[English] 日本語
Yorodumi- PDB-6cij: Cryo-EM structure of mouse RAG1/2 HFC complex containing partial ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cij | ||||||
---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of mouse RAG1/2 HFC complex containing partial HMGB1 linker(3.9 A) | ||||||
Components |
| ||||||
Keywords | RECOMBINATION/DNA / 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 | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å | ||||||
Authors | Chen, X. / Kim, M. / Chuenchor, W. / Cui, Y. / Zhang, X. / Zhou, Z.H. / Gellert, M. / Yang, W. | ||||||
Funding support | United States, 1items
| ||||||
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 |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6cij.cif.gz | 478.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6cij.ent.gz | 370.1 KB | Display | PDB format |
PDBx/mmJSON format | 6cij.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cij_validation.pdf.gz | 773.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6cij_full_validation.pdf.gz | 818.8 KB | Display | |
Data in XML | 6cij_validation.xml.gz | 61.3 KB | Display | |
Data in CIF | 6cij_validation.cif.gz | 93.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ci/6cij ftp://data.pdbj.org/pub/pdb/validation_reports/ci/6cij | HTTPS FTP |
-Related structure data
Related structure data | 7480MC 7470C 5zdzC 5ze0C 5ze1C 5ze2C 6cg0C 6cikC 6cilC 6cimC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-V(D)J recombination-activating protein ... , 2 types, 4 molecules ACDB
#1: Protein | Mass: 88670.805 Da / Num. of mol.: 2 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 #8: Protein | Mass: 58158.254 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 |
---|
-DNA chain , 6 types, 6 molecules FIJGLM
#2: DNA chain | Mass: 14268.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
---|---|
#3: DNA chain | Mass: 4880.164 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
#4: DNA chain | Mass: 6091.926 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
#5: DNA chain | Mass: 18809.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
#7: DNA chain | Mass: 9138.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
#9: DNA chain | Mass: 12655.191 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-Protein , 1 types, 1 molecules N
#6: Protein | Mass: 18897.885 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HMGB1, HMG1 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P09429 |
---|
-Non-polymers , 2 types, 4 molecules
#10: Chemical | #11: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: RAG1/2 in complex with nicked DNAs / Type: COMPLEX / Entity ID: #1-#9 / Source: RECOMBINANT |
---|---|
Source (natural) | Organism: Mus musculus (house mouse) |
Source (recombinant) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 57.6 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.12_2829: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software | Name: RELION / Version: 2.1 / Category: 3D reconstruction | ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 49624 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Target criteria: Correlation Coefficient | ||||||||||||||||||||||||
Refine LS restraints |
|