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Yorodumi- EMDB-32548: Cryo-EM structure of the AsCas12f1-sgRNAv1-dsDNA ternary complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32548 | ||||||||||||
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Title | Cryo-EM structure of the AsCas12f1-sgRNAv1-dsDNA ternary complex | ||||||||||||
Map data | |||||||||||||
Sample |
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Keywords | CRISPR / targeting / RNA BINDING PROTEIN-RNA-DNA complex | ||||||||||||
Function / homology | : / Transposase IS605, OrfB, C-terminal / Putative transposase DNA-binding domain / endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / RNA binding / metal ion binding / CRISPR-associated endodeoxyribonuclease Cas12f1 Function and homology information | ||||||||||||
Biological species | Acidibacillus sulfuroxidans (bacteria) / synthetic construct (others) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.69 Å | ||||||||||||
Authors | Wu Z / Liu D | ||||||||||||
Funding support | China, 3 items
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Citation | Journal: To Be Published Title: Structure-directed functional evolution of the miniature CRISPR-AsCas12f1 system Authors: Wu Z / Liu D / Pan D / Shen H / Ji Q | ||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32548.map.gz | 49.5 MB | EMDB map data format | |
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Header (meta data) | emd-32548-v30.xml emd-32548.xml | 13 KB 13 KB | Display Display | EMDB header |
Images | emd_32548.png | 81.1 KB | ||
Filedesc metadata | emd-32548.cif.gz | 5.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32548 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32548 | HTTPS FTP |
-Validation report
Summary document | emd_32548_validation.pdf.gz | 485.7 KB | Display | EMDB validaton report |
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Full document | emd_32548_full_validation.pdf.gz | 485.2 KB | Display | |
Data in XML | emd_32548_validation.xml.gz | 6.2 KB | Display | |
Data in CIF | emd_32548_validation.cif.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32548 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32548 | HTTPS FTP |
-Related structure data
Related structure data | 7wjuMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_32548.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.0773 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
-Entire : AsCas12f1-sgRNAv1-dsDNA ternary complex
Entire | Name: AsCas12f1-sgRNAv1-dsDNA ternary complex |
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Components |
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-Supramolecule #1: AsCas12f1-sgRNAv1-dsDNA ternary complex
Supramolecule | Name: AsCas12f1-sgRNAv1-dsDNA ternary complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Acidibacillus sulfuroxidans (bacteria) |
-Supramolecule #2: AsCas12f1
Supramolecule | Name: AsCas12f1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: synthetic construct (others) |
-Supramolecule #3: sgRNA1
Supramolecule | Name: sgRNA1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: synthetic construct (others) |
-Supramolecule #4: dsDNA
Supramolecule | Name: dsDNA / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3-#4 |
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-Macromolecule #1: OrfB_Zn_ribbon domain-containing protein
Macromolecule | Name: OrfB_Zn_ribbon domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Acidibacillus sulfuroxidans (bacteria) |
Molecular weight | Theoretical: 48.719742 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MIKVYRYEIV KPLDLDWKEF GTILRQLQQE TRFALNKATQ LAWEWMGFSS DYKDNHGEYP KSKDILGYTN VHGYAYHTIK TKAYRLNSG NLSQTIKRAT DRFKAYQKEI LRGDMSIPSY KRDIPLDLIK ENISVNRMNH GDYIASLSLL SNPAKQEMNV K RKISVIII ...String: MIKVYRYEIV KPLDLDWKEF GTILRQLQQE TRFALNKATQ LAWEWMGFSS DYKDNHGEYP KSKDILGYTN VHGYAYHTIK TKAYRLNSG NLSQTIKRAT DRFKAYQKEI LRGDMSIPSY KRDIPLDLIK ENISVNRMNH GDYIASLSLL SNPAKQEMNV K RKISVIII VRGAGKTIMD RILSGEYQVS ASQIIHDDRK NKWYLNISYD FEPQTRVLDL NKIMGIALGV AVAVYMAFQH TP ARYKLEG GEIENFRRQV ESRRISMLRQ GKYAGGARGG HGRDKRIKPI EQLRDKIANF RDTTNHRYSR YIVDMAIKEG CGT IQMEDL TNIRDIGSRF LQNWTYYDLQ QKIIYKAEEA GIKVIKIDPQ YTSQRCSECG NIDSGNRIGQ AIFKCRACGY EANA DYNAA RNIAIPNIDK IIAESIK UniProtKB: CRISPR-associated endodeoxyribonuclease Cas12f1 |
-Macromolecule #2: sgRNAv1
Macromolecule | Name: sgRNAv1 / type: rna / ID: 2 / Number of copies: 1 |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 61.643578 KDa |
Sequence | String: AUUCGUCGGU UCAGCGACGA UAAGCCGAGA AGUGCCAAUA AAACUGUUAA GUGGUUUGGU AACGCUCGGU AAGGUAGCCA AAAGGCUGA AACUCCGUGC ACAAAGACCG CACGGACGCU UCACAUAUAG CUCAUAAACA AGGGUUUGCG AGCUAGCUUG U GGAGUGUG AACCUGGCGU UUUUCCAUAG GCU |
-Macromolecule #3: Target strand
Macromolecule | Name: Target strand / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 9.260985 KDa |
Sequence | String: (DG)(DC)(DG)(DG)(DA)(DG)(DC)(DC)(DT)(DA) (DT)(DG)(DG)(DA)(DA)(DA)(DA)(DA)(DC)(DG) (DC)(DC)(DA)(DG)(DC)(DA)(DA)(DC)(DG) (DC) |
-Macromolecule #4: Non-target strand
Macromolecule | Name: Non-target strand / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 1.840227 KDa |
Sequence | String: (DG)(DC)(DG)(DT)(DT)(DG) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.5 µm |
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: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1770878 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |