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Yorodumi- EMDB-7480: Cryo-EM structure of mouse RAG1/2 HFC complex containing partial ... -
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-Basic information
Entry | Database: EMDB / ID: EMD-7480 | |||||||||
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Title | Cryo-EM structure of mouse RAG1/2 HFC complex containing partial HMGB1 linker(3.9 A) | |||||||||
Map data | Cryo-EM structure of mouse RAG1/2 HFC complex | |||||||||
Sample |
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Keywords | V(D)J recombination / RAG1/2 / RSS / Immunity / RECOMBINATION / RECOMBINATION-DNA complex | |||||||||
Function / homology | Function and homology information regulation of restriction endodeoxyribonuclease activity / regulation of tolerance induction / positive regulation of mismatch repair / regulation of T cell mediated immune response to tumor cell / negative regulation of apoptotic cell clearance / negative regulation of RNA polymerase II transcription preinitiation complex assembly / DNA geometric change / myeloid dendritic cell activation / T-helper 1 cell activation / mature B cell differentiation involved in immune response ...regulation of restriction endodeoxyribonuclease activity / regulation of tolerance induction / positive regulation of mismatch repair / regulation of T cell mediated immune response to tumor cell / negative regulation of apoptotic cell clearance / negative regulation of RNA polymerase II transcription preinitiation complex assembly / DNA geometric change / myeloid dendritic cell activation / T-helper 1 cell activation / mature B cell differentiation involved in immune response / C-X-C chemokine binding / T-helper 1 cell differentiation / positive regulation of dendritic cell differentiation / positive regulation of toll-like receptor 9 signaling pathway / negative regulation of CD4-positive, alpha-beta T cell differentiation / DNA recombinase complex / B cell homeostatic proliferation / DN2 thymocyte differentiation / negative regulation of T cell differentiation in thymus / endodeoxyribonuclease complex / neutrophil clearance / pre-B cell allelic exclusion / positive regulation of DNA ligation / positive regulation of interleukin-1 production / RAGE receptor binding / positive regulation of organ growth / Regulation of TLR by endogenous ligand / regulation of behavioral fear response / bubble DNA binding / alphav-beta3 integrin-HMGB1 complex / V(D)J recombination / negative regulation of T cell apoptotic process / Apoptosis induced DNA fragmentation / phosphatidylinositol-3,4-bisphosphate binding / inflammatory response to antigenic stimulus / positive regulation of monocyte chemotaxis / negative regulation of thymocyte apoptotic process / MyD88 deficiency (TLR2/4) / positive regulation of chemokine (C-X-C motif) ligand 2 production / supercoiled DNA binding / apoptotic cell clearance / phosphatidylinositol-3,5-bisphosphate binding / dendritic cell chemotaxis / T cell lineage commitment / DNA binding, bending / positive regulation of T cell differentiation / organ growth / IRAK4 deficiency (TLR2/4) / positive regulation of vascular endothelial cell proliferation / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / regulation of T cell differentiation / B cell lineage commitment / positive regulation of DNA binding / : / chemoattractant activity / T cell homeostasis / positive regulation of activated T cell proliferation / phosphatidylserine binding / phosphatidylinositol-3,4,5-trisphosphate binding / endoplasmic reticulum-Golgi intermediate compartment / TRAF6 mediated NF-kB activation / DNA topological change / positive regulation of interleukin-10 production / negative regulation of blood vessel endothelial cell migration / Advanced glycosylation endproduct receptor signaling / negative regulation of type II interferon production / T cell differentiation / Pyroptosis / positive regulation of blood vessel endothelial cell migration / protein autoubiquitination / positive regulation of autophagy / DNA polymerase binding / four-way junction DNA binding / activation of innate immune response / condensed chromosome / phosphatidylinositol-4,5-bisphosphate binding / methylated histone binding / positive regulation of interleukin-12 production / transcription repressor complex / B cell differentiation / phosphatidylinositol binding / thymus development / cytokine activity / positive regulation of interleukin-8 production / lipopolysaccharide binding / positive regulation of JNK cascade / TAK1-dependent IKK and NF-kappa-B activation / visual learning / RING-type E3 ubiquitin transferase / heterochromatin formation / autophagy / double-strand break repair via nonhomologous end joining / positive regulation of interleukin-6 production / ubiquitin-protein transferase activity / transcription corepressor activity / positive regulation of tumor necrosis factor production / ubiquitin protein ligase activity / neuron projection development / integrin binding / chromatin organization Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
Authors | Chen X / Kim M | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Mol Cell / Year: 2018 Title: Cracking the DNA Code for V(D)J Recombination. Authors: Min-Sung Kim / Watchalee Chuenchor / Xuemin Chen / Yanxiang Cui / Xing Zhang / Z Hong Zhou / Martin Gellert / Wei Yang / Abstract: To initiate V(D)J recombination for generating the adaptive immune response of vertebrates, RAG1/2 recombinase cleaves DNA at a pair of recombination signal sequences, the 12- and 23-RSS. We have ...To initiate V(D)J recombination for generating the adaptive immune response of vertebrates, RAG1/2 recombinase cleaves DNA at a pair of recombination signal sequences, the 12- and 23-RSS. We have determined crystal and cryo-EM structures of RAG1/2 with DNA in the pre-reaction and hairpin-forming complexes up to 2.75 Å resolution. Both protein and DNA exhibit structural plasticity and undergo dramatic conformational changes. Coding-flank DNAs extensively rotate, shift, and deform for nicking and hairpin formation. Two intertwined RAG1 subunits crisscross four times between the asymmetric pair of severely bent 12/23-RSS DNAs. Location-sensitive bending of 60° and 150° in 12- and 23-RSS spacers, respectively, must occur for RAG1/2 to capture the nonamers and pair the heptamers for symmetric double-strand breakage. DNA pairing is thus sequence-context dependent and structure specific, which partly explains the "beyond 12/23" restriction. Finally, catalysis in crystallo reveals the process of DNA hairpin formation and its stabilization by interleaved base stacking. | |||||||||
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_7480.map.gz | 8.4 MB | EMDB map data format | |
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Header (meta data) | emd-7480-v30.xml emd-7480.xml | 18.9 KB 18.9 KB | Display Display | EMDB header |
Images | emd_7480.png | 169.9 KB | ||
Filedesc metadata | emd-7480.cif.gz | 6.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-7480 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-7480 | HTTPS FTP |
-Validation report
Summary document | emd_7480_validation.pdf.gz | 379.1 KB | Display | EMDB validaton report |
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Full document | emd_7480_full_validation.pdf.gz | 378.7 KB | Display | |
Data in XML | emd_7480_validation.xml.gz | 6.4 KB | Display | |
Data in CIF | emd_7480_validation.cif.gz | 7.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7480 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-7480 | HTTPS FTP |
-Related structure data
Related structure data | 6cijMC 7470C 5zdzC 5ze0C 5ze1C 5ze2C 6cg0C 6cikC 6cilC 6cimC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_7480.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Cryo-EM structure of mouse RAG1/2 HFC complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 in complex with nicked DNAs
+Supramolecule #1: RAG1/2 in complex with nicked DNAs
+Macromolecule #1: V(D)J recombination-activating protein 1
+Macromolecule #6: High mobility group protein B1
+Macromolecule #8: V(D)J recombination-activating protein 2
+Macromolecule #2: DNA (46-MER)
+Macromolecule #3: DNA (5'-D(*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP*A)-3')
+Macromolecule #4: DNA (5'-D(P*CP*TP*GP*GP*AP*TP*CP*TP*GP*GP*CP*CP*TP*GP*TP*CP*TP*TP...
+Macromolecule #5: DNA (60-MER)
+Macromolecule #7: DNA (30-MER)
+Macromolecule #9: DNA (41-MER)
+Macromolecule #10: ZINC ION
+Macromolecule #11: CALCIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 57.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 49624 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: COMMON LINE |
-Atomic model buiding 1
Refinement | Protocol: RIGID BODY FIT / Target criteria: Correlation Coefficient |
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Output model | PDB-6cij: |