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- 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) | |||||||||
![]() | Cryo-EM structure of mouse RAG1/2 HFC complex | |||||||||
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![]() | V(D)J recombination / RAG1/2 / RSS / Immunity / RECOMBINATION / RECOMBINATION-DNA complex | |||||||||
Function / homology | ![]() 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 / mature B cell differentiation involved in immune response / T-helper 1 cell activation ...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 / 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 / positive regulation of toll-like receptor 9 signaling pathway / 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 / 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 / alphav-beta3 integrin-HMGB1 complex / bubble DNA binding / 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 / negative regulation of thymocyte apoptotic process / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of monocyte chemotaxis / MyD88 deficiency (TLR2/4) / supercoiled DNA binding / phosphatidylinositol-3,5-bisphosphate binding / apoptotic cell clearance / dendritic cell chemotaxis / DNA binding, bending / positive regulation of T cell differentiation / positive regulation of vascular endothelial cell proliferation / IRAK4 deficiency (TLR2/4) / regulation of T cell differentiation / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / organ growth / T cell lineage commitment / positive regulation of DNA binding / B cell lineage commitment / positive regulation of activated T cell proliferation / phosphatidylserine binding / chemoattractant activity / T cell homeostasis / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / phosphatidylinositol-3,4,5-trisphosphate binding / DNA topological change / TRAF6 mediated NF-kB activation / positive regulation of interleukin-10 production / Advanced glycosylation endproduct receptor signaling / 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 / Pyroptosis / protein autoubiquitination / positive regulation of autophagy / DNA polymerase binding / four-way junction DNA binding / condensed chromosome / methylated histone binding / phosphatidylinositol-4,5-bisphosphate binding / activation of innate immune response / positive regulation of interleukin-12 production / transcription repressor complex / phosphatidylinositol binding / B cell differentiation / 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 | ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
![]() | Chen X / Kim M | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 8.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.9 KB 18.9 KB | Display Display | ![]() |
Images | ![]() | 169.9 KB | ||
Filedesc metadata | ![]() | 6.7 KB | ||
Archive directory | ![]() ![]() | 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 ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Cryo-EM structure of mouse RAG1/2 HFC 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
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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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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.4 |
Vitrification | Cryogen name: ETHANE |
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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: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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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: |