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- EMDB-49109: The ligation (AMP-Lys) complex in the NHEJ pathway -

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Basic information

Entry
Database: EMDB / ID: EMD-49109
TitleThe ligation (AMP-Lys) complex in the NHEJ pathway
Map dataconsensus map for Ligation complex (AMP-Lys) in NHEJ pathway
Sample
  • Complex: The ligation (AMP-Lys) complex in the NHEJ pathway
    • Protein or peptide: x 6 types
    • DNA: x 4 types
  • Ligand: x 1 types
KeywordsNHEJ / ligation / XLF / PAXX / 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 / Ku70:Ku80 complex / DN2 thymocyte differentiation / negative regulation of t-circle formation / DNA ligase (ATP) / 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 / Ku70:Ku80 complex / DN2 thymocyte differentiation / negative regulation of t-circle formation / DNA ligase (ATP) / T cell receptor V(D)J recombination / DNA end binding / pro-B cell differentiation / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA ligase (ATP) activity / DNA-dependent protein kinase complex / DNA-dependent protein kinase-DNA ligase 4 complex / nonhomologous end joining complex / immunoglobulin V(D)J recombination / nucleotide-excision repair, DNA gap filling / single strand break repair / regulation of smooth muscle cell proliferation / cellular response to X-ray / V(D)J recombination / nuclear telomere cap complex / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / isotype switching / Cytosolic sensors of pathogen-associated DNA / IRF3-mediated induction of type I IFN / positive regulation of neurogenesis / regulation of telomere maintenance / recombinational repair / U3 snoRNA binding / protein localization to chromosome, telomeric region / DNA biosynthetic process / response to ionizing radiation / cellular response to lithium ion / cellular hyperosmotic salinity response / 2-LTR circle formation / telomeric DNA binding / hematopoietic stem cell proliferation / ligase activity / positive regulation of protein kinase activity / site of DNA damage / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / T cell differentiation / somatic stem cell population maintenance / 5'-deoxyribose-5-phosphate lyase activity / response to X-ray / hematopoietic stem cell differentiation / ATP-dependent activity, acting on DNA / chromosome organization / telomere maintenance via telomerase / SUMOylation of DNA damage response and repair proteins / condensed chromosome / DNA polymerase binding / neurogenesis / cellular response to ionizing radiation / telomere maintenance / activation of innate immune response / DNA helicase activity / cyclin binding / cellular response to leukemia inhibitory factor / B cell differentiation / central nervous system development / stem cell proliferation / response to gamma radiation / small-subunit processome / Nonhomologous End-Joining (NHEJ) / enzyme activator activity / cellular response to gamma radiation / protein-DNA complex / base-excision repair / double-strand break repair via nonhomologous end joining / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / establishment of integrated proviral latency / fibrillar center / positive regulation of fibroblast proliferation / site of double-strand break / double-strand break repair / T cell differentiation in thymus / double-stranded DNA binding / neuron apoptotic process / scaffold protein binding / fibroblast proliferation / secretory granule lumen / DNA recombination / molecular adaptor activity / transcription regulator complex / damaged DNA binding / in utero embryonic development / ficolin-1-rich granule lumen / negative regulation of neuron apoptotic process / chromosome, telomeric region / cell population proliferation / transcription cis-regulatory region binding / ribonucleoprotein complex / innate immune response / cell division
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 / : / Ku70 / Ku, C-terminal / Ku, C-terminal domain superfamily / Ku C terminal domain like / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / Ku80 / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / Ku70/Ku80 C-terminal arm / Ku70/Ku80 C-terminal arm / Ku70/Ku80, N-terminal alpha/beta / Ku70/Ku80 beta-barrel domain / Ku70/Ku80 N-terminal alpha/beta domain / Ku70 and Ku80 are 70kDa and 80kDa subunits of the Lupus Ku autoantigen / Ku70/Ku80 beta-barrel domain / SPOC-like, C-terminal domain superfamily / 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 / ATP-dependent DNA ligase family profile. / 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 / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / von Willebrand factor (vWF) type A domain / von Willebrand factor, type A / BRCT domain profile. / BRCT domain / BRCT domain superfamily / von Willebrand factor A-like domain superfamily / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
X-ray repair cross-complementing protein 6 / X-ray repair cross-complementing protein 5 / DNA ligase 4 / DNA repair protein XRCC4 / Protein PAXX / Non-homologous end-joining factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 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
DepositionFeb 7, 2025-
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

Downloads & links

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Map

FileDownload / File: emd_49109.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationconsensus map for Ligation complex (AMP-Lys) in NHEJ pathway
Voxel sizeX=Y=Z: 0.833 Å
Density
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.18115662 - 0.55033416
Average (Standard dev.)-0.000033109853 (±0.0132484585)
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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Sample components

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Entire : The ligation (AMP-Lys) complex in the NHEJ pathway

EntireName: The ligation (AMP-Lys) complex in the NHEJ pathway
Components
  • Complex: The ligation (AMP-Lys) complex in the NHEJ pathway
    • 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
    • Protein or peptide: Protein PAXX
    • DNA: DNA (39-MER)
    • DNA: DNA (38-MER)
    • DNA: DNA (35-MER)
    • DNA: DNA (34-MER)
  • Ligand: ADENOSINE MONOPHOSPHATE

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Supramolecule #1: The ligation (AMP-Lys) complex in the NHEJ pathway

SupramoleculeName: The ligation (AMP-Lys) complex in the NHEJ pathway / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 850 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: 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: 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 #7: DNA (39-MER)

MacromoleculeName: DNA (39-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.722289 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) (DC)

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Macromolecule #8: DNA (38-MER)

MacromoleculeName: DNA (38-MER) / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.811352 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)(DG)(DG)(DT) (DC)

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Macromolecule #9: DNA (35-MER)

MacromoleculeName: DNA (35-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 (34-MER)

MacromoleculeName: DNA (34-MER) / type: dna / ID: 10 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.807135 KDa
SequenceString:
(DA)(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 #11: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 11 / Number of copies: 1 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 47.39 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.6 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: NONE / Details: Ab initio map reconstituted by cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF
Details: The resolution was calculated by PostProcess in RELION with the composite half maps generated by "Combined_Focused_Maps" in Phenix.
Number images used: 78835
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial modelPDB ID:

9cq6


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-9n82:
The ligation (AMP-Lys) complex in the NHEJ pathway

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  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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