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Yorodumi- EMDB-20039: Cryo-EM structure of mouse RAG1/2 NFC complex (DNA1) with C2 symmetry -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20039 | |||||||||
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Title | Cryo-EM structure of mouse RAG1/2 NFC complex (DNA1) with C2 symmetry | |||||||||
Map data | Mouse RAG1/2 NFC complex | |||||||||
Sample |
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Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.44 Å | |||||||||
Authors | Chen X / Cui Y / Zhou ZH / Yang W / Gellert M | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2020 Title: Cutting antiparallel DNA strands in a single active site. Authors: Xuemin Chen / Yanxiang Cui / Robert B Best / Huaibin Wang / Z Hong Zhou / Wei Yang / Martin Gellert / Abstract: A single enzyme active site that catalyzes multiple reactions is a well-established biochemical theme, but how one nuclease site cleaves both DNA strands of a double helix has not been well ...A single enzyme active site that catalyzes multiple reactions is a well-established biochemical theme, but how one nuclease site cleaves both DNA strands of a double helix has not been well understood. In analyzing site-specific DNA cleavage by the mammalian RAG1-RAG2 recombinase, which initiates V(D)J recombination, we find that the active site is reconfigured for the two consecutive reactions and the DNA double helix adopts drastically different structures. For initial nicking of the DNA, a locally unwound and unpaired DNA duplex forms a zipper via alternating interstrand base stacking, rather than melting as generally thought. The second strand cleavage and formation of a hairpin-DNA product requires a global scissor-like movement of protein and DNA, delivering the scissile phosphate into the rearranged active site. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20039.map.gz | 5.3 MB | EMDB map data format | |
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Header (meta data) | emd-20039-v30.xml emd-20039.xml | 10.7 KB 10.7 KB | Display Display | EMDB header |
Images | emd_20039.png | 48.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20039 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20039 | HTTPS FTP |
-Related structure data
Related structure data | 6oemC 6oenC 6oeoC 6oepC 6oeqC 6oerC 6v0vC C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_20039.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Mouse RAG1/2 NFC complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : RAG1/2 Nick-forming complex (DNA1)
Entire | Name: RAG1/2 Nick-forming complex (DNA1) |
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Components |
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-Supramolecule #1: RAG1/2 Nick-forming complex (DNA1)
Supramolecule | Name: RAG1/2 Nick-forming complex (DNA1) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7 |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
Details | mouse RAG1/2 NFC complex (DNA2) |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 42.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Initial angle assignment | Type: NOT APPLICABLE |
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Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.44 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 109388 |