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Open data
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Basic information
Entry | Database: PDB / ID: 7nfc | ||||||
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Title | Cryo-EM structure of NHEJ super-complex (dimer) | ||||||
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Function / homology | ![]() DNA ligation involved in DNA recombination / FHA domain binding / positive regulation of chromosome organization / positive regulation of ligase activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chaplin, A.K. / Hardwick, S.W. / Kefala Stavridi, A. / Chirgadze, D.Y. / Blundell, T.L. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM of NHEJ supercomplexes provides insights into DNA repair. Authors: Amanda K Chaplin / Steven W Hardwick / Antonia Kefala Stavridi / Christopher J Buehl / Noah J Goff / Virginie Ropars / Shikang Liang / Taiana Maia De Oliveira / Dimitri Y Chirgadze / ...Authors: Amanda K Chaplin / Steven W Hardwick / Antonia Kefala Stavridi / Christopher J Buehl / Noah J Goff / Virginie Ropars / Shikang Liang / Taiana Maia De Oliveira / Dimitri Y Chirgadze / Katheryn Meek / Jean-Baptiste Charbonnier / Tom L Blundell / ![]() ![]() ![]() Abstract: Non-homologous end joining (NHEJ) is one of two critical mechanisms utilized in humans to repair DNA double-strand breaks (DSBs). Unrepaired or incorrect repair of DSBs can lead to apoptosis or ...Non-homologous end joining (NHEJ) is one of two critical mechanisms utilized in humans to repair DNA double-strand breaks (DSBs). Unrepaired or incorrect repair of DSBs can lead to apoptosis or cancer. NHEJ involves several proteins, including the Ku70/80 heterodimer, DNA-dependent protein kinase catalytic subunit (DNA-PKcs), X-ray cross-complementing protein 4 (XRCC4), XRCC4-like factor (XLF), and ligase IV. These core proteins bind DSBs and ligate the damaged DNA ends. However, details of the structural assembly of these proteins remain unclear. Here, we present cryo-EM structures of NHEJ supercomplexes that are composed of these core proteins and DNA, revealing the detailed structural architecture of this assembly. We describe monomeric and dimeric forms of this supercomplex and also propose the existence of alternate dimeric forms of long-range synaptic complexes. Finally, we show that mutational disruption of several structural features within these NHEJ complexes negatively affects DNA repair. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.9 MB | Display | ![]() |
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PDB format | ![]() | 1.6 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 12299MC ![]() 7nfeC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 4 types, 10 molecules AFKLNOMPQR
#1: Protein | Mass: 471375.406 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() References: UniProt: P78527, ![]() #4: Protein | ![]() Mass: 38337.703 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #5: Protein | ![]() Mass: 104124.953 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() #6: Protein | Mass: 33372.234 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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-X-ray repair cross-complementing protein ... , 2 types, 4 molecules BGCH
#2: Protein | Mass: 69945.039 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: Insect cell expression vector pTIE1 (others) References: UniProt: P12956, ![]() ![]() #3: Protein | Mass: 82812.438 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Production host: Insect cell expression vector pTIE1 (others) References: UniProt: P13010, ![]() |
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-DNA chain , 3 types, 4 molecules DEIJ
#7: DNA chain | Mass: 8335.403 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() | ||
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#8: DNA chain | Mass: 8619.629 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() #9: DNA chain | | Mass: 8350.414 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
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Molecular weight | Value: 1.6 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||||||||
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Source (recombinant) |
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Buffer solution | pH: 7.4 | ||||||||||||||||||||||||||||||||||||
Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | ||||||||||||||||||||||||||||||||||||
Vitrification![]() | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() ![]() |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 1.3 sec. / Electron dose: 46.8 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
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EM software |
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CTF correction![]() | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Particle selection | Num. of particles selected: 749185 | ||||||||||||||||||||||||
Symmetry | Point symmetry![]() | ||||||||||||||||||||||||
3D reconstruction![]() | Resolution: 4.14 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23421 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 294.33 Å2 | ||||||||||||||||||||||||
Refine LS restraints |
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