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- EMDB-40446: WT CRISPR-Cas12a with a 20bp R-loop and nontarget strand in the R... -
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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | WT CRISPR-Cas12a with a 20bp R-loop and nontarget strand in the RuvC active site. | |||||||||
![]() | 20bp R-loop unsharpened map | |||||||||
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![]() | CRISPR / R-loop / endonuclease / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA-RNA complex | |||||||||
Function / homology | ![]() Bacillus subtilis ribonuclease / : / deoxyribonuclease I / deoxyribonuclease I activity / defense response to virus / lyase activity / DNA binding / RNA binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
![]() | Strohkendl I / Taylor DW | |||||||||
Funding support | ![]()
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![]() | ![]() Title: WT CRISPR-Cas12a with a 20bp R-loop and nontarget strand in the RuvC active site. Authors: Strohkendl I / Taylor DW | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 62.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 17.1 KB 17.1 KB | Display Display | ![]() |
Images | ![]() | 57 KB | ||
Filedesc metadata | ![]() | 6.5 KB | ||
Others | ![]() ![]() | 116.2 MB 116.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8sfoMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | 20bp R-loop unsharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.94 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: 20bp R-loop half map A
File | emd_40446_half_map_1.map | ||||||||||||
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Annotation | 20bp R-loop half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: 20bp R-loop half map B
File | emd_40446_half_map_2.map | ||||||||||||
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Annotation | 20bp R-loop half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : WT AsCas12a incubated with 20bp-complementary target DNA.
Entire | Name: WT AsCas12a incubated with 20bp-complementary target DNA. |
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Components |
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-Supramolecule #1: WT AsCas12a incubated with 20bp-complementary target DNA.
Supramolecule | Name: WT AsCas12a incubated with 20bp-complementary target DNA. type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: CRISPR-associated endonuclease Cas12a
Macromolecule | Name: CRISPR-associated endonuclease Cas12a / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: deoxyribonuclease I |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 151.705234 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GAASMTQFEG FTNLYQVSKT LRFELIPQGK TLKHIQEQGF IEEDKARNDH YKELKPIIDR IYKTYADQCL QLVQLDWENL SAAIDSYRK EKTEETRNAL IEEQATYRNA IHDYFIGRTD NLTDAINKRH AEIYKGLFKA ELFNGKVLKQ LGTVTTTEHE N ALLRSFDK ...String: GAASMTQFEG FTNLYQVSKT LRFELIPQGK TLKHIQEQGF IEEDKARNDH YKELKPIIDR IYKTYADQCL QLVQLDWENL SAAIDSYRK EKTEETRNAL IEEQATYRNA IHDYFIGRTD NLTDAINKRH AEIYKGLFKA ELFNGKVLKQ LGTVTTTEHE N ALLRSFDK FTTYFSGFYE NRKNVFSAED ISTAIPHRIV QDNFPKFKEN CHIFTRLITA VPSLREHFEN VKKAIGIFVS TS IEEVFSF PFYNQLLTQT QIDLYNQLLG GISREAGTEK IKGLNEVLNL AIQKNDETAH IIASLPHRFI PLFKQILSDR NTL SFILEE FKSDEEVIQS FCKYKTLLRN ENVLETAEAL FNELNSIDLT HIFISHKKLE TISSALCDHW DTLRNALYER RISE LTGKI TKSAKEKVQR SLKHEDINLQ EIISAAGKEL SEAFKQKTSE ILSHAHAALD QPLPTTLKKQ EEKEILKSQL DSLLG LYHL LDWFAVDESN EVDPEFSARL TGIKLEMEPS LSFYNKARNY ATKKPYSVEK FKLNFQMPTL ASGWDVNKEK NNGAIL FVK NGLYYLGIMP KQKGRYKALS FEPTEKTSEG FDKMYYDYFP DAAKMIPKCS TQLKAVTAHF QTHTTPILLS NNFIEPL EI TKEIYDLNNP EKEPKKFQTA YAKKTGDQKG YREALCKWID FTRDFLSKYT KTTSIDLSSL RPSSQYKDLG EYYAELNP L LYHISFQRIA EKEIMDAVET GKLYLFQIYN KDFAKGHHGK PNLHTLYWTG LFSPENLAKT SIKLNGQAEL FYRPKSRMK RMAHRLGEKM LNKKLKDQKT PIPDTLYQEL YDYVNHRLSH DLSDEARALL PNVITKEVSH EIIKDRRFTS DKFFFHVPIT LNYQAANSP SKFNQRVNAY LKEHPETPII GIDRGERNLI YITVIDSTGK ILEQRSLNTI QQFDYQKKLD NREKERVAAR Q AWSVVGTI KDLKQGYLSQ VIHEIVDLMI HYQAVVVLEN LNFGFKSKRT GIAEKAVYQQ FEKMLIDKLN CLVLKDYPAE KV GGVLNPY QLTDQFTSFA KMGTQSGFLF YVPAPYTSKI DPLTGFVDPF VWKTIKNHES RKHFLEGFDF LHYDVKTGDF ILH FKMNRN LSFQRGLPGF MPAWDIVFEK NETQFDAKGT PFIAGKRIVP VIENHRFTGR YRDLYPANEL IALLEEKGIV FRDG SNILP KLLENDDSHA IDTMVALIRS VLQMRNSNAA TGEDYINSPV RDLNGVCFDS RFQNPEWPMD ADANGAYHIA LKGQL LLNH LKESKDLKLQ NGISNQDWLA YIQELRN UniProtKB: CRISPR-associated endonuclease Cas12a |
-Macromolecule #2: RNA (39-MER)
Macromolecule | Name: RNA (39-MER) / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 15.351995 KDa |
Sequence | String: UUUUUAAUUU CUACUCUUGU AGAUGUGAUA AGUGGAAUGC CAUGUGGA |
-Macromolecule #3: DNA (40-MER)
Macromolecule | Name: DNA (40-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 17.211082 KDa |
Sequence | String: (DA)(DG)(DC)(DA)(DC)(DA)(DG)(DT)(DA)(DG) (DC)(DT)(DA)(DC)(DT)(DC)(DC)(DA)(DC)(DA) (DT)(DG)(DG)(DC)(DA)(DT)(DT)(DC)(DC) (DA)(DC)(DT)(DT)(DA)(DT)(DC)(DA)(DC)(DT) (DA) (DA)(DA)(DA)(DG)(DA)(DT) ...String: (DA)(DG)(DC)(DA)(DC)(DA)(DG)(DT)(DA)(DG) (DC)(DT)(DA)(DC)(DT)(DC)(DC)(DA)(DC)(DA) (DT)(DG)(DG)(DC)(DA)(DT)(DT)(DC)(DC) (DA)(DC)(DT)(DT)(DA)(DT)(DC)(DA)(DC)(DT) (DA) (DA)(DA)(DA)(DG)(DA)(DT)(DC)(DG) (DG)(DA)(DA)(DG)(DA)(DG)(DC)(DG) |
-Macromolecule #4: DNA (35-MER)
Macromolecule | Name: DNA (35-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 17.299061 KDa |
Sequence | String: (DC)(DG)(DC)(DT)(DC)(DT)(DT)(DC)(DC)(DG) (DA)(DT)(DC)(DT)(DT)(DT)(DT)(DA)(DG)(DT) (DG)(DA)(DT)(DA)(DA)(DG)(DT)(DG)(DG) (DA)(DA)(DT)(DG)(DC)(DC)(DA)(DT)(DG)(DT) (DG) (DG)(DA)(DG)(DT)(DA)(DG) ...String: (DC)(DG)(DC)(DT)(DC)(DT)(DT)(DC)(DC)(DG) (DA)(DT)(DC)(DT)(DT)(DT)(DT)(DA)(DG)(DT) (DG)(DA)(DT)(DA)(DA)(DG)(DT)(DG)(DG) (DA)(DA)(DT)(DG)(DC)(DC)(DA)(DT)(DG)(DT) (DG) (DG)(DA)(DG)(DT)(DA)(DG)(DC)(DT) (DA)(DC)(DT)(DG)(DT)(DG)(DC)(DT) |
-Macromolecule #5: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 7 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 49.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm |
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Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 154794 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |