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Yorodumi- EMDB-20033: Cryo-EM structure of mouse RAG1/2 12RSS-NFC/23RSS-PRC complex (DNA1) -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20033 | |||||||||
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Title | Cryo-EM structure of mouse RAG1/2 12RSS-NFC/23RSS-PRC complex (DNA1) | |||||||||
Map data | RAG1/2 12RSS-NFC/23RSS-PRC | |||||||||
Sample |
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Keywords | V(D)J recombination / DNA Transposition / RAG / SCID / RECOMBINATION / RECOMBINATION-DNA complex | |||||||||
Function / homology | Function and homology information mature B cell differentiation involved in immune response / DNA recombinase complex / B cell homeostatic proliferation / DN2 thymocyte differentiation / negative regulation of T cell differentiation in thymus / endodeoxyribonuclease complex / pre-B cell allelic exclusion / positive regulation of organ growth / regulation of behavioral fear response / V(D)J recombination ...mature B cell differentiation involved in immune response / DNA recombinase complex / B cell homeostatic proliferation / DN2 thymocyte differentiation / negative regulation of T cell differentiation in thymus / endodeoxyribonuclease complex / pre-B cell allelic exclusion / positive regulation of organ growth / regulation of behavioral fear response / V(D)J recombination / negative regulation of T cell apoptotic process / phosphatidylinositol-3,4-bisphosphate binding / negative regulation of thymocyte apoptotic process / phosphatidylinositol-3,5-bisphosphate binding / positive regulation of T cell differentiation / regulation of T cell differentiation / organ growth / T cell lineage commitment / B cell lineage commitment / T cell homeostasis / phosphatidylinositol-3,4,5-trisphosphate binding / T cell differentiation / protein autoubiquitination / phosphatidylinositol-4,5-bisphosphate binding / methylated histone binding / phosphatidylinositol binding / B cell differentiation / thymus development / visual learning / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / chromatin organization / histone binding / T cell differentiation in thymus / endonuclease activity / DNA recombination / adaptive immune response / sequence-specific DNA binding / Hydrolases; Acting on ester bonds / defense response to bacterium / chromatin binding / protein homodimerization activity / zinc ion binding / nucleoplasm / identical protein binding / nucleus / metal ion binding Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) / Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||
Authors | Chen X / Cui Y / Zhou ZH / Yang W / Gellert M | |||||||||
Funding support | United States, 1 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_20033.map.gz | 77.2 MB | EMDB map data format | |
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Header (meta data) | emd-20033-v30.xml emd-20033.xml | 16.6 KB 16.6 KB | Display Display | EMDB header |
Images | emd_20033.png | 57.2 KB | ||
Filedesc metadata | emd-20033.cif.gz | 6.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20033 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20033 | HTTPS FTP |
-Related structure data
Related structure data | 6oepMC 6oemC 6oenC 6oeoC 6oeqC 6oerC 6v0vC C: citing same article (ref.) M: atomic model generated by this map |
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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_20033.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | RAG1/2 12RSS-NFC/23RSS-PRC | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : mouse RAG1/2 12RSS-NFC/23RSS-PRC complex (DNA1)
Entire | Name: mouse RAG1/2 12RSS-NFC/23RSS-PRC complex (DNA1) |
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Components |
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-Supramolecule #1: mouse RAG1/2 12RSS-NFC/23RSS-PRC complex (DNA1)
Supramolecule | Name: mouse RAG1/2 12RSS-NFC/23RSS-PRC complex (DNA1) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: Mus musculus (house mouse) |
-Macromolecule #1: V(D)J recombination-activating protein 1
Macromolecule | Name: V(D)J recombination-activating protein 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 119.388352 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MAASLPSTLS FSSAPDEIQH PQIKFSEWKF KLFRVRSFEK APEEAQKEKD SSEGKPYLEQ SPVVPEKPGG QNSILTQRAL KLHPKFSKK FHADGKSSDK AVHQARLRHF CRICGNRFKS DGHSRRYPVH GPVDAKTQSL FRKKEKRVTS WPDLIARIFR I DVKADVDS ...String: MAASLPSTLS FSSAPDEIQH PQIKFSEWKF KLFRVRSFEK APEEAQKEKD SSEGKPYLEQ SPVVPEKPGG QNSILTQRAL KLHPKFSKK FHADGKSSDK AVHQARLRHF CRICGNRFKS DGHSRRYPVH GPVDAKTQSL FRKKEKRVTS WPDLIARIFR I DVKADVDS IHPTEFCHDC WSIMHRKFSS SHSQVYFPRK VTVEWHPHTP SCDICFTAHR GLKRKRHQPN VQLSKKLKTV LN HARRDRR KRTQARVSSK EVLKKISNCS KIHLSTKLLA VDFPAHFVKS ISCQICEHIL ADPVETSCKH LFCRICILRC LKV MGSYCP SCRYPCFPTD LESPVKSFLN ILNSLMVKCP AQDCNEEVSL EKYNHHVSSH KESKETLVHI NKGGRPRQHL LSLT RRAQK HRLRELKIQV KEFADKEEGG DVKAVCLTLF LLALRARNEH RQADELEAIM QGRGSGLQPA VCLAIRVNTF LSCSQ YHKM YRTVKAITGR QIFQPLHALR NAEKVLLPGY HPFEWQPPLK NVSSRTDVGI IDGLSGLASS VDEYPVDTIA KRFRYD SAL VSALMDMEED ILEGMRSQDL DDYLNGPFTV VVKESCDGMG DVSEKHGSGP AVPEKAVRFS FTVMRITIEH GSQNVKV FE EPKPNSELCC KPLCLMLADE SDHETLTAIL SPLIAEREAM KSSELTLEMG GIPRTFKFIF RGTGYDEKLV REVEGLEA S GSVYICTLCD TTRLEASQNL VFHSITRSHA ENLQRYEVWR SNPYHESVEE LRDRVKGVSA KPFIETVPSI DALHCDIGN AAEFYKIFQL EIGEVYKHPN ASKEERKRWQ ATLDKHLRKR MNLKPIMRMN GNFARKLMTQ ETVDAVCELI PSEERHEALR ELMDLYLKM KPVWRSSCPA KECPESLCQY SFNSQRFAEL LSTKFKYRYE GKITNYFHKT LAHVPEIIER DGSIGAWASE G NQSGNKLF RRFRKMNARQ SKCYEMEDVL KHHWLYTSKY LQKFMNAHNA LKSSGFTMNS KETLGDPLGI EDSLESQDSM EF UniProtKB: V(D)J recombination-activating protein 1 |
-Macromolecule #2: V(D)J recombination-activating protein 2
Macromolecule | Name: V(D)J recombination-activating protein 2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 59.13841 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MSLQMVTVGH NIALIQPGFS LMNFDGQVFF FGQKGWPKRS CPTGVFHFDI KQNHLKLKPA IFSKDSCYLP PLRYPATCSY KGSIDSDKH QYIIHGGKTP NNELSDKIYI MSVACKNNKK VTFRCTEKDL VGDVPEPRYG HSIDVVYSRG KSMGVLFGGR S YMPSTQRT ...String: MSLQMVTVGH NIALIQPGFS LMNFDGQVFF FGQKGWPKRS CPTGVFHFDI KQNHLKLKPA IFSKDSCYLP PLRYPATCSY KGSIDSDKH QYIIHGGKTP NNELSDKIYI MSVACKNNKK VTFRCTEKDL VGDVPEPRYG HSIDVVYSRG KSMGVLFGGR S YMPSTQRT TEKWNSVADC LPHVFLIDFE FGCATSYILP ELQDGLSFHV SIARNDTVYI LGGHSLASNI RPANLYRIRV DL PLGTPAV NCTVLPGGIS VSSAILTQTN NDEFVIVGGY QLENQKRMVC SLVSLGDNTI EISEMETPDW TSDIKHSKIW FGS NMGNGT IFLGIPGDNK QAMSEAFYFY TLRCSEEDLS EDQKIVSNSQ TSTEDPGDST PFEDSEEFCF SAEATSFDGD DEFD TYNED DEDDESVTGY WITCCPTCDV DINTWVPFYS TELNKPAMIY CSHGDGHWVH AQCMDLEERT LIHLSEGSNK YYCNE HVQI ARALQTPKRN PPLQKPPMKS LHKKGSGKVL TPAKKSFLRR LFD UniProtKB: V(D)J recombination-activating protein 2 |
-Macromolecule #3: DNA (46-MER)
Macromolecule | Name: DNA (46-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Molecular weight | Theoretical: 15.528942 KDa |
Sequence | String: (DC)(DG)(DG)(DG)(DT)(DT)(DT)(DT)(DT)(DG) (DT)(DT)(DA)(DA)(DG)(DG)(DG)(DC)(DT)(DG) (DT)(DA)(DT)(DC)(DA)(DC)(DT)(DG)(DT) (DG)(DT)(DA)(DA)(DG)(DA)(DC)(DA)(DG)(DG) (DC) (DC)(DA)(DG)(DA)(DT)(DC)(DC)(DA) (DG)(DG) |
-Macromolecule #4: DNA (46-MER)
Macromolecule | Name: DNA (46-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Molecular weight | Theoretical: 15.275817 KDa |
Sequence | String: (DC)(DC)(DT)(DG)(DG)(DA)(DT)(DC)(DT)(DG) (DG)(DC)(DC)(DT)(DG)(DT)(DC)(DT)(DT)(DA) (DC)(DA)(DC)(DA)(DG)(DT)(DG)(DA)(DT) (DA)(DC)(DA)(DG)(DC)(DC)(DC)(DT)(DT)(DA) (DA) (DC)(DA)(DA)(DA)(DA)(DA)(DC)(DC) (DC)(DG) |
-Macromolecule #5: DNA (57-MER)
Macromolecule | Name: DNA (57-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Molecular weight | Theoretical: 18.809023 KDa |
Sequence | String: (DC)(DG)(DG)(DG)(DT)(DT)(DT)(DT)(DT)(DG) (DT)(DC)(DT)(DG)(DG)(DC)(DT)(DT)(DC)(DA) (DC)(DA)(DC)(DT)(DT)(DG)(DA)(DT)(DT) (DT)(DG)(DC)(DA)(DT)(DC)(DA)(DC)(DT)(DG) (DT) (DG)(DT)(DA)(DA)(DG)(DA) ...String: (DC)(DG)(DG)(DG)(DT)(DT)(DT)(DT)(DT)(DG) (DT)(DC)(DT)(DG)(DG)(DC)(DT)(DT)(DC)(DA) (DC)(DA)(DC)(DT)(DT)(DG)(DA)(DT)(DT) (DT)(DG)(DC)(DA)(DT)(DC)(DA)(DC)(DT)(DG) (DT) (DG)(DT)(DA)(DA)(DG)(DA)(DC)(DA) (DG)(DG)(DC)(DC)(DA)(DG)(DA)(DT)(DC)(DC) (DA)(DG) (DG) |
-Macromolecule #6: DNA (57-MER)
Macromolecule | Name: DNA (57-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) |
Molecular weight | Theoretical: 18.792076 KDa |
Sequence | String: (DC)(DC)(DT)(DG)(DG)(DA)(DT)(DC)(DT)(DG) (DG)(DC)(DC)(DT)(DG)(DT)(DC)(DT)(DT)(DA) (DC)(DA)(DC)(DA)(DG)(DT)(DG)(DA)(DT) (DG)(DC)(DA)(DA)(DA)(DT)(DC)(DA)(DA)(DG) (DT) (DG)(DT)(DG)(DA)(DA)(DG) ...String: (DC)(DC)(DT)(DG)(DG)(DA)(DT)(DC)(DT)(DG) (DG)(DC)(DC)(DT)(DG)(DT)(DC)(DT)(DT)(DA) (DC)(DA)(DC)(DA)(DG)(DT)(DG)(DA)(DT) (DG)(DC)(DA)(DA)(DA)(DT)(DC)(DA)(DA)(DG) (DT) (DG)(DT)(DG)(DA)(DA)(DG)(DC)(DC) (DA)(DG)(DA)(DC)(DA)(DA)(DA)(DA)(DA)(DC) (DC)(DC) (DG) |
-Macromolecule #7: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 7 / Number of copies: 3 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #8: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 8 / Number of copies: 2 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Details: unspecified |
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: 42.0 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: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 107398 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |