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Open data
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Basic information
Entry | Database: PDB / ID: 6oer | ||||||
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Title | Cryo-EM structure of mouse RAG1/2 NFC complex (DNA2) | ||||||
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![]() | RECOMBINATION/DNA / V(D)J recombination / DNA Transposition / RAG / SCID / RECOMBINATION / RECOMBINATION-DNA complex | ||||||
Function / homology | ![]() non-sequence-specific DNA binding, bending / DNA-binding transcription factor binding => GO:0140297 / regulation of restriction endodeoxyribonuclease activity / heterochromatin formation => GO:0031507 / regulation of tolerance induction / positive regulation of mismatch repair / negative regulation of apoptotic cell clearance / negative regulation of RNA polymerase II transcription preinitiation complex assembly / DNA geometric change / mature B cell differentiation involved in immune response ...non-sequence-specific DNA binding, bending / DNA-binding transcription factor binding => GO:0140297 / regulation of restriction endodeoxyribonuclease activity / heterochromatin formation => GO:0031507 / regulation of tolerance induction / positive regulation of mismatch repair / negative regulation of apoptotic cell clearance / negative regulation of RNA polymerase II transcription preinitiation complex assembly / DNA geometric change / mature B cell differentiation involved in immune response / T-helper 1 cell activation / C-X-C chemokine binding / T-helper 1 cell differentiation / positive regulation of dendritic cell differentiation / DNA recombinase complex / negative regulation of CD4-positive, alpha-beta T cell differentiation / B cell homeostatic proliferation / DN2 thymocyte differentiation / negative regulation of T cell differentiation in thymus / endodeoxyribonuclease complex / neutrophil clearance / double-stranded DNA endonuclease activity / pre-B cell allelic exclusion / positive regulation of interleukin-1 production / positive regulation of organ growth / regulation of behavioral fear response / alphav-beta3 integrin-HMGB1 complex / bubble DNA binding / V(D)J recombination / negative regulation of T cell apoptotic process / phosphatidylinositol-3,4-bisphosphate binding / inflammatory response to antigenic stimulus / negative regulation of thymocyte apoptotic process / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of monocyte chemotaxis / supercoiled DNA binding / phosphatidylinositol-3,5-bisphosphate binding / positive regulation of T cell differentiation / DNA binding, bending / positive regulation of vascular endothelial cell proliferation / regulation of T cell differentiation / organ growth / T cell lineage commitment / B cell lineage commitment / positive regulation of activated T cell proliferation / phosphatidylserine binding / T cell homeostasis / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / positive regulation of interleukin-10 production / negative regulation of blood vessel endothelial cell migration / negative regulation of type II interferon production / endoplasmic reticulum-Golgi intermediate compartment / T cell differentiation / positive regulation of blood vessel endothelial cell migration / positive regulation of DNA binding / protein autoubiquitination / positive regulation of autophagy / DNA polymerase binding / four-way junction DNA binding / condensed chromosome / methylated histone binding / phosphatidylinositol-4,5-bisphosphate binding / positive regulation of interleukin-12 production / activation of innate immune response / transcription repressor complex / phosphatidylinositol binding / B cell differentiation / thymus development / positive regulation of interleukin-8 production / lipopolysaccharide binding / positive regulation of JNK cascade / RING-type E3 ubiquitin transferase / visual learning / autophagy / ubiquitin-protein transferase activity / chemotaxis / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / ubiquitin protein ligase activity / integrin binding / chromatin organization / histone binding / positive regulation of cytosolic calcium ion concentration / T cell differentiation in thymus / endonuclease activity / DNA recombination / adaptive immune response / sequence-specific DNA binding / damaged DNA binding / transcription coactivator activity / Hydrolases; Acting on ester bonds / positive regulation of ERK1 and ERK2 cascade / transcription cis-regulatory region binding / lyase activity / endosome / defense response to bacterium / positive regulation of apoptotic process / DNA repair / innate immune response Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.29 Å | ||||||
![]() | Chen, X. / Cui, Y. / Zhou, Z.H. / Yang, W. / Gellert, M. | ||||||
Funding support | ![]()
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![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 471.6 KB | Display | ![]() |
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PDB format | ![]() | 356 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 946.2 KB | Display | ![]() |
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Full document | ![]() | 987.6 KB | Display | |
Data in XML | ![]() | 60.8 KB | Display | |
Data in CIF | ![]() | 93.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 20035MC ![]() 6oemC ![]() 6oenC ![]() 6oeoC ![]() 6oepC ![]() 6oeqC ![]() 6v0vC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
-V(D)J recombination-activating protein ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 119388.352 Da / Num. of mol.: 2 / Mutation: E962Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P15919, Hydrolases; Acting on ester bonds, RING-type E3 ubiquitin transferase #2: Protein | Mass: 59138.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-DNA chain , 4 types, 4 molecules FIGJ
#3: DNA chain | Mass: 15503.931 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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#4: DNA chain | Mass: 15275.817 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#5: DNA chain | Mass: 18784.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
#6: DNA chain | Mass: 18792.076 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
-Protein , 1 types, 1 molecules H
#7: Protein | Mass: 18897.885 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() ![]() |
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-Non-polymers , 2 types, 6 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/CA.gif)
#8: Chemical | #9: Chemical | ChemComp-CA / |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: RAG1/2 Nick-forming complex (DNA2) / Type: COMPLEX / Entity ID: #1-#7 / Source: MULTIPLE SOURCES |
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Molecular weight | Units: MEGADALTONS / Experimental value: YES |
Buffer solution | pH: 7.4 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: unspecified |
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 |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 333280 / Symmetry type: POINT | ||||||||||||||||||||||||
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