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- EMDB-45807: The gap-filling complex with Pol mu engaged in the NHEJ pathway -

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Basic information

Entry
Database: EMDB / ID: EMD-45807
TitleThe gap-filling complex with Pol mu engaged in the NHEJ pathway
Map datacomposite map for NHEJ gap-filling complex
Sample
  • Complex: A gap-filling complex with Pol mu engaged
    • Protein or peptide: x 6 types
    • DNA: x 4 types
  • Protein or peptide: x 1 types
  • Ligand: x 2 types
KeywordsNHEJ / DNA gap / fill-in synthesis / ligation / XLF / PAXX / Polymerase mu / DNA repair / Ligase IV / LIGASE-TRANSFERASE-DNA complex
Function / homology
Function and homology information


FHA domain binding / positive regulation of chromosome organization / positive regulation of ligase activity / DNA ligase IV complex / DNA ligase activity / DN2 thymocyte differentiation / DNA double-strand break attachment to nuclear envelope / DNA ligase (ATP) / Ku70:Ku80 complex / T cell receptor V(D)J recombination ...FHA domain binding / positive regulation of chromosome organization / positive regulation of ligase activity / DNA ligase IV complex / DNA ligase activity / DN2 thymocyte differentiation / DNA double-strand break attachment to nuclear envelope / DNA ligase (ATP) / Ku70:Ku80 complex / T cell receptor V(D)J recombination / negative regulation of t-circle formation / pro-B cell differentiation / DNA end binding / DNA ligase (ATP) activity / small-subunit processome assembly / positive regulation of lymphocyte differentiation / 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 / V(D)J recombination / regulation of smooth muscle cell proliferation / cellular response to X-ray / double-strand break repair via classical nonhomologous end joining / isotype switching / nuclear telomere cap complex / Cytosolic sensors of pathogen-associated DNA / protein localization to site of double-strand break / IRF3-mediated induction of type I IFN / recombinational repair / regulation of telomere maintenance / positive regulation of neurogenesis / U3 snoRNA binding / DNA biosynthetic process / protein localization to chromosome, telomeric region / cellular response to lithium ion / cellular hyperosmotic salinity response / 2-LTR circle formation / response to ionizing radiation / hematopoietic stem cell proliferation / ligase activity / telomeric DNA binding / DNA 3'-5' helicase / positive regulation of protein kinase activity / T cell differentiation / somatic stem cell population maintenance / 5'-deoxyribose-5-phosphate lyase activity / hematopoietic stem cell differentiation / response to X-ray / chromosome organization / ATP-dependent activity, acting on DNA / site of DNA damage / telomere maintenance via telomerase / SUMOylation of DNA damage response and repair proteins / somatic hypermutation of immunoglobulin genes / condensed chromosome / DNA polymerase binding / neurogenesis / activation of innate immune response / DNA helicase activity / telomere maintenance / B cell differentiation / cyclin binding / DNA-(apurinic or apyrimidinic site) lyase / central nervous system development / stem cell proliferation / cellular response to leukemia inhibitory factor / response to gamma radiation / cellular response to ionizing radiation / Nonhomologous End-Joining (NHEJ) / small-subunit processome / enzyme activator activity / protein-DNA complex / cellular response to gamma radiation / base-excision repair / double-strand break repair via nonhomologous end joining / establishment of integrated proviral latency / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / positive regulation of fibroblast proliferation / fibrillar center / T cell differentiation in thymus / double-strand break repair / site of double-strand break / neuron apoptotic process / double-stranded DNA binding / fibroblast proliferation / scaffold protein binding / secretory granule lumen / DNA recombination / transcription regulator complex / protein-macromolecule adaptor activity / DNA-directed DNA polymerase / ficolin-1-rich granule lumen / in utero embryonic development / negative regulation of neuron apoptotic process / molecular adaptor activity / damaged DNA binding / DNA-directed DNA polymerase activity
Similarity search - Function
Protein PAXX / : / PAXX, PAralog of XRCC4 and XLF, also called C9orf142 / XLF, N-terminal / : / : / XLF N-terminal domain / XLF protein coiled-coil region / DNA ligase IV domain / DNA ligase IV ...Protein PAXX / : / PAXX, PAralog of XRCC4 and XLF, also called C9orf142 / XLF, N-terminal / : / : / XLF N-terminal domain / XLF protein coiled-coil region / 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 / Ku70, bridge and pillars domain superfamily / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / : / DNA ligase N terminus / Ku70 / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / ATP-dependent DNA ligase AMP-binding site. / ATP-dependent DNA ligase signature 2. / DNA ligase, ATP-dependent, C-terminal / Ku80 / ATP dependent DNA ligase C terminal region / Ku70/Ku80 C-terminal arm / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 N-terminal alpha/beta domain / DNA ligase, ATP-dependent, conserved site / ATP-dependent DNA ligase family profile. / DNA-directed DNA/RNA polymerase mu / 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 / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / SAP domain superfamily / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / 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 / BRCA1 C Terminus (BRCT) domain / DNA polymerase beta, palm domain / DNA polymerase beta palm / breast cancer carboxy-terminal domain / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase X family / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase, thumb domain superfamily / DNA polymerase beta thumb / von Willebrand factor (vWF) type A domain / BRCT domain profile. / von Willebrand factor, type A / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily / von Willebrand factor A-like domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
DNA repair protein Ku70 / X-ray repair cross-complementing protein 5 / DNA ligase 4 / DNA repair protein XRCC4 / Protein PAXX / Non-homologous end-joining factor 1 / DNA-directed DNA/RNA polymerase mu
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsLi J / Liu L / Gellert M / Yang W
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
CitationJournal: Nature / Year: 2025
Title: Dynamic assemblies and coordinated reactions of non-homologous end joining.
Authors: Lan Liu / Jun Li / Metztli Cisneros-Aguirre / Arianna Merkell / Jeremy M Stark / Martin Gellert / Wei Yang /
Abstract: Non-homologous end joining (NHEJ) is the main repair pathway of double-strand DNA breaks in higher eukaryotes. Here we report reconstitution of the final steps of NHEJ and structures of DNA ...Non-homologous end joining (NHEJ) is the main repair pathway of double-strand DNA breaks in higher eukaryotes. Here we report reconstitution of the final steps of NHEJ and structures of DNA polymerase μ and ligase IV (LIG4) engaged in gap filling and end joining. These reactions take place in a flexible ω-shaped framework composed of XRCC4 and XLF. Two broken DNA ends, each encircled by Ku70-Ku80 internally, are docked onto the ω frame, mediated by LIG4. DNA polymerase and ligase attached to each ω arm repair only one broken strand of a defined polarity; the final steps of NHEJ requires coordination and toggling of a pair of such enzymes. The facilitators XLF and PAXX additively stimulate NHEJ reactions. As DNA-end sensor and protector, LIG4 replaces DNA-PKcs for end joining and bridges the two DNA ends for polymerase to fill remaining gaps. These assemblies present new targets for NHEJ inhibition to enhance efficacy of radiotherapy and accuracy of gene editing.
History
DepositionJul 19, 2024-
Header (metadata) releaseApr 23, 2025-
Map releaseApr 23, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45807.png

Downloads & links

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Map

FileDownload / File: emd_45807.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcomposite map for NHEJ gap-filling complex
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 426.496 Å		0.83 Å/pix.
x 512 pix.
= 426.496 Å		0.83 Å/pix.
x 512 pix.
= 426.496 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.833 Å
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Histogram (log scale)
Contour LevelBy AUTHOR: 8.0
Minimum - Maximum-45.604965 - 83.839775000000003
Average (Standard dev.)0.009839301 (±1.4478338)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 426.496 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_45807_msk_1.map
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Additional map: Postprocessed (by RELION) map for model building and validation

Fileemd_45807_additional_1.map
AnnotationPostprocessed (by RELION) map for model building and validation
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Additional map: DeepEMhancer sharpened map for model building

Fileemd_45807_additional_2.map
AnnotationDeepEMhancer sharpened map for model building
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Half map: half 1 map

Fileemd_45807_half_map_1.map
Annotationhalf 1 map
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Half map: half 2 map

Fileemd_45807_half_map_2.map
Annotationhalf 2 map
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Sample components

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Entire : A gap-filling complex with Pol mu engaged

EntireName: A gap-filling complex with Pol mu engaged
Components
  • Complex: A gap-filling complex with Pol mu engaged
    • Protein or peptide: X-ray repair cross-complementing protein 6
    • Protein or peptide: X-ray repair cross-complementing protein 5
    • Protein or peptide: Non-homologous end-joining factor 1
    • Protein or peptide: DNA repair protein XRCC4
    • Protein or peptide: DNA ligase 4
    • DNA: DNA (38-MER)
    • DNA: DNA (42-MER)
    • DNA: DNA (34-MER)
    • DNA: DNA (37-MER)
    • Protein or peptide: DNA-directed DNA/RNA polymerase mu
  • Protein or peptide: Protein PAXX
  • Ligand: MAGNESIUM ION
  • Ligand: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine

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Supramolecule #1: A gap-filling complex with Pol mu engaged

SupramoleculeName: A gap-filling complex with Pol mu engaged / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5, #7-#11
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 967 KDa

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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: 2 / 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 #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: 2 / Enantiomer: LEVO
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 #3: Non-homologous end-joining factor 1

MacromoleculeName: Non-homologous end-joining factor 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.625535 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPVMEELEQG LLMQPWAWLQ LAENSLLAKV FITKQGYALL VSDLQQVWHE QVDTSVVSQR AKELNKRLTA PPAAFLCHLD NLLRPLLKD AAHPSEATFS CDCVADALIL RVRSELSGLP FYWNFHCMLA SPSLVSQHLI RPLMGMSLAL QCQVRELATL L HMKDLEIQ ...String:
GPVMEELEQG LLMQPWAWLQ LAENSLLAKV FITKQGYALL VSDLQQVWHE QVDTSVVSQR AKELNKRLTA PPAAFLCHLD NLLRPLLKD AAHPSEATFS CDCVADALIL RVRSELSGLP FYWNFHCMLA SPSLVSQHLI RPLMGMSLAL QCQVRELATL L HMKDLEIQ DYQESGATLI RDRLKTEPFE ENSFLEQFMI EKLPEACSIG DGKPFVMNLQ DLYMAVTTQE VQVGQKHQGA GD PHTSNSA SLQGIDSQCV NQPEQLVSSA PTLSAPEKES TGTSGPLQRP QLSKVKRKKP RGLFS

UniProtKB: Non-homologous end-joining factor 1

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Macromolecule #4: DNA repair protein XRCC4

MacromoleculeName: DNA repair protein XRCC4 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.337703 KDa
Recombinant expressionOrganism: Homo sapiens (human)
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 ligase 4

MacromoleculeName: DNA ligase 4 / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA ligase (ATP)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 104.37825 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GPVMAASQTS QTVASHVPFA DLCSTLERIQ KSKGRAEKIR HFREFLDSWR KFHDALHKNH KDVTDSFYPA MRLILPQLER ERMAYGIKE TMLAKLYIEL LNLPRDGKDA LKLLNYRTPT GTHGDAGDFA MIAYFVLKPR CLQKGSLTIQ QVNDLLDSIA S NNSAKRKD ...String:
GPVMAASQTS QTVASHVPFA DLCSTLERIQ KSKGRAEKIR HFREFLDSWR KFHDALHKNH KDVTDSFYPA MRLILPQLER ERMAYGIKE TMLAKLYIEL LNLPRDGKDA LKLLNYRTPT GTHGDAGDFA MIAYFVLKPR CLQKGSLTIQ QVNDLLDSIA S NNSAKRKD LIKKSLLQLI TQSSALEQKW LIRMIIKDLK LGVSQQTIFS VFHNDAAELH NVTTDLEKVC RQLHDPSVGL SD ISITLFS AFKPMLAAIA DIEHIEKDMK HQSFYIETKL DGERMQMHKD GDVYKYFSRN GYNYTDQFGA SPTEGSLTPF IHN AFKADI QICILDGEMM AYNPNTQTFM QKGTKFDIKR MVEDSDLQTC YCVFDVLMVN NKKLGHETLR KRYEILSSIF TPIP GRIEI VQKTQAHTKN EVIDALNEAI DKREEGIMVK QPLSIYKPDK RGEGWLKIKP EYVSGLMDEL DILIVGGYWG KGSRG GMMS HFLCAVAEKP PPGEKPSVFH TLSRVGSGCT MKELYDLGLK LAKYWKPFHR KAPPSSILCG TEKPEVYIEP CNSVIV QIK AAEIVPSDMY KTGCTLRFPR IEKIRDDKEW HECMTLDDLE QLRGKASGKL ASKHLYIGGD DEPQEKKRKA APKMKKV IG IIEHLKAPNL TNVNKISNIF EDVEFCVMSG TDSQPKPDLE NRIAEFGGYI VQNPGPDTYC VIAGSENIRV KNIILSNK H DVVKPAWLLE CFKTKSFVPW QPRFMIHMCP STKEHFAREY DCYGDSYFID TDLNQLKEVF SGIKNSNEQT PEEMASLIA DLEYRYSWDC SPLSMFRRHT VYLDSYAVIN DLSTKNEGTR LAIKALELRF HGAKVVSCLA EGVSHVIIGE DHSRVADFKA FRRTFKRKF KILKESWVTD SIDKCELQEE NQYLI

UniProtKB: DNA ligase 4

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Macromolecule #6: Protein PAXX

MacromoleculeName: Protein PAXX / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.282197 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SQDPMDPLSP PLCTLPPGPE PPRFVCYCEG EESGEGDRGG FNLYVTDAAE LWSTCFTPDS LAALKARFGL SAAEDITPR FRAACEQQAV ALTLQEDRAS LTLSGGPSAL AFDLSKVPGP EAAPRLRALT LGLAKRVWSL ERRLAAAEET A VSPRKSPR ...String:
MGSSHHHHHH SQDPMDPLSP PLCTLPPGPE PPRFVCYCEG EESGEGDRGG FNLYVTDAAE LWSTCFTPDS LAALKARFGL SAAEDITPR FRAACEQQAV ALTLQEDRAS LTLSGGPSAL AFDLSKVPGP EAAPRLRALT LGLAKRVWSL ERRLAAAEET A VSPRKSPR PAGPQLFLPD PDPQRGGPGP GVRRRCPGES LINPGFKSKK PAGGVDFDET

UniProtKB: Protein PAXX

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Macromolecule #11: DNA-directed DNA/RNA polymerase mu

MacromoleculeName: DNA-directed DNA/RNA polymerase mu / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA-directed DNA polymerase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 56.973672 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HHHHHHSSGL EVLFQGPHML PKRRRARVGS PSGDAASSTP PSTRFPGVAI YLVEPRMGRS RRAFLTGLAR SKGFRVLDAC SSEATHVVM EETSAEEAVS WQERRMAAAP PGCTPPALLD ISWLTESLGA GQPVPVECRH RLEVAGPRKG PLSPAWMPAY A CQRPTPLT ...String:
HHHHHHSSGL EVLFQGPHML PKRRRARVGS PSGDAASSTP PSTRFPGVAI YLVEPRMGRS RRAFLTGLAR SKGFRVLDAC SSEATHVVM EETSAEEAVS WQERRMAAAP PGCTPPALLD ISWLTESLGA GQPVPVECRH RLEVAGPRKG PLSPAWMPAY A CQRPTPLT HHNTGLSEAL EILAEAAGFE GSEGRLLTFC RAASVLKALP SPVTTLSQLQ GLPHFGEHSS RVVQELLEHG VC EEVERVR RSERYQTMKL FTQIFGVGVK TADRWYREGL RTLDDLREQP QKLTQQQKAG LQHHQDLSTP VLRSDVDALQ QVV EEAVGQ ALPGATVTLT GGFRRGKLQG HDVDFLITHP KEGQEAGLLP RVMCRLQDQG LILYHQHQHS CCESPTRLAQ QSHM DAFER SFCIFRLPQP PGAAVGGSTR PCPSWKAVRV DLVVAPVSQF PFALLGWTGS KLFQRELRRF SRKEKGLWLN SHGLF DPEQ KTFFQAASEE DIFRHLGLEY LPPEQRNA

UniProtKB: DNA-directed DNA/RNA polymerase mu

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Macromolecule #7: DNA (38-MER)

MacromoleculeName: DNA (38-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.737299 KDa
SequenceString: (DC)(DG)(DC)(DG)(DC)(DC)(DC)(DA)(DG)(DC) (DT)(DT)(DT)(DC)(DC)(DC)(DA)(DG)(DC)(DT) (DA)(DA)(DT)(DA)(DA)(DA)(DC)(DT)(DA) (DA)(DA)(DA)(DA)(DC)(DT)(DA)(DT)(DG)(DC) (DA) (DT)(DG)(DC)(DT)(DC)(DT) ...String:
(DC)(DG)(DC)(DG)(DC)(DC)(DC)(DA)(DG)(DC) (DT)(DT)(DT)(DC)(DC)(DC)(DA)(DG)(DC)(DT) (DA)(DA)(DT)(DA)(DA)(DA)(DC)(DT)(DA) (DA)(DA)(DA)(DA)(DC)(DT)(DA)(DT)(DG)(DC) (DA) (DT)(DG)(DC)(DT)(DC)(DT)(DA)(DC) (DT)(DG)(DC)(DT)(DT)(DC)(DT)(DG)(DA)(DT) (DC)(DT) (DA)(DG)(DT)(DC)(DG)(DA)(DC) (DT)

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Macromolecule #8: DNA (42-MER)

MacromoleculeName: DNA (42-MER) / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.795354 KDa
SequenceString: (DC)(DG)(DC)(DG)(DC)(DC)(DC)(DA)(DG)(DC) (DT)(DT)(DT)(DC)(DC)(DC)(DA)(DG)(DC)(DT) (DA)(DA)(DT)(DA)(DA)(DA)(DC)(DT)(DA) (DA)(DA)(DA)(DA)(DC)(DA)(DT)(DT)(DC)(DG) (DT) (DT)(DC)(DA)(DC)(DG)(DT) ...String:
(DC)(DG)(DC)(DG)(DC)(DC)(DC)(DA)(DG)(DC) (DT)(DT)(DT)(DC)(DC)(DC)(DA)(DG)(DC)(DT) (DA)(DA)(DT)(DA)(DA)(DA)(DC)(DT)(DA) (DA)(DA)(DA)(DA)(DC)(DA)(DT)(DT)(DC)(DG) (DT) (DT)(DC)(DA)(DC)(DG)(DT)(DG)(DA) (DG)(DT)(DT)(DC)(DC)(DA)(DG)(DT)(DA)(DC) (DA)(DA) (DG)(DT)(DC)(DT)(DA)(DG)(DT) (DC)

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Macromolecule #9: DNA (34-MER)

MacromoleculeName: DNA (34-MER) / type: dna / ID: 9 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.865188 KDa
SequenceString:
(DG)(DA)(DC)(DT)(DA)(DG)(DA)(DT)(DC)(DA) (DG)(DA)(DA)(DG)(DC)(DA)(DG)(DT)(DA)(DG) (DA)(DG)(DC)(DA)(DT)(DG)(DC)(DA)(DT) (DA)(DG)(DT)(DT)(DT)(DT)(DT)(DA)(DG)(DT) (DT) (DT)(DA)(DT)(DT)(DG)(DG)(DG)(DC) (DG)(DC)(DG)

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Macromolecule #10: DNA (37-MER)

MacromoleculeName: DNA (37-MER) / type: dna / ID: 10 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.493929 KDa
SequenceString:
(DG)(DA)(DC)(DT)(DT)(DG)(DT)(DA)(DC)(DT) (DG)(DG)(DA)(DA)(DC)(DT)(DC)(DA)(DC)(DG) (DT)(DG)(DA)(DA)(DC)(DG)(DA)(DA)(DT) (DG)(DT)(DT)(DT)(DT)(DT)(DA)(DG)(DT)(DT) (DT) (DA)(DT)(DT)(DG)(DG)(DG)(DC)(DG) (DC)(DG)

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Macromolecule #12: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 12 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #13: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]a...

MacromoleculeName: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine
type: ligand / ID: 13 / Number of copies: 1 / Formula: DZ4
Molecular weightTheoretical: 490.197 Da
Chemical component information

ChemComp-DZ4:
2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]adenosine

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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

Concentration0.35 mg/mL
BufferpH: 7.9
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
EMDB ID:

23509

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF
Details: The resolution is calculated by the postprocess in RELION with the two composite half maps. The composite maps were generated by Phenix.combine_focused_maps
Number images used: 891208
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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