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- PDB-5ze1: Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in 2mM... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5ze1 | ||||||
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Title | Hairpin Forming Complex, RAG1/2-Nicked 12RSS/23RSS complex in 2mM Mn2+ for 10 min at 4'C | ||||||
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![]() | DNA BINDING PROTEIN / V(D)J recombination / RAG1-2-12RSS-23RSS complex / Hairpin forming complex | ||||||
Function / homology | ![]() positive regulation of myeloid progenitor cell differentiation / Apoptosis induced DNA fragmentation / open form four-way junction DNA binding / calcium-dependent protein kinase regulator activity / crossed form four-way junction DNA binding / plasmacytoid dendritic cell activation / Advanced glycosylation endproduct receptor signaling / Pyroptosis / Regulation of TLR by endogenous ligand / regulation of tolerance induction ...positive regulation of myeloid progenitor cell differentiation / Apoptosis induced DNA fragmentation / open form four-way junction DNA binding / calcium-dependent protein kinase regulator activity / crossed form four-way junction DNA binding / plasmacytoid dendritic cell activation / Advanced glycosylation endproduct receptor signaling / Pyroptosis / Regulation of TLR by endogenous ligand / regulation of tolerance induction / regulation of T cell mediated immune response to tumor cell / positive regulation of toll-like receptor 2 signaling pathway / positive regulation of myeloid cell differentiation / DNA geometric change / myeloid dendritic cell activation / mature B cell differentiation involved in immune response / TRAF6 mediated NF-kB activation / bent DNA binding / glycolipid binding / DNA recombinase complex / positive regulation of toll-like receptor 9 signaling pathway / positive regulation of glycogen catabolic process / B cell homeostatic proliferation / DN2 thymocyte differentiation / negative regulation of T cell differentiation in thymus / endodeoxyribonuclease complex / positive regulation of toll-like receptor 4 signaling pathway / TAK1-dependent IKK and NF-kappa-B activation / neutrophil clearance / pre-B cell allelic exclusion / endothelial cell chemotaxis / positive regulation of DNA ligation / eye development / RAGE receptor binding / positive regulation of organ growth / regulation of behavioral fear response / induction of positive chemotaxis / bubble DNA binding / V(D)J recombination / myeloid cell differentiation / myeloid progenitor cell differentiation / negative regulation of T cell apoptotic process / regulation of nucleotide-excision repair / macrophage activation involved in immune response / phosphatidylinositol-3,4-bisphosphate binding / positive regulation of innate immune response / positive regulation of monocyte chemotactic protein-1 production / negative regulation of thymocyte apoptotic process / cellular response to interleukin-7 / glycogen catabolic process / supercoiled DNA binding / phosphatidylinositol-3,5-bisphosphate binding / apoptotic cell clearance / endothelial cell proliferation / DNA binding, bending / positive regulation of T cell differentiation / positive regulation of mesenchymal cell proliferation / regulation of T cell differentiation / organ growth / positive regulation of wound healing / T cell lineage commitment / B cell lineage commitment / protein kinase activator activity / positive regulation of sprouting angiogenesis / phosphatidylserine binding / T cell homeostasis / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of interferon-alpha production / endoplasmic reticulum-Golgi intermediate compartment / T cell differentiation / protein autoubiquitination / positive regulation of autophagy / four-way junction DNA binding / response to glucocorticoid / phosphatidylinositol-4,5-bisphosphate binding / methylated histone binding / positive regulation of interferon-beta production / Neutrophil degranulation / positive regulation of mitotic cell cycle / phosphatidylinositol binding / B cell differentiation / thymus development / positive regulation of interleukin-1 beta production / cytokine activity / lung development / peptide binding / visual learning / RING-type E3 ubiquitin transferase / base-excision repair / autophagy / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of interleukin-6 production / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / positive regulation of tumor necrosis factor production / double-stranded RNA binding / chromatin organization / chromosome / heparin binding / single-stranded DNA binding Similarity search - Function | ||||||
Biological species | ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Kim, M.S. / Chuenchor, W. / Chen, X. / Gellert, M. / Yang, W. | ||||||
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
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 534.6 KB | Display | ![]() |
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PDB format | ![]() | 413.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 7470C ![]() 7480C ![]() 5zdzC ![]() 5ze0C ![]() 5ze2C ![]() 6cg0C ![]() 6cijC ![]() 6cikC ![]() 6cilC ![]() 6cimC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 3 types, 5 molecules ACBDN
#1: Protein | Mass: 71871.305 Da / Num. of mol.: 2 / Fragment: UNP residues 384-1008 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: 43225.711 Da / Num. of mol.: 2 / Fragment: UNP residues 1-387 / Mutation: M1V Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein | | Mass: 18897.885 Da / Num. of mol.: 1 / Fragment: UNP residues 1-163 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-DNA chain , 6 types, 6 molecules FIJGLM
#4: DNA chain | Mass: 13978.961 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#5: DNA chain | Mass: 4864.165 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#6: DNA chain | Mass: 4855.150 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#7: DNA chain | Mass: 16640.654 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#8: DNA chain | Mass: 9138.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#9: DNA chain | Mass: 12036.805 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 5 types, 61 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/MN.gif)
![](data/chem/img/EDO.gif)
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![](data/chem/img/HOH.gif)
![](data/chem/img/MN.gif)
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#10: Chemical | #11: Chemical | ChemComp-MN / #12: Chemical | ChemComp-EDO / | #13: Chemical | #14: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.38 Å3/Da / Density % sol: 63.6 % Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 100mM MES (pH 6.8), 15% PEG 3350, 200mM Potassium formate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3→50 Å / Num. obs: 163362 / % possible obs: 99.82 % / Redundancy: 5.2 % / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 3→3.11 Å |
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Processing
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Refinement | Method to determine structure: ![]() Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→36.679 Å
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Refine LS restraints |
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LS refinement shell |
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