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Open data
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Basic information
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Title | CryoEM structure of Ku heterodimer bound to DNA and PAXX | |||||||||
![]() | Ku70/80 heterodimer bound to DNA and PAXX | |||||||||
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Function / homology | ![]() Ku70:Ku80 complex / negative regulation of t-circle formation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Hardwick SW / Kefala-Stavridi A / Chirgadze DY / Blundell TL / Chaplin AK | |||||||||
Funding support | ![]()
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![]() | ![]() Title: PAXX binding to the NHEJ machinery explains functional redundancy with XLF. Authors: Murielle Seif-El-Dahan / Antonia Kefala-Stavridi / Philippe Frit / Steven W Hardwick / Dima Y Chirgadze / Taiana Maia De Oliviera / Jessica Andreani / Sébastien Britton / Nadia Barboule / ...Authors: Murielle Seif-El-Dahan / Antonia Kefala-Stavridi / Philippe Frit / Steven W Hardwick / Dima Y Chirgadze / Taiana Maia De Oliviera / Jessica Andreani / Sébastien Britton / Nadia Barboule / Madeleine Bossaert / Arun Prasad Pandurangan / Katheryn Meek / Tom L Blundell / Virginie Ropars / Patrick Calsou / Jean-Baptiste Charbonnier / Amanda K Chaplin / ![]() ![]() ![]() Abstract: Nonhomologous end joining is a critical mechanism that repairs DNA double-strand breaks in human cells. In this work, we address the structural and functional role of the accessory protein PAXX ...Nonhomologous end joining is a critical mechanism that repairs DNA double-strand breaks in human cells. In this work, we address the structural and functional role of the accessory protein PAXX [paralog of x-ray repair cross-complementing protein 4 (XRCC4) and XRCC4-like factor (XLF)] in this mechanism. Here, we report high-resolution cryo-electron microscopy (cryo-EM) and x-ray crystallography structures of the PAXX C-terminal Ku-binding motif bound to Ku70/80 and cryo-EM structures of PAXX bound to two alternate DNA-dependent protein kinase (DNA-PK) end-bridging dimers, mediated by either Ku80 or XLF. We identify residues critical for the Ku70/PAXX interaction in vitro and in cells. We demonstrate that PAXX and XLF can bind simultaneously to the Ku heterodimer and act as structural bridges in alternate forms of DNA-PK dimers. Last, we show that engagement of both proteins provides a complementary advantage for DNA end synapsis and end joining in cells. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 194.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.6 KB 21.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 17.4 KB | Display | ![]() |
Images | ![]() | 58.9 KB | ||
Others | ![]() ![]() | 194.5 MB 194.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7zwaMC ![]() 7zygC ![]() 8ascC ![]() 8bh3C ![]() 8bhvC ![]() 8bhyC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Ku70/80 heterodimer bound to DNA and PAXX | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.65 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_14995_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_14995_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Ku70/80 heterodimer bound to DNA and PAXX
Entire | Name: Ku70/80 heterodimer bound to DNA and PAXX |
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Components |
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-Supramolecule #1: Ku70/80 heterodimer bound to DNA and PAXX
Supramolecule | Name: Ku70/80 heterodimer bound to DNA and PAXX / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 150 KDa |
-Macromolecule #1: X-ray repair cross-complementing protein 6
Macromolecule | Name: X-ray repair cross-complementing protein 6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO EC number: ![]() |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 69.945039 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #2: X-ray repair cross-complementing protein 5
Macromolecule | Name: X-ray repair cross-complementing protein 5 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO EC number: ![]() |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 82.812438 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #3: Protein PAXX
Macromolecule | Name: Protein PAXX / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 21.663498 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MDPLSPPLCT LPPGPEPPRF VCYCEGEESG EGDRGGFNLY VTDAAELWST CFTPDSLAAL KARFGLSAAE DITPRFRAAC EQQAVALTL QEDRASLTLS GGPSALAFDL SKVPGPEAAP RLRALTLGLA KRVWSLERRL AAAEETAVSP RKSPRPAGPQ L FLPDPDPQ ...String: MDPLSPPLCT LPPGPEPPRF VCYCEGEESG EGDRGGFNLY VTDAAELWST CFTPDSLAAL KARFGLSAAE DITPRFRAAC EQQAVALTL QEDRASLTLS GGPSALAFDL SKVPGPEAAP RLRALTLGLA KRVWSLERRL AAAEETAVSP RKSPRPAGPQ L FLPDPDPQ RGGPGPGVRR RCPGESLINP GFKSKKPAGG VDFDET |
-Macromolecule #4: DNA (5'-D(P*GP*AP*TP*CP*CP*CP*TP*CP*TP*AP*GP*AP*TP*AP*T)-3')
Macromolecule | Name: DNA (5'-D(P*GP*AP*TP*CP*CP*CP*TP*CP*TP*AP*GP*AP*TP*AP*T)-3') type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 4.543972 KDa |
Sequence | String: (DG)(DA)(DT)(DC)(DC)(DC)(DT)(DC)(DT)(DA) (DG)(DA)(DT)(DA)(DT) |
-Macromolecule #5: DNA (5'-D(P*CP*GP*AP*TP*AP*TP*CP*TP*AP*GP*AP*GP*GP*GP*AP*TP*C)-3')
Macromolecule | Name: DNA (5'-D(P*CP*GP*AP*TP*AP*TP*CP*TP*AP*GP*AP*GP*GP*GP*AP*TP*C)-3') type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 4.96224 KDa |
Sequence | String: (DG)(DA)(DT)(DA)(DT)(DC)(DT)(DA)(DG)(DA) (DG)(DG)(DG)(DA)(DT)(DC) |
-Macromolecule #6: PHOSPHATE ION
Macromolecule | Name: PHOSPHATE ION / type: ligand / ID: 6 / Number of copies: 1 / Formula: PO4 |
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Molecular weight | Theoretical: 94.971 Da |
Chemical component information | ![]() ChemComp-PO4: |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 2 mg/mL |
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Buffer | pH: 8 |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 6924 / Average exposure time: 1.25 sec. / Average electron dose: 44.39 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |