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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | WT CRISPR-Cas12a with a 5bp R-loop | |||||||||
![]() | 5bp 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: 3.4 Å | |||||||||
![]() | Strohkendl I / Taylor DW | |||||||||
Funding support | ![]()
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![]() | ![]() Title: WT CRISPR-Cas12a with a 5bp R-loop 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) | ![]() ![]() | 16.4 KB 16.4 KB | Display Display | ![]() |
Images | ![]() | 58.9 KB | ||
Filedesc metadata | ![]() | 6.4 KB | ||
Others | ![]() ![]() | 116 MB 116 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8sfhMC 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 | 5bp R-loop unsharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.833 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: 5bp R-loop half map A
File | emd_40441_half_map_1.map | ||||||||||||
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Annotation | 5bp R-loop half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: 5bp R-loop half map B
File | emd_40441_half_map_2.map | ||||||||||||
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Annotation | 5bp R-loop half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : WT AsCas12a incubated with 8bp-complementary target DNA.
Entire | Name: WT AsCas12a incubated with 8bp-complementary target DNA. |
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Components |
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-Supramolecule #1: WT AsCas12a incubated with 8bp-complementary target DNA.
Supramolecule | Name: WT AsCas12a incubated with 8bp-complementary target DNA. type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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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: 151.418953 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MTQFEGFTNL YQVSKTLRFE LIPQGKTLKH IQEQGFIEED KARNDHYKEL KPIIDRIYKT YADQCLQLVQ LDWENLSAAI DSYRKEKTE ETRNALIEEQ ATYRNAIHDY FIGRTDNLTD AINKRHAEIY KGLFKAELFN GKVLKQLGTV TTTEHENALL R SFDKFTTY ...String: MTQFEGFTNL YQVSKTLRFE LIPQGKTLKH IQEQGFIEED KARNDHYKEL KPIIDRIYKT YADQCLQLVQ LDWENLSAAI DSYRKEKTE ETRNALIEEQ ATYRNAIHDY FIGRTDNLTD AINKRHAEIY KGLFKAELFN GKVLKQLGTV TTTEHENALL R SFDKFTTY FSGFYENRKN VFSAEDISTA IPHRIVQDNF PKFKENCHIF TRLITAVPSL REHFENVKKA IGIFVSTSIE EV FSFPFYN QLLTQTQIDL YNQLLGGISR EAGTEKIKGL NEVLNLAIQK NDETAHIIAS LPHRFIPLFK QILSDRNTLS FIL EEFKSD EEVIQSFCKY KTLLRNENVL ETAEALFNEL NSIDLTHIFI SHKKLETISS ALCDHWDTLR NALYERRISE LTGK ITKSA KEKVQRSLKH EDINLQEIIS AAGKELSEAF KQKTSEILSH AHAALDQPLP TTLKKQEEKE ILKSQLDSLL GLYHL LDWF AVDESNEVDP EFSARLTGIK LEMEPSLSFY NKARNYATKK PYSVEKFKLN FQMPTLASGW DVNKEKNNGA ILFVKN GLY YLGIMPKQKG RYKALSFEPT EKTSEGFDKM YYDYFPDAAK MIPKCSTQLK AVTAHFQTHT TPILLSNNFI EPLEITK EI YDLNNPEKEP KKFQTAYAKK TGDQKGYREA LCKWIDFTRD FLSKYTKTTS IDLSSLRPSS QYKDLGEYYA ELNPLLYH I SFQRIAEKEI MDAVETGKLY LFQIYNKDFA KGHHGKPNLH TLYWTGLFSP ENLAKTSIKL NGQAELFYRP KSRMKRMAH RLGEKMLNKK LKDQKTPIPD TLYQELYDYV NHRLSHDLSD EARALLPNVI TKEVSHEIIK DRRFTSDKFF FHVPITLNYQ AANSPSKFN QRVNAYLKEH PETPIIGIDR GERNLIYITV IDSTGKILEQ RSLNTIQQFD YQKKLDNREK ERVAARQAWS V VGTIKDLK QGYLSQVIHE IVDLMIHYQA VVVLENLNFG FKSKRTGIAE KAVYQQFEKM LIDKLNCLVL KDYPAEKVGG VL NPYQLTD QFTSFAKMGT QSGFLFYVPA PYTSKIDPLT GFVDPFVWKT IKNHESRKHF LEGFDFLHYD VKTGDFILHF KMN RNLSFQ RGLPGFMPAW DIVFEKNETQ FDAKGTPFIA GKRIVPVIEN HRFTGRYRDL YPANELIALL EEKGIVFRDG SNIL PKLLE NDDSHAIDTM VALIRSVLQM RNSNAATGED YINSPVRDLN GVCFDSRFQN PEWPMDADAN GAYHIALKGQ LLLNH LKES KDLKLQNGIS NQDWLAYIQE LRN UniProtKB: CRISPR-associated endonuclease Cas12a |
-Macromolecule #2: RNA (27-MER)
Macromolecule | Name: RNA (27-MER) / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 8.598088 KDa |
Sequence | String: AAUUUCUACU CUUGUAGAUG UGAUAAG |
-Macromolecule #3: DNA (32-MER)
Macromolecule | Name: DNA (32-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 9.882405 KDa |
Sequence | String: (DA)(DC)(DC)(DG)(DT)(DA)(DA)(DG)(DG)(DT) (DC)(DT)(DT)(DA)(DT)(DC)(DA)(DC)(DT)(DA) (DA)(DA)(DA)(DG)(DA)(DT)(DC)(DG)(DG) (DA)(DA)(DG) |
-Macromolecule #4: DNA (32-MER)
Macromolecule | Name: DNA (32-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 9.797312 KDa |
Sequence | String: (DC)(DT)(DT)(DC)(DC)(DG)(DA)(DT)(DC)(DT) (DT)(DT)(DT)(DA)(DG)(DT)(DG)(DA)(DT)(DA) (DA)(DG)(DA)(DC)(DC)(DT)(DT)(DA)(DC) (DG)(DG)(DT) |
-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 KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 e/Å2 |
Electron beam | Acceleration voltage: 300 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 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: INSILICO MODEL |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 60595 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |