyribose-5-phosphate lyase activity / hematopoietic stem cell differentiation / somitogenesis / ATP-dependent activity, acting on DNA / ectopic germ cell programmed cell death / site of DNA damage / telomere maintenance via telomerase / interstrand cross-link repair / mitotic G1 DNA damage checkpoint signaling / neurogenesis / activation of innate immune response / positive regulation of erythrocyte differentiation / DNA helicase activity / B cell differentiation / telomere maintenance / cyclin binding / DNA-(apurinic or apyrimidinic site) lyase / positive regulation of translation / cellular response to leukemia inhibitory factor / response to gamma radiation / protein modification process / Nonhomologous End-Joining (NHEJ) / small-subunit processome / peptidyl-serine phosphorylation / enzyme activator activity / protein-DNA complex / cellular response to gamma radiation / regulation of circadian rhythm / brain development / double-strand break repair via nonhomologous end joining / protein destabilization / 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 / T cell differentiation in thymus / rhythmic process / double-strand break repair / E3 ubiquitin ligases ubiquitinate target proteins / heart development / double-stranded DNA binding / scaffold protein binding / secretory granule lumen / endonuclease activity / DNA recombination / transcription regulator complex / ficolin-1-rich granule lumen / damaged DNA binding / Hydrolases; Acting on ester bonds / RNA polymerase II-specific DNA-binding transcription factor binding / adaptive immune response / protein phosphorylation / chromosome, telomeric region
Similarity search - Function
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 ...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, 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 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 / : / DNA repair metallo-beta-lactamase / DNA repair metallo-beta-lactamase / 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 / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / von Willebrand factor A-like domain superfamily / Armadillo-like helical / Armadillo-type fold / Protein kinase-like domain superfamily
Similarity search - Domain/homology
DNA repair protein Ku70 / X-ray repair cross-complementing protein 5 / DNA-dependent protein kinase catalytic subunit / Protein artemis
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsLiu L / Li J
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)M.G., DK036167 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)W.Y., DK036147 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK036144 United States
CitationJournal: Mol Cell / Year: 2022
Title: Autophosphorylation transforms DNA-PK from protecting to processing DNA ends.
Authors: Lan Liu / Xuemin Chen / Jun Li / Huaibin Wang / Christopher J Buehl / Noah J Goff / Katheryn Meek / Wei Yang / Martin Gellert /
Abstract: The DNA-dependent protein kinase (DNA-PK) initially protects broken DNA ends but then promotes their processing during non-homologous end joining (NHEJ). Before ligation by NHEJ, DNA hairpin ends ...The DNA-dependent protein kinase (DNA-PK) initially protects broken DNA ends but then promotes their processing during non-homologous end joining (NHEJ). Before ligation by NHEJ, DNA hairpin ends generated during V(D)J recombination must be opened by the Artemis nuclease, together with autophosphorylated DNA-PK. Structures of DNA-PK bound to DNA before and after phosphorylation, and in complex with Artemis and a DNA hairpin, reveal an essential functional switch. When bound to open DNA ends in its protection mode, DNA-PK is inhibited for cis-autophosphorylation of the so-called ABCDE cluster but activated for phosphorylation of other targets. In contrast, DNA hairpin ends promote cis-autophosphorylation. Phosphorylation of four Thr residues in ABCDE leads to gross structural rearrangement of DNA-PK, widening the DNA binding groove for Artemis recruitment and hairpin cleavage. Meanwhile, Artemis locks DNA-PK into the kinase-inactive state. Kinase activity and autophosphorylation of DNA-PK are regulated by different DNA ends, feeding forward to coordinate NHEJ events.
History
DepositionOct 6, 2021-
Header (metadata) releaseJan 12, 2022-
Map releaseJan 12, 2022-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7sgl
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25113.png

Downloads & links

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Map

FileDownload / File: emd_25113.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 480 pix.
= 399.84 Å		0.83 Å/pix.
x 480 pix.
= 399.84 Å		0.83 Å/pix.
x 480 pix.
= 399.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0056 / Movie #1: 0.006
Minimum - Maximum-0.023507146 - 0.06320549
Average (Standard dev.)-0.000028083343 (±0.0016734427)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 399.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8330.8330.833
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z399.840399.840399.840
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0240.063-0.000

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Supplemental data

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Mask #1

Fileemd_25113_msk_1.map
Projections & Slices
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Half map: #1

Fileemd_25113_half_map_1.map
Projections & Slices
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Half map: #2

Fileemd_25113_half_map_2.map
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Sample components

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Entire : Complex of DNA-PKcs, KU70, Ku80, Artemis and DNA

EntireName: Complex of DNA-PKcs, KU70, Ku80, Artemis and DNA
Components
  • Complex: Complex of DNA-PKcs, KU70, Ku80, Artemis and DNA
    • Protein or peptide: DNA-dependent protein kinase catalytic subunit
    • Protein or peptide: X-ray repair cross-complementing protein 6
    • Protein or peptide: X-ray repair cross-complementing protein 5
    • Protein or peptide: Protein artemis
    • DNA: Hairpin_1
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: INOSITOL HEXAKISPHOSPHATE
  • Ligand: ZINC ION

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Supramolecule #1: Complex of DNA-PKcs, KU70, Ku80, Artemis and DNA

SupramoleculeName: Complex of DNA-PKcs, KU70, Ku80, Artemis and DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Molecular weightTheoretical: 720 KDa

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Macromolecule #1: DNA-dependent protein kinase catalytic subunit

MacromoleculeName: DNA-dependent protein kinase catalytic subunit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 469.993031 KDa
SequenceString: MAGSGAGVRC SLLRLQETLS AADRCGAALA GHQLIRGLGQ ECVLSSSPAV LALQTSLVFS RDFGLLVFVR KSLNSIEFRE CREEILKFL CIFLEKMGQK IAPYSVEIKN TCTSVYTKDR AAKCKIPALD LLIKLLQTFR SSRLMDEFKI GELFSKFYGE L ALKKKIPD ...String:
MAGSGAGVRC SLLRLQETLS AADRCGAALA GHQLIRGLGQ ECVLSSSPAV LALQTSLVFS RDFGLLVFVR KSLNSIEFRE CREEILKFL CIFLEKMGQK IAPYSVEIKN TCTSVYTKDR AAKCKIPALD LLIKLLQTFR SSRLMDEFKI GELFSKFYGE L ALKKKIPD TVLEKVYELL GLLGEVHPSE MINNAENLFR AFLGELKTQM TSAVREPKLP VLAGCLKGLS SLLCNFTKSM EE DPQTSRE IFNFVLKAIR PQIDLKRYAV PSAGLRLFAL HASQFSTCLL DNYVSLFEVL LKWCAHTNVE LKKAALSALE SFL KQVSNM VAKNAEMHKN KLQYFMEQFY GIIRNVDSNN KELSIAIRGY GLFAGPCKVI NAKDVDFMYV ELIQRCKQMF LTQT DTGDD RVYQMPSFLQ SVASVLLYLD TVPEVYTPVL EHLVVMQIDS FPQYSPKMQL VCCRAIVKVF LALAAKGPVL RNCIS TVVH QGLIRICSKP VVLPKGPESE SEDHRASGEV RTGKWKVPTY KDYVDLFRHL LSSDQMMDSI LADEAFFSVN SSSESL NHL LYDEFVKSVL KIVEKLDLTL EIQTVGEQEN GDEAPGVWMI PTSDPAANLH PAKPKDFSAF INLVEFCREI LPEKQAE FF EPWVYSFSYE LILQSTRLPL ISGFYKLLSI TVRNAKKIKY FEGVSPKSLK HSPEDPEKYS CFALFVKFGK EVAVKMKQ Y KDELLASCLT FLLSLPHNII ELDVRAYVPA LQMAFKLGLS YTPLAEVGLN ALEEWSIYID RHVMQPYYKD ILPCLDGYL KTSALSDETK NNWEVSALSR AAQKGFNKVV LKHLKKTKNL SSNEAISLEE IRIRVVQMLG SLGGQINKNL LTVTSSDEMM KSYVAWDRE KRLSFAVPFR EMKPVIFLDV FLPRVTELAL TASDRQTKVA ACELLHSMVM FMLGKATQMP EGGQGAPPMY Q LYKRTFPV LLRLACDVDQ VTRQLYEPLV MQLIHWFTNN KKFESQDTVA LLEAILDGIV DPVDSTLRDF CGRCIREFLK WS IKQITPQ QQEKSPVNTK SLFKRLYSLA LHPNAFKRLG ASLAFNNIYR EFREEESLVE QFVFEALVIY MESLALAHAD EKS LGTIQQ CCDAIDHLCR IIEKKHVSLN KAKKRRLPRG FPPSASLCLL DLVKWLLAHC GRPQTECRHK SIELFYKFVP LLPG NRSPN LWLKDVLKEE GVSFLINTFE GGGCGQPSGI LAQPTLLYLR GPFSLQATLC WLDLLLAALE CYNTFIGERT VGALQ VLGT EAQSSLLKAV AFFLESIAMH DIIAAEKCFG TGAAGNRTSP QEGERYNYSK CTVVVRIMEF TTTLLNTSPE GWKLLK KDL CNTHLMRVLV QTLCEPASIG FNIGDVQVMA HLPDVCVNLM KALKMSPYKD ILETHLREKI TAQSIEELCA VNLYGPD AQ VDRSRLAAVV SACKQLHRAG LLHNILPSQS TDLHHSVGTE LLSLVYKGIA PGDERQCLPS LDLSCKQLAS GLLELAFA F GGLCERLVSL LLNPAVLSTA SLGSSQGSVI HFSHGEYFYS LFSETINTEL LKNLDLAVLE LMQSSVDNTK MVSAVLNGM LDQSFRERAN QKHQGLKLAT TILQHWKKCD SWWAKDSPLE TKMAVLALLA KILQIDSSVS FNTSHGSFPE VFTTYISLLA DTKLDLHLK GQAVTLLPFF TSLTGGSLEE LRRVLEQLIV AHFPMQSREF PPGTPRFNNY VDCMKKFLDA LELSQSPMLL E LMTEVLCR EQQHVMEELF QSSFRRIARR GSCVTQVGLL ESVYEMFRKD DPRLSFTRQS FVDRSLLTLL WHCSLDALRE FF STIVVDA IDVLKSRFTK LNESTFDTQI TKKMGYYKIL DVMYSRLPKD DVHAKESKIN QVFHGSCITE GNELTKTLIK LCY DAFTEN MAGENQLLER RRLYHCAAYN CAISVICCVF NELKFYQGFL FSEKPEKNLL IFENLIDLKR RYNFPVEVEV PMER KKKYI EIRKEAREAA NGDSDGPSYM SSLSYLADST LSEEMSQFDF STGVQSYSYS SQDPRPATGR FRRREQRDPT VHDDV LELE MDELNRHECM APLTALVKHM HRSLGPPQGE EDSVPRDLPS WMKFLHGKLG NPIVPLNIRL FLAKLVINTE EVFRPY AKH WLSPLLQLAA SENNGGEGIH YMVVEIVATI LSWTGLATPT GVPKDEVLAN RLLNFLMKHV FHPKRAVFRH NLEIIKT LV ECWKDCLSIP YRLIFEKFSG KDPNSKDNSV GIQLLGIVMA NDLPPYDPQC GIQSSEYFQA LVNNMSFVRY KEVYAAAA E VLGLILRYVM ERKNILEESL CELVAKQLKQ HQNTMEDKFI VCLNKVTKSF PPLADRFMNA VFFLLPKFHG VLKTLCLEV VLCRVEGMTE LYFQLKSKDF VQVMRHRDDE RQKVCLDIIY KMMPKLKPVE LRELLNPVVE FVSHPSTTCR EQMYNILMWI HDNYRDPES ETDNDSQEIF KLAKDVLIQG LIDENPGLQL IIRNFWSHET RLPSNTLDRL LALNSLYSPK IEVHFLSLAT N FLLEMTSM SPDYPNPMFE HPLSECEFQE YTIDSDWRFR STVLTPMFVE (TPO)QASQGTLQT RTQEGSLSAR WPVAGQIR A (TPO)QQQHDF(TPO)L(TPO) QTADGRSSFD WLTGSSTDPL VDHTSPSSDS LLFAHKRSER LQRAPLKSVG PDFGKKR LG LPGDEVDNKV KGAAGRTDLL RLRRRFMRDQ EKLSLMYARK GVAEQKREKE IKSELKMKQD AQVVLYRSYR HGDLPDIQ I KHSSLITPLQ AVAQRDPIIA KQLFSSLFSG ILKEMDKFKT LSEKNNITQK LLQDFNRFLN TTFSFFPPFV SCIQDISCQ HAALLSLDPA AVSAGCLASL QQPVGIRLLE EALLRLLPAE LPAKRVRGKA RLPPDVLRWV ELAKLYRSIG EYDVLRGIFT SEIGTKQIT QSALLAEARS DYSEAAKQYD EALNKQDWVD GEPTEAEKDF WELASLDCYN HLAEWKSLEY CSTASIDSEN P PDLNKIWS EPFYQETYLP YMIRSKLKLL LQGEADQSLL TFIDKAMHGE LQKAILELHY SQELSLLYLL QDDVDRAKYY IQ NGIQSFM QNYSSIDVLL HQSRLTKLQS VQALTEIQEF ISFISKQGNL SSQVPLKRLL NTWTNRYPDA KMDPMNIWDD IIT NRCFFL SKIEEKLTPL PEDNSMNVDQ DGDPSDRMEV QEQEEDISSL IRSCKFSMKM KMIDSARKQN NFSLAMKLLK ELHK ESKTR DDWLVSWVQS YCRLSHCRSR SQGCSEQVLT VLKTVSLLDE NNVSSYLSKN ILAFRDQNIL LGTTYRIIAN ALSSE PACL AEIEEDKARR ILELSGSSSE DSEKVIAGLY QRAFQHLSEA VQAAEEEAQP PSWSCGPAAG VIDAYMTLAD FCDQQL RKE EENASVIDSA ELQAYPALVV EKMLKALKLN SNEARLKFPR LLQIIERYPE ETLSLMTKEI SSVPCWQFIS WISHMVA LL DKDQAVAVQH SVEEITDNYP QAIVYPFIIS SESYSFKDTS TGHKNKEFVA RIKSKLDQGG VIQDFINALD QLSNPELL F KDWSNDVRAE LAKTPVNKKN IEKMYERMYA ALGDPKAPGL GAFRRKFIQT FGKEFDKHFG KGGSKLLRMK LSDFNDITN MLLLKMNKDS KPPGNLKECS PWMSDFKVEF LRNELEIPGQ YDGRGKPLPE YHVRIAGFDE RVTVMASLRR PKRIIIRGHD EREHPFLVK GGEDLRQDQR VEQLFQVMNG ILAQDSACSQ RALQLRTYSV VPMTSRLGLI EWLENTVTLK DLLLNTMSQE E KAAYLSDP RAPPCEYKDW LTKMSGKHDV GAYMLMYKGA NRTETVTSFR KRESKVPADL LKRAFVRMST SPEAFLALRS HF ASSHALI CISHWILGIG DRHLNNFMVA METGGVIGID FGHAFGSATQ FLPVPELMPF RLTRQFINLM LPMKETGLMY SIM VHALRA FRSDPGLLTN TMDVFVKEPS FDWKNFEQKM LKKGGSWIQE INVAEKNWYP RQKICYAKRK LAGANPAVIT CDEL LLGHE KAPAFRDYVA VARGSKDHNI RAQEPESGLS EETQVKCLMD QATDPNILGR TWEGWEPWM

UniProtKB: DNA-dependent protein kinase catalytic subunit

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Macromolecule #2: X-ray repair cross-complementing protein 6

MacromoleculeName: X-ray repair cross-complementing protein 6 / 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: 70.198336 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPVMSGWESY YKTEGDEEAE EEQEENLEAS GDYKYSGRDS LIFLVDASKA MFESQSEDEL TPFDMSIQCI QSVYISKIIS SDRDLLAVV FYGTEKDKNS VNFKNIYVLQ ELDNPGAKRI LELDQFKGQQ GQKRFQDMMG HGSDYSLSEV LWVCANLFSD V QFKMSHKR ...String:
GPVMSGWESY YKTEGDEEAE EEQEENLEAS GDYKYSGRDS LIFLVDASKA MFESQSEDEL TPFDMSIQCI QSVYISKIIS SDRDLLAVV FYGTEKDKNS VNFKNIYVLQ ELDNPGAKRI LELDQFKGQQ GQKRFQDMMG HGSDYSLSEV LWVCANLFSD V QFKMSHKR IMLFTNEDNP HGNDSAKASR ARTKAGDLRD TGIFLDLMHL KKPGGFDISL FYRDIISIAE DEDLRVHFEE SS KLEDLLR KVRAKETRKR ALSRLKLKLN KDIVISVGIY NLVQKALKPP PIKLYRETNE PVKTKTRTFN TSTGGLLLPS DTK RSQIYG SRQIILEKEE TEELKRFDDP GLMLMGFKPL VLLKKHHYLR PSLFVYPEES LVIGSSTLFS ALLIKCLEKE VAAL CRYTP RRNIPPYFVA LVPQEEELDD QKIQVTPPGF QLVFLPFADD KRKMPFTEKI MATPEQVGKM KAIVEKLRFT YRSDS FENP VLQQHFRNLE ALALDLMEPE QAVDLTLPKV EAMNKRLGSL VDEFKELVYP PDYNPEGKVT KRKHDNEGSG SKRPKV EYS EEELKTHISK GTLGKFTVPM LKEACRAYGL KSGLKKQELL EALTKHFQD

UniProtKB: DNA repair protein Ku70

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Macromolecule #3: X-ray repair cross-complementing protein 5

MacromoleculeName: X-ray repair cross-complementing protein 5 / type: protein_or_peptide / ID: 3 / 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: 82.812438 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Macromolecule #4: Protein artemis

MacromoleculeName: Protein artemis / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 79.479359 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSSFEGQMAE YPTISIDRFD RENLRARAYF LSHCHKDHMK GLRAPTLKRR LECSLKVYLY CSPVTKELLL TSPKYRFWKK RIISIEIET PTQISLVDEA SGEKEEIVVT LLPAGHCPGS VMFLFQGNNG TVLYTGDFRL AQGEAARMEL LHSGGRVKDI Q SVYLDTTF ...String:
MSSFEGQMAE YPTISIDRFD RENLRARAYF LSHCHKDHMK GLRAPTLKRR LECSLKVYLY CSPVTKELLL TSPKYRFWKK RIISIEIET PTQISLVDEA SGEKEEIVVT LLPAGHCPGS VMFLFQGNNG TVLYTGDFRL AQGEAARMEL LHSGGRVKDI Q SVYLDTTF CDPRFYQIPS REECLSGVLE LVRSWITRSP YHVVWLNCKA AYGYEYLFTN LSEELGVQVH VNKLDMFRNM PE ILHHLTT DRNTQIHACR HPKAEEYFQW SKLPCGITSR NRIPLHIISI KPSTMWFGER SRKTNVIVRT GESSYRACFS FHS SYSEIK DFLSYLCPVN AYPNVIPVGT TMDKVVEILK PLCRSSQSTE PKYKPLGKLK RARTVHRDSE EEDDYLFDDP LPIP LRHKV PYPETFHPEV FSMTAVSEKQ PEKLRQTPGC CRAECMQSSR FTNFVDCEES NSESEEEVGI PASLQGDLGS VLHLQ KADG DVPQWEVFFK RNDEITDESL ENFPSSTVAG GSQSPKLFSD SDGESTHISS QNSSQSTHIT EQGSQGWDSQ SDTVLL SSQ ERNSGDITSL DKADYRPTIK ENIPASLMEQ NVICPKDTYS DLKSRDKDVT IVPSTGEPTT LSSETHIPEE KSLLNLS TN ADSQSSSDFE VPSTPEAELP KREHLQYLYE KLATGESIAV KKRKCSLLDT AAALEVLFQ

UniProtKB: Protein artemis

+
Macromolecule #5: Hairpin_1

MacromoleculeName: Hairpin_1 / type: dna / ID: 5 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 16.636688 KDa
SequenceString: (DT)(DC)(DA)(DG)(DA)(DA)(DG)(DC)(DA)(DG) (DT)(DA)(DG)(DA)(DG)(DC)(DA)(DT)(DG)(DC) (DA)(DT)(DA)(DT)(DA)(DT)(DG)(DC)(DA) (DT)(DG)(DC)(DT)(DC)(DT)(DA)(DC)(DT)(DG) (DC) (DT)(DT)(DC)(DT)(DG)(DA) ...String:
(DT)(DC)(DA)(DG)(DA)(DA)(DG)(DC)(DA)(DG) (DT)(DA)(DG)(DA)(DG)(DC)(DA)(DT)(DG)(DC) (DA)(DT)(DA)(DT)(DA)(DT)(DG)(DC)(DA) (DT)(DG)(DC)(DT)(DC)(DT)(DA)(DC)(DT)(DG) (DC) (DT)(DT)(DC)(DT)(DG)(DA)(DC)(DG) (DA)(DT)(DA)(DT)(DC)(DG)

+
Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 7 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #8: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 8 / Number of copies: 1 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE

+
Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

-
Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
25.0 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid
100.0 mMPotassium chlorideKCl
1.0 mMDithiothreitol
GridModel: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

22624

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 161380
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 3.1.0)
Final angle assignmentType: COMMON LINE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-7sgl:
DNA-PK complex of DNA end processing

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