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- EMDB-23509: NHEJ Short-range synaptic complex -

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Basic information

Entry
Database: EMDB / ID: EMD-23509
TitleNHEJ Short-range synaptic complex
Map dataSynaptic complex
Sample
  • Complex: Short-range synaptic complex of NHEJ
    • Protein or peptide: X-ray repair cross-complementing protein 6
    • Protein or peptide: X-ray repair cross-complementing protein 5
    • DNA: DNA (26-MER)
    • DNA: DNA (5'-D(P*GP*TP*TP*CP*TP*TP*AP*GP*TP*AP*TP*AP*TP*A)-3')
    • Protein or peptide: DNA repair protein XRCC4
    • Protein or peptide: Non-homologous end-joining factor 1
    • DNA: DNA (5'-D(P*TP*AP*TP*AP*TP*AP*CP*TP*AP*AP*GP*AP*AP*C)-3')
    • DNA: DNA (26-MER)
    • DNA: DNA (5'-D(P*CP*AP*AP*TP*GP*AP*AP*AP*CP*GP*GP*AP*AP*CP*AP*GP*TP*CP*AP*G)-3')
    • Protein or peptide: DNA ligase 4
KeywordsNHEJ / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


DNA ligation involved in DNA recombination / FHA domain binding / positive regulation of chromosome organization / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / DNA ligase activity / Ku70:Ku80 complex / DN2 thymocyte differentiation / negative regulation of t-circle formation ...DNA ligation involved in DNA recombination / FHA domain binding / positive regulation of chromosome organization / positive regulation of ligase activity / DNA ligase IV complex / DNA ligation involved in DNA repair / DNA ligase activity / Ku70:Ku80 complex / DN2 thymocyte differentiation / negative regulation of t-circle formation / DNA ligase (ATP) / DNA end binding / T cell receptor V(D)J recombination / pro-B cell differentiation / DNA ligase (ATP) activity / small-subunit processome assembly / positive regulation of lymphocyte differentiation / DNA-dependent protein kinase complex / nucleotide-excision repair, DNA gap filling / DNA-dependent protein kinase-DNA ligase 4 complex / single strand break repair / cellular response to X-ray / immunoglobulin V(D)J recombination / nonhomologous end joining complex / protein localization to site of double-strand break / DNA ligation / nuclear telomere cap complex / regulation of smooth muscle cell proliferation / V(D)J recombination / isotype switching / Cytosolic sensors of pathogen-associated DNA / double-strand break repair via classical nonhomologous end joining / IRF3-mediated induction of type I IFN / recombinational repair / regulation of telomere maintenance / U3 snoRNA binding / positive regulation of neurogenesis / protein localization to chromosome, telomeric region / cellular response to fatty acid / hematopoietic stem cell proliferation / cellular hyperosmotic salinity response / response to ionizing radiation / telomeric DNA binding / DNA biosynthetic process / positive regulation of catalytic activity / cellular response to lithium ion / 2-LTR circle formation / site of DNA damage / somatic stem cell population maintenance / ligase activity / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / enzyme activator activity / 5'-deoxyribose-5-phosphate lyase activity / T cell differentiation / response to X-ray / chromosome organization / hematopoietic stem cell differentiation / positive regulation of protein kinase activity / ATP-dependent activity, acting on DNA / SUMOylation of DNA damage response and repair proteins / DNA polymerase binding / condensed chromosome / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / DNA helicase activity / activation of innate immune response / telomere maintenance / cellular response to leukemia inhibitory factor / neurogenesis / small-subunit processome / cyclin binding / B cell differentiation / central nervous system development / stem cell proliferation / cellular response to ionizing radiation / protein-DNA complex / response to gamma radiation / Nonhomologous End-Joining (NHEJ) / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cellular response to gamma radiation / fibrillar center / double-strand break repair via nonhomologous end joining / establishment of integrated proviral latency / double-strand break repair / positive regulation of fibroblast proliferation / site of double-strand break / T cell differentiation in thymus / fibroblast proliferation / double-stranded DNA binding / scaffold protein binding / neuron apoptotic process / secretory granule lumen / DNA recombination / in utero embryonic development / negative regulation of neuron apoptotic process / cell population proliferation / ficolin-1-rich granule lumen / transcription regulator complex / damaged DNA binding / chromosome, telomeric region
Similarity search - Function
XLF, N-terminal / XLF-Cernunnos, XRcc4-like factor, NHEJ component / DNA ligase IV domain / DNA ligase IV / DNA ligase 4 / DNA Ligase 4, adenylation domain / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / DNA double-strand break repair and V(D)J recombination protein XRCC4 / XRCC4-like, N-terminal domain superfamily ...XLF, N-terminal / XLF-Cernunnos, XRcc4-like factor, NHEJ component / DNA ligase IV domain / DNA ligase IV / DNA ligase 4 / DNA Ligase 4, adenylation domain / XRCC4, N-terminal domain superfamily / DNA repair protein XRCC4 / DNA double-strand break repair and V(D)J recombination protein XRCC4 / 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, N-terminal alpha/beta / Ku70/Ku80 beta-barrel domain / Ku70/Ku80 C-terminal arm / 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 signature 2. / ATP-dependent DNA ligase AMP-binding site. / 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 / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / DNA repair protein XRCC4-like, C-terminal / 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 / Non-homologous end-joining factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.4 Å
AuthorsHe Y / Chen S
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM135651 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM008382 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129547 United States
American Cancer SocietyIRG-15-173-2 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)P01CA092584 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM047251 United States
CitationJournal: Nature / Year: 2021
Title: Structural basis of long-range to short-range synaptic transition in NHEJ.
Authors: Siyu Chen / Linda Lee / Tasmin Naila / Susan Fishbain / Annie Wang / Alan E Tomkinson / Susan P Lees-Miller / Yuan He /
Abstract: DNA double-strand breaks (DSBs) are a highly cytotoxic form of DNA damage and the incorrect repair of DSBs is linked to carcinogenesis. The conserved error-prone non-homologous end joining (NHEJ) ...DNA double-strand breaks (DSBs) are a highly cytotoxic form of DNA damage and the incorrect repair of DSBs is linked to carcinogenesis. The conserved error-prone non-homologous end joining (NHEJ) pathway has a key role in determining the effects of DSB-inducing agents that are used to treat cancer as well as the generation of the diversity in antibodies and T cell receptors. Here we applied single-particle cryo-electron microscopy to visualize two key DNA-protein complexes that are formed by human NHEJ factors. The Ku70/80 heterodimer (Ku), the catalytic subunit of the DNA-dependent protein kinase (DNA-PKcs), DNA ligase IV (LigIV), XRCC4 and XLF form a long-range synaptic complex, in which the DNA ends are held approximately 115 Å apart. Two DNA end-bound subcomplexes comprising Ku and DNA-PKcs are linked by interactions between the DNA-PKcs subunits and a scaffold comprising LigIV, XRCC4, XLF, XRCC4 and LigIV. The relative orientation of the DNA-PKcs molecules suggests a mechanism for autophosphorylation in trans, which leads to the dissociation of DNA-PKcs and the transition into the short-range synaptic complex. Within this complex, the Ku-bound DNA ends are aligned for processing and ligation by the XLF-anchored scaffold, and a single catalytic domain of LigIV is stably associated with a nick between the two Ku molecules, which suggests that the joining of both strands of a DSB involves both LigIV molecules.
History
DepositionFeb 18, 2021-
Header (metadata) releaseApr 14, 2021-
Map releaseApr 14, 2021-
UpdateAug 16, 2023-
Current statusAug 16, 2023Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7lsy
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23509.png

Downloads & links

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Map

FileDownload / File: emd_23509.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSynaptic complex
Voxel sizeX=Y=Z: 1.66 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.0053695086 - 0.5519546
Average (Standard dev.)0.00089410075 (±0.009972619)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-96-96-96
Dimensions192192192
Spacing192192192
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.661.661.66
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z318.720318.720318.720
α/β/γ90.00090.00090.000
start NX/NY/NZ645365
NX/NY/NZ139143124
MAP C/R/S123
start NC/NR/NS-96-96-96
NC/NR/NS192192192
D min/max/mean-0.0050.5520.001

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Supplemental data

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Sample components

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Entire : Short-range synaptic complex of NHEJ

EntireName: Short-range synaptic complex of NHEJ
Components
  • Complex: Short-range synaptic complex of NHEJ
    • Protein or peptide: X-ray repair cross-complementing protein 6
    • Protein or peptide: X-ray repair cross-complementing protein 5
    • DNA: DNA (26-MER)
    • DNA: DNA (5'-D(P*GP*TP*TP*CP*TP*TP*AP*GP*TP*AP*TP*AP*TP*A)-3')
    • Protein or peptide: DNA repair protein XRCC4
    • Protein or peptide: Non-homologous end-joining factor 1
    • DNA: DNA (5'-D(P*TP*AP*TP*AP*TP*AP*CP*TP*AP*AP*GP*AP*AP*C)-3')
    • DNA: DNA (26-MER)
    • DNA: DNA (5'-D(P*CP*AP*AP*TP*GP*AP*AP*AP*CP*GP*GP*AP*AP*CP*AP*GP*TP*CP*AP*G)-3')
    • Protein or peptide: DNA ligase 4

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Supramolecule #1: Short-range synaptic complex of NHEJ

SupramoleculeName: Short-range synaptic complex of NHEJ / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#10
Molecular weightTheoretical: 720 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: 68.872875 KDa
Recombinant expressionOrganism: unidentified baculovirus
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 LKKQELL

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
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: unidentified baculovirus
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 #5: DNA repair protein XRCC4

MacromoleculeName: DNA repair protein XRCC4 / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.337703 KDa
Recombinant expressionOrganism: unidentified baculovirus
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 #6: Non-homologous end-joining factor 1

MacromoleculeName: Non-homologous end-joining factor 1 / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.372234 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEELEQGLLM QPWAWLQLAE NSLLAKVFIT KQGYALLVSD LQQVWHEQVD TSVVSQRAKE LNKRLTAPPA AFLCHLDNLL RPLLKDAAH PSEATFSCDC VADALILRVR SELSGLPFYW NFHCMLASPS LVSQHLIRPL MGMSLALQCQ VRELATLLHM K DLEIQDYQ ...String:
MEELEQGLLM QPWAWLQLAE NSLLAKVFIT KQGYALLVSD LQQVWHEQVD TSVVSQRAKE LNKRLTAPPA AFLCHLDNLL RPLLKDAAH PSEATFSCDC VADALILRVR SELSGLPFYW NFHCMLASPS LVSQHLIRPL MGMSLALQCQ VRELATLLHM K DLEIQDYQ ESGATLIRDR LKTEPFEENS FLEQFMIEKL PEACSIGDGK PFVMNLQDLY MAVTTQEVQV GQKHQGAGDP HT SNSASLQ GIDSQCVNQP EQLVSSAPTL SAPEKESTGT SGPLQRPQLS KVKRKKPRGL FS

UniProtKB: Non-homologous end-joining factor 1

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Macromolecule #10: DNA ligase 4

MacromoleculeName: DNA ligase 4 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO / EC number: DNA ligase (ATP)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 104.124953 KDa
Recombinant expressionOrganism: unidentified baculovirus
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 #3: DNA (26-MER)

MacromoleculeName: DNA (26-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.936151 KDa
SequenceString:
(DT)(DA)(DT)(DA)(DT)(DA)(DC)(DT)(DA)(DA) (DG)(DA)(DA)(DC)(DT)(DT)(DC)(DT)(DG)(DA) (DC)(DT)(DG)(DT)(DT)(DC)

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Macromolecule #4: DNA (5'-D(P*GP*TP*TP*CP*TP*TP*AP*GP*TP*AP*TP*AP*TP*A)-3')

MacromoleculeName: DNA (5'-D(P*GP*TP*TP*CP*TP*TP*AP*GP*TP*AP*TP*AP*TP*A)-3')
type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.284812 KDa
SequenceString:
(DG)(DT)(DT)(DC)(DT)(DT)(DA)(DG)(DT)(DA) (DT)(DA)(DT)(DA)

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Macromolecule #7: DNA (5'-D(P*TP*AP*TP*AP*TP*AP*CP*TP*AP*AP*GP*AP*AP*C)-3')

MacromoleculeName: DNA (5'-D(P*TP*AP*TP*AP*TP*AP*CP*TP*AP*AP*GP*AP*AP*C)-3')
type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.27183 KDa
SequenceString:
(DT)(DA)(DT)(DA)(DT)(DA)(DC)(DT)(DA)(DA) (DG)(DA)(DA)(DC)

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Macromolecule #8: DNA (26-MER)

MacromoleculeName: DNA (26-MER) / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 7.964145 KDa
SequenceString:
(DC)(DG)(DT)(DT)(DT)(DC)(DA)(DT)(DT)(DG) (DT)(DT)(DG)(DT)(DT)(DC)(DT)(DT)(DA)(DG) (DT)(DA)(DT)(DA)(DT)(DA)

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Macromolecule #9: DNA (5'-D(P*CP*AP*AP*TP*GP*AP*AP*AP*CP*GP*GP*AP*AP*CP*AP*GP*TP*CP...

MacromoleculeName: DNA (5'-D(P*CP*AP*AP*TP*GP*AP*AP*AP*CP*GP*GP*AP*AP*CP*AP*GP*TP*CP*AP*G)-3')
type: dna / ID: 9 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.185046 KDa
SequenceString:
(DC)(DA)(DA)(DT)(DG)(DA)(DA)(DA)(DC)(DG) (DG)(DA)(DA)(DC)(DA)(DG)(DT)(DC)(DA)(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

BufferpH: 7.9
Component:
ConcentrationNameFormula
10.0 mMHEPES
50.0 mMPotassium chlorideKCl
10.0 mMMagnesium chlorideMgCl2
2.5 %glycerol
0.05 %NP-40
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 200 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Support film - Film thickness: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 101.325 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 30000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 11520 pixel / Digitization - Dimensions - Height: 8184 pixel / Number grids imaged: 2 / Number real images: 32723 / Average exposure time: 0.0426 sec. / Average electron dose: 46.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1766936
Startup modelType of model: INSILICO MODEL
In silico model: Negative staining map reconstructed ab-initio from CryoSPARC
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software: (Name: EMAN, cryoSPARC)
Final 3D classificationNumber classes: 10 / Avg.num./class: 180000 / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 8.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 175866

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient
Output model

PDB-7lsy:
NHEJ Short-range synaptic complex

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