+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21003 | |||||||||
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Title | Cryo-EM structure of mouse WT RAG1/2 NFC complex (DNA0) | |||||||||
Map data | Structure of mouse WT RAG1/2 NFC complex (DNA0) | |||||||||
Sample |
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Keywords | V(D)J recombination / RAG / SCID / RECOMBINATION / RECOMBINATION-DNA complex | |||||||||
Function / homology | Function and homology information mature B cell differentiation involved in immune response / DNA recombinase complex / endodeoxyribonuclease complex / B cell homeostatic proliferation / DN2 thymocyte differentiation / negative regulation of T cell differentiation in thymus / 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 / endodeoxyribonuclease complex / B cell homeostatic proliferation / DN2 thymocyte differentiation / negative regulation of T cell differentiation in thymus / 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 / methylated histone binding / phosphatidylinositol-4,5-bisphosphate binding / phosphatidylinositol binding / B cell differentiation / thymus development / visual learning / RING-type E3 ubiquitin transferase / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / T cell differentiation in thymus / chromatin organization / histone binding / endonuclease activity / DNA recombination / sequence-specific DNA binding / adaptive immune response / Hydrolases; Acting on ester bonds / defense response to bacterium / chromatin binding / protein homodimerization activity / zinc ion binding / nucleoplasm / identical protein binding / metal ion binding / nucleus Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) / Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.61 Å | |||||||||
Authors | Chen X / Yang W | |||||||||
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_21003.map.gz | 4.3 MB | EMDB map data format | |
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Header (meta data) | emd-21003-v30.xml emd-21003.xml | 13.7 KB 13.7 KB | Display Display | EMDB header |
Images | emd_21003.png | 57.2 KB | ||
Filedesc metadata | emd-21003.cif.gz | 6.2 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21003 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21003 | HTTPS FTP |
-Related structure data
Related structure data | 6v0vMC 6oemC 6oenC 6oeoC 6oepC 6oeqC 6oerC 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_21003.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of mouse WT RAG1/2 NFC complex (DNA0) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 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 Nick-forming complex (DNA0)
Entire | Name: RAG1/2 Nick-forming complex (DNA0) |
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Components |
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-Supramolecule #1: RAG1/2 Nick-forming complex (DNA0)
Supramolecule | Name: RAG1/2 Nick-forming complex (DNA0) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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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: 1 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 88.524625 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: NCSKIHLSTK LLAVDFPAHF VKSISCQICE HILADPVETS CKHLFCRICI LRCLKVMGSY CPSCRYPCFP TDLESPVKSF LNILNSLMV KCPAQDCNEE VSLEKYNHHV SSHKESKETL VHINKGGRPR QHLLSLTRRA QKHRLRELKI QVKEFADKEE G GDVKAVCL ...String: NCSKIHLSTK LLAVDFPAHF VKSISCQICE HILADPVETS CKHLFCRICI LRCLKVMGSY CPSCRYPCFP TDLESPVKSF LNILNSLMV KCPAQDCNEE VSLEKYNHHV SSHKESKETL VHINKGGRPR QHLLSLTRRA QKHRLRELKI QVKEFADKEE G GDVKAVCL TLFLLALRAR NEHRQADELE AIMQGRGSGL QPAVCLAIRV NTFLSCSQYH KMYRTVKAIT GRQIFQPLHA LR NAEKVLL PGYHPFEWQP PLKNVSSRTD VGIIDGLSGL ASSVDEYPVD TIAKRFRYDS ALVSALMDME EDILEGMRSQ DLD DYLNGP FTVVVKESCD GMGDVSEKHG SGPAVPEKAV RFSFTVMRIT IEHGSQNVKV FEEPKPNSEL CCKPLCLMLA DESD HETLT AILSPLIAER EAMKSSELTL EMGGIPRTFK FIFRGTGYDE KLVREVEGLE ASGSVYICTL CDTTRLEASQ NLVFH SITR SHAENLQRYE VWRSNPYHES VEELRDRVKG VSAKPFIETV PSIDALHCDI GNAAEFYKIF QLEIGEVYKH PNASKE ERK RWQATLDKHL RKRMNLKPIM RMNGNFARKL MTQETVDAVC ELIPSEERHE ALRELMDLYL KMKPVWRSSC PAKECPE SL CQYSFNSQRF AELLSTKFKY RYEGKITNYF HKTLAHVPEI IERDGSIGAW ASEGNESGNK LFRRFRKMNA RQSKCYEM E DVLKHHWLYT SKYLQKFMNA HNALKSSGFT MNSKETLGDP LGIEDSLESQ DSME 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: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Mus musculus (house mouse) |
Molecular weight | Theoretical: 58.158254 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 ARALQAPKRN PPLQKPPMKS LHKKGSGKVL TPAKKS UniProtKB: V(D)J recombination-activating protein 2 |
-Macromolecule #3: DNA (30-MER)
Macromolecule | Name: DNA (30-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 14.268144 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) |
-Macromolecule #4: DNA (30-MER)
Macromolecule | Name: DNA (30-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 14.064058 KDa |
Sequence | String: (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: CALCIUM ION
Macromolecule | Name: CALCIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: CA |
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Molecular weight | Theoretical: 40.078 Da |
-Macromolecule #6: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 6 / Number of copies: 1 / 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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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 45.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 111362 |