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- EMDB-51249: DNA-PK Ku80 mediated dimer bound to DNA polymerase Lambda and DNA... -

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Basic information

Entry
Database: EMDB / ID: EMD-51249
TitleDNA-PK Ku80 mediated dimer bound to DNA polymerase Lambda and DNA ligase 4/XRCC4
Map data
Sample
  • Complex: Ku80 mediated dimer of DNA-PK bound to Polymerase Lambda and XRCC4/DNA ligase IV
    • Protein or peptide: DNA ligase 4
    • Protein or peptide: X-ray repair cross-complementing protein 5
    • Protein or peptide: Protein PAXX
    • Protein or peptide: DNA repair protein XRCC4
    • Protein or peptide: DNA-dependent protein kinase catalytic subunit
    • Protein or peptide: X-ray repair cross-complementing protein 6
    • DNA: DNA
    • DNA: DNA
    • Protein or peptide: DNA polymerase lambda
KeywordsKinase / complex / DNA-binding / DNA BINDING PROTEIN
Function / homology
Function and homology information


FHA domain binding / positive regulation of chromosome organization / DN2 thymocyte differentiation / positive regulation of ligase activity / DNA ligase IV complex / positive regulation of platelet formation / DNA ligase activity / DNA double-strand break attachment to nuclear envelope / Ku70:Ku80 complex / T cell receptor V(D)J recombination ...FHA domain binding / positive regulation of chromosome organization / DN2 thymocyte differentiation / positive regulation of ligase activity / DNA ligase IV complex / positive regulation of platelet formation / DNA ligase activity / DNA double-strand break attachment to nuclear envelope / Ku70:Ku80 complex / T cell receptor V(D)J recombination / DNA ligase (ATP) / negative regulation of t-circle formation / pro-B cell differentiation / DNA end binding / DNA-dependent protein kinase activity / small-subunit processome assembly / DNA ligase (ATP) activity / 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 / nucleotide-excision repair, DNA gap filling / single strand break repair / 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 / isotype switching / double-strand break repair via classical nonhomologous end joining / nuclear telomere cap complex / Cytosolic sensors of pathogen-associated DNA / protein localization to site of double-strand break / telomere capping / IRF3-mediated induction of type I IFN / regulation of hematopoietic stem cell differentiation / recombinational repair / regulation of telomere maintenance / protein localization to chromosome, telomeric region / U3 snoRNA binding / positive regulation of neurogenesis / peptidyl-threonine phosphorylation / maturation of 5.8S rRNA / T cell lineage commitment / cellular response to lithium ion / cellular hyperosmotic salinity response / DNA biosynthetic process / positive regulation of double-strand break repair via nonhomologous end joining / negative regulation of cGAS/STING signaling pathway / B cell lineage commitment / 2-LTR circle formation / hematopoietic stem cell proliferation / AMP binding / ligase activity / telomeric repeat DNA binding / negative regulation of protein phosphorylation / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / DNA 3'-5' helicase / somatic stem cell population maintenance / 5'-deoxyribose-5-phosphate lyase activity / chromosome organization / hematopoietic stem cell differentiation / response to X-ray / ectopic germ cell programmed cell death / somitogenesis / ATP-dependent activity, acting on DNA / telomere maintenance via telomerase / SUMOylation of DNA damage response and repair proteins / somatic hypermutation of immunoglobulin genes / site of DNA damage / base-excision repair, gap-filling / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / DNA polymerase binding / activation of innate immune response / neurogenesis / positive regulation of erythrocyte differentiation / telomere maintenance / cyclin binding / stem cell proliferation / DNA helicase activity / DNA-(apurinic or apyrimidinic site) lyase / protein modification process / cellular response to leukemia inhibitory factor / central nervous system development / cellular response to ionizing radiation / peptidyl-serine phosphorylation / positive regulation of translation / response to gamma radiation / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / small-subunit processome / cellular response to gamma radiation / protein-DNA complex / regulation of circadian rhythm / brain development / base-excision repair
Similarity search - Function
Protein PAXX / : / PAXX, PAralog of XRCC4 and XLF, also called C9orf142 / DNA ligase IV domain / DNA ligase IV / DNA ligase 4 / DNA Ligase 4, adenylation domain / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / : ...Protein PAXX / : / PAXX, PAralog of XRCC4 and XLF, also called C9orf142 / DNA ligase IV domain / DNA ligase IV / DNA ligase 4 / DNA Ligase 4, adenylation domain / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / : / : / : / XRCC4 N-terminal domain / XRCC4 coiled-coil / XRCC4 C-terminal region / XRCC4-like, N-terminal 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, bridge and pillars domain superfamily / : / Ku70 / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / Ku80 / Ku70/Ku80 C-terminal arm / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 N-terminal alpha/beta domain / ATP-dependent DNA ligase AMP-binding site. / ATP-dependent DNA ligase signature 2. / DNA ligase, ATP-dependent, C-terminal / ATP dependent DNA ligase C terminal region / DNA ligase, ATP-dependent, conserved site / Ku70/Ku80 beta-barrel domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen / Ku70/Ku80 beta-barrel domain / ATP-dependent DNA ligase family profile. / SPOC-like, C-terminal domain superfamily / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / SAP domain superfamily / DNA repair protein XRCC4-like, C-terminal / 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. / BRCA1 C Terminus (BRCT) domain / DNA polymerase family X, beta-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / Phosphatidylinositol 3- and 4-kinases signature 1. / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / breast cancer carboxy-terminal domain / DNA-directed DNA polymerase X / DNA polymerase X family / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase beta-like, N-terminal domain / DNA polymerase lambda lyase domain superfamily / Helix-hairpin-helix domain / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase, thumb domain superfamily / DNA polymerase beta thumb / 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 / BRCT domain profile. / von Willebrand factor, type A / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily
Similarity search - Domain/homology
DNA repair protein Ku70 / DNA repair protein Ku80 / DNA ligase 4 / DNA-dependent protein kinase catalytic subunit / DNA repair protein XRCC4 / Protein PAXX / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.25 Å
AuthorsChaplin AK / Amin H / Zahid S / Hardwick SW
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/X00029X/1 United Kingdom
The Lister Institute of Preventive Medicine United Kingdom
CitationJournal: Nat Commun / Year: 2025
Title: Structural and functional insights into the interaction between Ku70/80 and Pol X family polymerases in NHEJ.
Authors: Philippe Frit / Himani Amin / Sayma Zahid / Nadia Barboule / Chloe Hall / Gurdip Matharu / Steven W Hardwick / Jeanne Chauvat / Sébastien Britton / Dima Y Chirgadze / Virginie Ropars / Jean- ...Authors: Philippe Frit / Himani Amin / Sayma Zahid / Nadia Barboule / Chloe Hall / Gurdip Matharu / Steven W Hardwick / Jeanne Chauvat / Sébastien Britton / Dima Y Chirgadze / Virginie Ropars / Jean-Baptiste Charbonnier / Patrick Calsou / Amanda K Chaplin /
Abstract: Non-homologous end joining (NHEJ) is the main repair pathway for double-strand DNA breaks (DSBs) in mammals. DNA polymerases lambda (Pol λ) and mu (Pol μ), members of the Pol X family, play a key ...Non-homologous end joining (NHEJ) is the main repair pathway for double-strand DNA breaks (DSBs) in mammals. DNA polymerases lambda (Pol λ) and mu (Pol μ), members of the Pol X family, play a key role in this process. However, their interaction within the NHEJ complexes is unclear. Here, we present cryo-EM structures of Pol λ in complex with the DNA-PK long-range synaptic complex, and Pol μ bound to Ku70/80-DNA. These structures identify interaction sites between Ku70/80 and Pol X BRCT domains. Using mutants at the proteins interface in functional assays including cell transfection with an original gap-filling reporter, we define the role of the BRCT domain in the recruitment and activity of the two Pol X members in NHEJ and in their contribution to cell survival following DSBs. Finally, we propose a unified model for the interaction of all Pol X members with Ku70/80.
History
DepositionAug 5, 2024-
Header (metadata) releaseAug 13, 2025-
Map releaseAug 13, 2025-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51249.png

Downloads & links

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Map

FileDownload / File: emd_51249.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

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Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 320 pix.
= 417.28 Å		1.3 Å/pix.
x 320 pix.
= 417.28 Å		1.3 Å/pix.
x 320 pix.
= 417.28 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.304 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 0.211
Minimum - Maximum-0.17788844 - 0.6955113
Average (Standard dev.)0.0019756726 (±0.034080233)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 417.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51249_msk_1.map
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Additional map: Locally refined composite map

Fileemd_51249_additional_1.map
AnnotationLocally refined composite map
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Half map: #2

Fileemd_51249_half_map_1.map
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Half map: #1

Fileemd_51249_half_map_2.map
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Sample components

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Entire : Ku80 mediated dimer of DNA-PK bound to Polymerase Lambda and XRCC...

EntireName: Ku80 mediated dimer of DNA-PK bound to Polymerase Lambda and XRCC4/DNA ligase IV
Components
  • Complex: Ku80 mediated dimer of DNA-PK bound to Polymerase Lambda and XRCC4/DNA ligase IV
    • Protein or peptide: DNA ligase 4
    • Protein or peptide: X-ray repair cross-complementing protein 5
    • Protein or peptide: Protein PAXX
    • Protein or peptide: DNA repair protein XRCC4
    • Protein or peptide: DNA-dependent protein kinase catalytic subunit
    • Protein or peptide: X-ray repair cross-complementing protein 6
    • DNA: DNA
    • DNA: DNA
    • Protein or peptide: DNA polymerase lambda

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Supramolecule #1: Ku80 mediated dimer of DNA-PK bound to Polymerase Lambda and XRCC...

SupramoleculeName: Ku80 mediated dimer of DNA-PK bound to Polymerase Lambda and XRCC4/DNA ligase IV
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 800 KDa

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Macromolecule #1: DNA ligase 4

MacromoleculeName: DNA ligase 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA ligase (ATP)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 104.124953 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MAASQTSQTV ASHVPFADLC STLERIQKSK GRAEKIRHFR EFLDSWRKFH DALHKNHKDV TDSFYPAMRL ILPQLERERM AYGIKETML AKLYIELLNL PRDGKDALKL LNYRTPTGTH GDAGDFAMIA YFVLKPRCLQ KGSLTIQQVN DLLDSIASNN S AKRKDLIK ...String:
MAASQTSQTV ASHVPFADLC STLERIQKSK GRAEKIRHFR EFLDSWRKFH DALHKNHKDV TDSFYPAMRL ILPQLERERM AYGIKETML AKLYIELLNL PRDGKDALKL LNYRTPTGTH GDAGDFAMIA YFVLKPRCLQ KGSLTIQQVN DLLDSIASNN S AKRKDLIK KSLLQLITQS SALEQKWLIR MIIKDLKLGV SQQTIFSVFH NDAAELHNVT TDLEKVCRQL HDPSVGLSDI SI TLFSAFK PMLAAIADIE HIEKDMKHQS FYIETKLDGE RMQMHKDGDV YKYFSRNGYN YTDQFGASPT EGSLTPFIHN AFK ADIQIC ILDGEMMAYN PNTQTFMQKG TKFDIKRMVE DSDLQTCYCV FDVLMVNNKK LGHETLRKRY EILSSIFTPI PGRI EIVQK TQAHTKNEVI DALNEAIDKR EEGIMVKQPL SIYKPDKRGE GWLKIKPEYV SGLMDELDIL IVGGYWGKGS RGGMM SHFL CAVAEKPPPG EKPSVFHTLS RVGSGCTMKE LYDLGLKLAK YWKPFHRKAP PSSILCGTEK PEVYIEPCNS VIVQIK AAE IVPSDMYKTG CTLRFPRIEK IRDDKEWHEC MTLDDLEQLR GKASGKLASK HLYIGGDDEP QEKKRKAAPK MKKVIGI IE HLKAPNLTNV NKISNIFEDV EFCVMSGTDS QPKPDLENRI AEFGGYIVQN PGPDTYCVIA GSENIRVKNI ILSNKHDV V KPAWLLECFK TKSFVPWQPR FMIHMCPSTK EHFAREYDCY GDSYFIDTDL NQLKEVFSGI KNSNEQTPEE MASLIADLE YRYSWDCSPL SMFRRHTVYL DSYAVINDLS TKNEGTRLAI KALELRFHGA KVVSCLAEGV SHVIIGEDHS RVADFKAFRR TFKRKFKIL KESWVTDSID KCELQEENQY LI

UniProtKB: DNA ligase 4

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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: 82.812438 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
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: DNA repair protein Ku80

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Macromolecule #3: Protein PAXX

MacromoleculeName: Protein PAXX / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 21.663498 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDPLSPPLCT LPPGPEPPRF VCYCEGEESG EGDRGGFNLY VTDAAELWST CFTPDSLAAL KARFGLSAAE DITPRFRAAC EQQAVALTL QEDRASLTLS GGPSALAFDL SKVPGPEAAP RLRALTLGLA KRVWSLERRL AAAEETAVSP RKSPRPAGPQ L FLPDPDPQ ...String:
MDPLSPPLCT LPPGPEPPRF VCYCEGEESG EGDRGGFNLY VTDAAELWST CFTPDSLAAL KARFGLSAAE DITPRFRAAC EQQAVALTL QEDRASLTLS GGPSALAFDL SKVPGPEAAP RLRALTLGLA KRVWSLERRL AAAEETAVSP RKSPRPAGPQ L FLPDPDPQ RGGPGPGVRR RCPGESLINP GFKSKKPAGG VDFDET

UniProtKB: Protein PAXX

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Macromolecule #4: DNA repair protein XRCC4

MacromoleculeName: DNA repair protein XRCC4 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.337703 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MERKISRIHL VSEPSITHFL QVSWEKTLES GFVITLTDGH SAWTGTVSES EISQEADDMA MEKGKYVGEL RKALLSGAGP ADVYTFNFS KESCYFFFEK NLKDVSFRLG SFNLEKVENP AEVIRELICY CLDTIAENQA KNEHLQKENE RLLRDWNDVQ G RFEKCVSA ...String:
MERKISRIHL VSEPSITHFL QVSWEKTLES GFVITLTDGH SAWTGTVSES EISQEADDMA MEKGKYVGEL RKALLSGAGP ADVYTFNFS KESCYFFFEK NLKDVSFRLG SFNLEKVENP AEVIRELICY CLDTIAENQA KNEHLQKENE RLLRDWNDVQ G RFEKCVSA KEALETDLYK RFILVLNEKK TKIRSLHNKL LNAAQEREKD IKQEGETAIC SEMTADRDPV YDESTDEESE NQ TDLSGLA SAAVSKDDSI ISSLDVTDIA PSRKRRQRMQ RNLGTEPKMA PQENQLQEKE NSRPDSSLPE TSKKEHISAE NMS LETLRN SSPEDLFDEI

UniProtKB: DNA repair protein XRCC4

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Macromolecule #5: DNA-dependent protein kinase catalytic subunit

MacromoleculeName: DNA-dependent protein kinase catalytic subunit / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 469.673219 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 TQASQGTLQT RTQEGSLSAR WPVAGQIRAT QQ QHDFTLT QTADGRSSFD WLTGSSTDPL VDHTSPSSDS LLFAHKRSER LQRAPLKSVG PDFGKKRLGL PGDEVDNKVK GAA GRTDLL RLRRRFMRDQ EKLSLMYARK GVAEQKREKE IKSELKMKQD AQVVLYRSYR HGDLPDIQIK HSSLITPLQA VAQR DPIIA KQLFSSLFSG ILKEMDKFKT LSEKNNITQK LLQDFNRFLN TTFSFFPPFV SCIQDISCQH AALLSLDPAA VSAGC LASL QQPVGIRLLE EALLRLLPAE LPAKRVRGKA RLPPDVLRWV ELAKLYRSIG EYDVLRGIFT SEIGTKQITQ SALLAE ARS DYSEAAKQYD EALNKQDWVD GEPTEAEKDF WELASLDCYN HLAEWKSLEY CSTASIDSEN PPDLNKIWSE PFYQETY LP YMIRSKLKLL LQGEADQSLL TFIDKAMHGE LQKAILELHY SQELSLLYLL QDDVDRAKYY IQNGIQSFMQ NYSSIDVL L HQSRLTKLQS VQALTEIQEF ISFISKQGNL SSQVPLKRLL NTWTNRYPDA KMDPMNIWDD IITNRCFFLS KIEEKLTPL PEDNSMNVDQ DGDPSDRMEV QEQEEDISSL IRSCKFSMKM KMIDSARKQN NFSLAMKLLK ELHKESKTRD DWLVSWVQSY CRLSHCRSR SQGCSEQVLT VLKTVSLLDE NNVSSYLSKN ILAFRDQNIL LGTTYRIIAN ALSSEPACLA EIEEDKARRI L ELSGSSSE DSEKVIAGLY QRAFQHLSEA VQAAEEEAQP PSWSCGPAAG VIDAYMTLAD FCDQQLRKEE ENASVIDSAE LQ AYPALVV EKMLKALKLN SNEARLKFPR LLQIIERYPE ETLSLMTKEI SSVPCWQFIS WISHMVALLD KDQAVAVQHS VEE ITDNYP QAIVYPFIIS SESYSFKDTS TGHKNKEFVA RIKSKLDQGG VIQDFINALD QLSNPELLFK DWSNDVRAEL AKTP VNKKN IEKMYERMYA ALGDPKAPGL GAFRRKFIQT FGKEFDKHFG KGGSKLLRMK LSDFNDITNM LLLKMNKDSK PPGNL KECS PWMSDFKVEF LRNELEIPGQ YDGRGKPLPE YHVRIAGFDE RVTVMASLRR PKRIIIRGHD EREHPFLVKG GEDLRQ DQR VEQLFQVMNG ILAQDSACSQ RALQLRTYSV VPMTSRLGLI EWLENTVTLK DLLLNTMSQE EKAAYLSDPR APPCEYK DW LTKMSGKHDV GAYMLMYKGA NRTETVTSFR KRESKVPADL LKRAFVRMST SPEAFLALRS HFASSHALIC ISHWILGI G DRHLNNFMVA METGGVIGID FGHAFGSATQ FLPVPELMPF RLTRQFINLM LPMKETGLMY SIMVHALRAF RSDPGLLTN TMDVFVKEPS FDWKNFEQKM LKKGGSWIQE INVAEKNWYP RQKICYAKRK LAGANPAVIT CDELLLGHEK APAFRDYVAV ARGSKDHNI RAQEPESGLS EETQVKCLMD QATDPNILGR TWEGWEPWM

UniProtKB: DNA-dependent protein kinase catalytic subunit

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

MacromoleculeName: X-ray repair cross-complementing protein 6 / type: protein_or_peptide / ID: 6 / 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: 69.945039 KDa
Recombinant expressionOrganism: Insect cell expression vector pTIE1 (others)
SequenceString: MSGWESYYKT EGDEEAEEEQ EENLEASGDY KYSGRDSLIF LVDASKAMFE SQSEDELTPF DMSIQCIQSV YISKIISSDR DLLAVVFYG TEKDKNSVNF KNIYVLQELD NPGAKRILEL DQFKGQQGQK RFQDMMGHGS DYSLSEVLWV CANLFSDVQF K MSHKRIML ...String:
MSGWESYYKT EGDEEAEEEQ EENLEASGDY KYSGRDSLIF LVDASKAMFE SQSEDELTPF DMSIQCIQSV YISKIISSDR DLLAVVFYG TEKDKNSVNF KNIYVLQELD NPGAKRILEL DQFKGQQGQK RFQDMMGHGS DYSLSEVLWV CANLFSDVQF K MSHKRIML FTNEDNPHGN DSAKASRART KAGDLRDTGI FLDLMHLKKP GGFDISLFYR DIISIAEDED LRVHFEESSK LE DLLRKVR AKETRKRALS RLKLKLNKDI VISVGIYNLV QKALKPPPIK LYRETNEPVK TKTRTFNTST GGLLLPSDTK RSQ IYGSRQ IILEKEETEE LKRFDDPGLM LMGFKPLVLL KKHHYLRPSL FVYPEESLVI GSSTLFSALL IKCLEKEVAA LCRY TPRRN IPPYFVALVP QEEELDDQKI QVTPPGFQLV FLPFADDKRK MPFTEKIMAT PEQVGKMKAI VEKLRFTYRS DSFEN PVLQ QHFRNLEALA LDLMEPEQAV DLTLPKVEAM NKRLGSLVDE FKELVYPPDY NPEGKVTKRK HDNEGSGSKR PKVEYS EEE LKTHISKGTL GKFTVPMLKE ACRAYGLKSG LKKQELLEAL TKHFQD

UniProtKB: DNA repair protein Ku70

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Macromolecule #9: DNA polymerase lambda

MacromoleculeName: DNA polymerase lambda / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 63.571238 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MDPRGILKAF PKRQKIHADA SSKVLAKIPR REEGEEAEEW LSSLRAHVVR TGIGRARAEL FEKQIVQHGG QLCPAQGPGV THIVVDEGM DYERALRLLR LPQLPPGAQL VKSAWLSLCL QERRLVDVAG FSIFIPSRYL DHPQPSKAEQ DASIPPGTHE A LLQTALSP ...String:
MDPRGILKAF PKRQKIHADA SSKVLAKIPR REEGEEAEEW LSSLRAHVVR TGIGRARAEL FEKQIVQHGG QLCPAQGPGV THIVVDEGM DYERALRLLR LPQLPPGAQL VKSAWLSLCL QERRLVDVAG FSIFIPSRYL DHPQPSKAEQ DASIPPGTHE A LLQTALSP PPPPTRPVSP PQKAKEAPNT QAQPISDDEA SDGEETQVSA ADLEALISGH YPTSLEGDCE PSPAPAVLDK WV CAQPSSQ KATNHNLHIT EKLEVLAKAY SVQGDKWRAL GYAKAINALK SFHKPVTSYQ EACSIPGIGK RMAEKIIEIL ESG HLRKLD HISESVPVLE LFSNIWGAGT KTAQMWYQQG FRSLEDIRSQ ASLTTQQAIG LKHYSDFLER MPREEATEIE QTVQ KAAQA FNSGLLCVAC GSYRRGKATC GDVDVLITHP DGRSHRGIFS RLLDSLRQEG FLTDDLVSQE ENGQQQKYLG VCRLP GPGR RHRRLDIIVV PYSEFACALL YFTGSAHFNR SMRALAKTKG MSLSEHALST AVVRNTHGCK VGPGRVLPTP TEKDVF RLL GLPYREPAER DW

UniProtKB: DNA polymerase lambda

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Macromolecule #7: DNA

MacromoleculeName: DNA / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.632012 KDa
SequenceString:
(DC)(DT)(DA)(DA)(DT)(DA)(DA)(DA)(DC)(DT) (DA)(DA)(DA)(DA)(DA)(DC)(DT)(DA)(DT)(DT) (DA)(DT)(DT)(DA)(DT)

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Macromolecule #8: DNA

MacromoleculeName: DNA / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.748026 KDa
SequenceString:
(DT)(DA)(DA)(DT)(DA)(DA)(DT)(DA)(DG)(DT) (DT)(DT)(DT)(DT)(DA)(DG)(DT)(DT)(DT)(DA) (DT)(DT)(DG)(DG)(DG)

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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

Concentration2 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 11487 / Average exposure time: 1.04 sec. / Average electron dose: 51.96 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 / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000
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

Particle selectionNumber selected: 603711
CTF correctionSoftware - Name: Warp / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 14964
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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