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- EMDB-23510: NHEJ Long-range synaptic complex -

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Basic information

Entry
Database: EMDB / ID: EMD-23510
TitleNHEJ Long-range synaptic complex
Map dataPre-synaptic complex
Sample
  • Complex: Long-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
    • Protein or peptide: DNA-dependent protein kinase catalytic subunit
    • Protein or peptide: Unknown peptide
    • DNA: DNA (31-MER)
    • DNA: DNA (30-MER)
    • Protein or peptide: DNA repair protein XRCC4
    • Protein or peptide: Non-homologous end-joining factor 1
    • Protein or peptide: DNA ligase 4
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsNHEJ / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


DNA ligation involved in DNA recombination / T cell receptor V(D)J recombination / FHA domain binding / positive regulation of chromosome organization / positive regulation of ligase activity / pro-B cell differentiation / DNA ligase IV complex / positive regulation of lymphocyte differentiation / DNA ligation involved in DNA repair / small-subunit processome assembly ...DNA ligation involved in DNA recombination / T cell receptor V(D)J recombination / FHA domain binding / positive regulation of chromosome organization / positive regulation of ligase activity / pro-B cell differentiation / DNA ligase IV complex / positive regulation of lymphocyte differentiation / DNA ligation involved in DNA repair / small-subunit processome assembly / DNA ligase activity / Ku70:Ku80 complex / DNA-dependent protein kinase complex / DN2 thymocyte differentiation / immunoglobulin V(D)J recombination / negative regulation of t-circle formation / DNA end binding / DNA ligase (ATP) / DNA-dependent protein kinase-DNA ligase 4 complex / MHC class II antigen presentation / nonhomologous end joining complex / DNA ligase (ATP) activity / cellular response to X-ray / regulation of smooth muscle cell proliferation / single strand break repair / Cytosolic sensors of pathogen-associated DNA / nucleotide-excision repair, DNA gap filling / Neutrophil degranulation / DNA ligation / V(D)J recombination / IRF3-mediated induction of type I IFN / nuclear telomere cap complex / double-strand break repair via classical nonhomologous end joining / isotype switching / protein localization to site of double-strand break / positive regulation of catalytic activity / entry into host cell by a symbiont-containing vacuole / U3 snoRNA binding / recombinational repair / regulation of telomere maintenance / protein localization to chromosome, telomeric region / cellular response to fatty acid / positive regulation of neurogenesis / cellular hyperosmotic salinity response / hematopoietic stem cell proliferation / response to ionizing radiation / cellular response to lithium ion / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / DNA biosynthetic process / telomeric DNA binding / 2-LTR circle formation / ligase activity / : / site of DNA damage / somatic stem cell population maintenance / protein autoprocessing / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / response to X-ray / T cell differentiation / 5'-deoxyribose-5-phosphate lyase activity / hematopoietic stem cell differentiation / positive regulation of protein kinase activity / chromosome organization / ATP-dependent activity, acting on DNA / SUMOylation of DNA damage response and repair proteins / DNA polymerase binding / condensed chromosome / activation of innate immune response / transport vesicle / enzyme activator activity / positive regulation of telomere maintenance via telomerase / DNA helicase activity / telomere maintenance / cyclin binding / neurogenesis / B cell differentiation / protein-DNA complex / stem cell proliferation / response to gamma radiation / cellular response to leukemia inhibitory factor / central nervous system development / small-subunit processome / cellular response to ionizing 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 / protein processing / double-strand break repair via nonhomologous end joining / establishment of integrated proviral latency / positive regulation of fibroblast proliferation / double-strand break repair / site of double-strand break / T cell differentiation in thymus / double-stranded DNA binding / scaffold protein binding / fibroblast proliferation / secretory granule lumen / in utero embryonic development / neuron apoptotic process
Similarity search - Function
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 ...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 / Ku80 / 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 / DNA ligase, ATP-dependent / DNA ligase, ATP-dependent, N-terminal / DNA ligase, ATP-dependent, N-terminal domain superfamily / DNA ligase N terminus / 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. / SAP domain superfamily / DNA ligase, ATP-dependent, central / ATP dependent DNA ligase domain / Pepsin-like domain / DNA repair protein XRCC4-like, C-terminal / SAP domain / SAP motif profile. / 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 / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase 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 / Plasmepsin X / DNA repair protein XRCC4 / Non-homologous end-joining factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 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
National Institutes of Health/National Cancer Institute (NIH/NCI)P01CA092584 United States
American Cancer SocietyIRG-15-173-21 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-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7lt3
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23510.png

Downloads & links

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Map

FileDownload / File: emd_23510.map.gz / Format: CCP4 / Size: 93 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPre-synaptic complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 290 pix.
= 319. Å		1.1 Å/pix.
x 290 pix.
= 319. Å		1.1 Å/pix.
x 290 pix.
= 319. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.00888776 - 1.8737493
Average (Standard dev.)0.004466961 (±0.042242248)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-145-145-145
Dimensions290290290
Spacing290290290
CellA=B=C: 319.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z290290290
origin x/y/z0.0000.0000.000
length x/y/z319.000319.000319.000
α/β/γ90.00090.00090.000
start NX/NY/NZ645365
NX/NY/NZ139143124
MAP C/R/S123
start NC/NR/NS-145-145-145
NC/NR/NS290290290
D min/max/mean-0.0091.8740.004

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Supplemental data

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Sample components

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Entire : Long-range synaptic Complex of NHEJ

EntireName: Long-range synaptic Complex of NHEJ
Components
  • Complex: Long-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
    • Protein or peptide: DNA-dependent protein kinase catalytic subunit
    • Protein or peptide: Unknown peptide
    • DNA: DNA (31-MER)
    • DNA: DNA (30-MER)
    • Protein or peptide: DNA repair protein XRCC4
    • Protein or peptide: Non-homologous end-joining factor 1
    • Protein or peptide: DNA ligase 4
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: Long-range synaptic Complex of NHEJ

SupramoleculeName: Long-range synaptic Complex of NHEJ / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#9 / Details: DNAPKcs-Ku-XRCC4-LigIV-XLF
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.66 MDa

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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: 69.945039 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 LKKQELLEAL TKHFQD

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 #3: DNA-dependent protein kinase catalytic subunit

MacromoleculeName: DNA-dependent protein kinase catalytic subunit / type: protein_or_peptide / ID: 3 / Number of copies: 2 / 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: Plasmepsin X

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Macromolecule #4: Unknown peptide

MacromoleculeName: Unknown peptide / type: protein_or_peptide / ID: 4 / Details: Maybe a part of PRKDC / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 1.720111 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)

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Macromolecule #7: DNA repair protein XRCC4

MacromoleculeName: DNA repair protein XRCC4 / type: protein_or_peptide / ID: 7 / 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 #8: Non-homologous end-joining factor 1

MacromoleculeName: Non-homologous end-joining factor 1 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 33.372234 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
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 #9: DNA ligase 4

MacromoleculeName: DNA ligase 4 / type: protein_or_peptide / ID: 9 / 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 #5: DNA (31-MER)

MacromoleculeName: DNA (31-MER) / type: dna / ID: 5 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.510159 KDa
SequenceString:
(DT)(DC)(DT)(DA)(DA)(DG)(DA)(DA)(DC)(DT) (DC)(DT)(DG)(DA)(DT)(DG)(DT)(DC)(DA)(DG) (DT)(DA)(DG)(DA)(DT)(DT)(DA)(DC)(DA) (DC)(DT)

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Macromolecule #6: DNA (30-MER)

MacromoleculeName: DNA (30-MER) / type: dna / ID: 6 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.236976 KDa
SequenceString:
(DG)(DT)(DG)(DT)(DA)(DA)(DT)(DC)(DT)(DA) (DC)(DT)(DG)(DA)(DC)(DA)(DT)(DC)(DA)(DG) (DA)(DG)(DT)(DT)(DC)(DT)(DT)(DA)(DG) (DA)

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Macromolecule #10: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 10 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*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

BufferpH: 7.9
Component:
ConcentrationNameFormula
10.0 mMHEPES
50.0 mMKCl
10.0 mMMgCl2
2.5 %glycerol
1.0 mMDTT
0.05 %NP-40
GridModel: Quantifoil R3.5/1 / Material: COPPER / Mesh: 400 / 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

MicroscopeJEOL 3200FS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Digitization - Frames/image: 1-30 / Number grids imaged: 4 / Number real images: 17114 / Average exposure time: 0.3 sec. / Average electron dose: 76.5 e/Å2
Electron beamAcceleration voltage: 200 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: 2.0 µm / Nominal magnification: 30000
Sample stageSpecimen holder model: JEOL / Cooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 1119381
Startup modelType of model: INSILICO MODEL
In silico model: Negative staining map reconstructed ab-initio from Cryosparc
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 329784
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software: (Name: EMAN, cryoSPARC)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 5 / Avg.num./class: 220000 / Software - Name: RELION (ver. 3.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6erh

source_name: PDB, initial_model_type: experimental model

1jey

source_name: PDB, initial_model_type: experimental model

5luq

source_name: PDB, initial_model_type: experimental model

5y3r

source_name: PDB, initial_model_type: experimental model

6zha

source_name: PDB, initial_model_type: experimental model

2r9a

source_name: PDB, initial_model_type: experimental model

3ii6

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient
Output model

PDB-7lt3:
NHEJ Long-range synaptic complex

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