+Open data
-Basic information
Entry | Database: PDB / ID: 6oer | ||||||
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Title | Cryo-EM structure of mouse RAG1/2 NFC complex (DNA2) | ||||||
Components |
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Keywords | RECOMBINATION/DNA / V(D)J recombination / DNA Transposition / RAG / SCID / RECOMBINATION / RECOMBINATION-DNA complex | ||||||
Function / homology | Function and homology information non-sequence-specific DNA binding, bending / DNA-binding transcription factor binding => GO:0140297 / regulation of restriction endodeoxyribonuclease activity / regulation of tolerance induction / heterochromatin formation => GO:0031507 / 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 / regulation of tolerance induction / heterochromatin formation => GO:0031507 / 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 / T-helper 1 cell differentiation / C-X-C chemokine binding / positive regulation of dendritic cell differentiation / DNA recombinase complex / endodeoxyribonuclease 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 / neutrophil clearance / regulation of behavioral fear response / pre-B cell allelic exclusion / positive regulation of organ growth / positive regulation of interleukin-1 production / bubble DNA binding / alphav-beta3 integrin-HMGB1 complex / V(D)J recombination / negative regulation of T cell apoptotic process / phosphatidylinositol-3,4-bisphosphate binding / positive regulation of chemokine (C-X-C motif) ligand 2 production / inflammatory response to antigenic stimulus / supercoiled DNA binding / negative regulation of thymocyte apoptotic process / phosphatidylinositol-3,5-bisphosphate binding / positive regulation of monocyte chemotaxis / DNA binding, bending / positive regulation of T cell differentiation / positive regulation of vascular endothelial cell proliferation / regulation of T cell differentiation / organ growth / T cell lineage commitment / phosphatidylserine binding / positive regulation of activated T cell proliferation / B cell lineage commitment / T cell homeostasis / negative regulation of blood vessel endothelial cell migration / 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 type II interferon production / T cell differentiation / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of blood vessel endothelial cell migration / positive regulation of DNA binding / protein autoubiquitination / DNA polymerase binding / positive regulation of autophagy / four-way junction DNA binding / condensed chromosome / methylated histone binding / phosphatidylinositol-4,5-bisphosphate binding / transcription repressor complex / activation of innate immune response / positive regulation of interleukin-12 production / 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 / positive regulation of interleukin-6 production / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / chemotaxis / integrin binding / positive regulation of tumor necrosis factor production / T cell differentiation in thymus / chromatin organization / positive regulation of cytosolic calcium ion concentration / histone binding / endonuclease activity / DNA recombination / sequence-specific DNA binding / adaptive immune response / damaged DNA binding / Hydrolases; Acting on ester bonds / transcription coactivator activity / 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 / chromatin binding Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Escherichia coli K-12 (bacteria) Equus caballus (horse) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.29 Å | ||||||
Authors | Chen, X. / Cui, Y. / Zhou, Z.H. / Yang, W. / Gellert, M. | ||||||
Funding support | United States, 1items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6oer.cif.gz | 471.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6oer.ent.gz | 356 KB | Display | PDB format |
PDBx/mmJSON format | 6oer.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oe/6oer ftp://data.pdbj.org/pub/pdb/validation_reports/oe/6oer | HTTPS FTP |
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-Related structure data
Related structure data | 20035MC 6oemC 6oenC 6oeoC 6oepC 6oeqC 6v0vC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Mus musculus (house mouse) / Gene: Rag1 / Production host: Homo sapiens (human) 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.) Mus musculus (house mouse) / Gene: Rag2, Rag-2 / Production host: Homo sapiens (human) / References: UniProt: P21784 |
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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.) Escherichia coli K-12 (bacteria) |
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#4: DNA chain | Mass: 15275.817 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli K-12 (bacteria) |
#5: DNA chain | Mass: 18784.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli K-12 (bacteria) |
#6: DNA chain | Mass: 18792.076 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Escherichia coli K-12 (bacteria) |
-Protein , 1 types, 1 molecules H
#7: Protein | Mass: 18897.885 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Equus caballus (horse) / References: UniProt: Q08IE6 |
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-Non-polymers , 2 types, 6 molecules
#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 |
-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 |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-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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