+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35926 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the AsCas12f-YHAM-sgRNAS3-5v7-target DNA | |||||||||
Map data | ||||||||||
Sample |
| |||||||||
Keywords | CRISPR-Cas / RNA BINDING PROTEIN-DNA COMPLEX / RNA BINDING PROTEIN / RNA BINDING PROTEIN-DNA-RNA 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 | Sulfoacidibacillus thermotolerans (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.91 Å | |||||||||
Authors | Hino T / Omura NS / Nakagawa R / Togashi T / Takeda NS / Hiramoto T / Tasaka S / Hirano H / Tokuyama T / Uosaki H ...Hino T / Omura NS / Nakagawa R / Togashi T / Takeda NS / Hiramoto T / Tasaka S / Hirano H / Tokuyama T / Uosaki H / Ishiguro H / Yamano H / Ozaki Y / Motooka D / Mori H / Kirita Y / Kise Y / Itoh Y / Matoba S / Aburatani H / Yachie N / Siksnys V / Ohmori T / Hoshino A / Nureki O | |||||||||
Funding support | Japan, 1 items
| |||||||||
Citation | Journal: To Be Published Title: Minimal and most efficient genome editing Cas enzyme Authors: Hino T / Omura NS / Nakagawa R / Togashi T / Takeda NS / Hiramoto T / Tasaka S / Hirano H / Tokuyama T / Uosaki H / Ishiguro H / Yamano H / Ozaki Y / Motooka D / Mori H / Kirita Y / Kise Y / ...Authors: Hino T / Omura NS / Nakagawa R / Togashi T / Takeda NS / Hiramoto T / Tasaka S / Hirano H / Tokuyama T / Uosaki H / Ishiguro H / Yamano H / Ozaki Y / Motooka D / Mori H / Kirita Y / Kise Y / Itoh Y / Matoba S / Aburatani H / Yachie N / Siksnys V / Ohmori T / Hoshino A / Nureki O | |||||||||
History |
|
-Structure visualization
Supplemental images |
---|
-Downloads & links
-EMDB archive
Map data | emd_35926.map.gz | 4.5 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-35926-v30.xml emd-35926.xml | 17.9 KB 17.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_35926_fsc.xml | 6.5 KB | Display | FSC data file |
Images | emd_35926.png | 140.8 KB | ||
Others | emd_35926_half_map_1.map.gz emd_35926_half_map_2.map.gz | 4.5 MB 4.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35926 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35926 | HTTPS FTP |
-Validation report
Summary document | emd_35926_validation.pdf.gz | 711.2 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_35926_full_validation.pdf.gz | 710.8 KB | Display | |
Data in XML | emd_35926_validation.xml.gz | 11.2 KB | Display | |
Data in CIF | emd_35926_validation.cif.gz | 14.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35926 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35926 | HTTPS FTP |
-Related structure data
Related structure data | 8j1jMC 8j12C 8j3rC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_35926.map.gz / Format: CCP4 / Size: 4.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Voxel size | X=Y=Z: 1.328 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Half map: #2
File | emd_35926_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_35926_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : AsCas12f-YHAM-sgRNAS3-5v7-target DNA
Entire | Name: AsCas12f-YHAM-sgRNAS3-5v7-target DNA |
---|---|
Components |
|
-Supramolecule #1: AsCas12f-YHAM-sgRNAS3-5v7-target DNA
Supramolecule | Name: AsCas12f-YHAM-sgRNAS3-5v7-target DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
---|---|
Source (natural) | Organism: Sulfoacidibacillus thermotolerans (bacteria) |
-Macromolecule #1: Transposase IS605 OrfB C-terminal domain-containing protein
Macromolecule | Name: Transposase IS605 OrfB C-terminal domain-containing protein type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: Sulfoacidibacillus thermotolerans (bacteria) |
Molecular weight | Theoretical: 49.966105 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MGHHHHHHGS MIKVYRYEIV KPLDLDWKEF GTILRQLQQE TRFALNKATQ LAWEWMGYSS DYKDNHGEYP KSKDILGYTN VHGYAYHTI KTKAYRLNSG NLSQTIKRAT DRFKAYQKEI LRGDMSIPSY KRDIPLDLIK ENISVNRMNH GDYIASLSLL S NPAKQEMN ...String: MGHHHHHHGS MIKVYRYEIV KPLDLDWKEF GTILRQLQQE TRFALNKATQ LAWEWMGYSS DYKDNHGEYP KSKDILGYTN VHGYAYHTI KTKAYRLNSG NLSQTIKRAT DRFKAYQKEI LRGDMSIPSY KRDIPLDLIK ENISVNRMNH GDYIASLSLL S NPAKQEMN VKRKISVIII VRGAGKTIMD RILSGEYQVH ASQIIHDDRK NKWYLNISYD FEPQTRVLDL NKIMGIDLGV AV AAYMAFQ HTPARYKLEG GEIENFRRQV ESRRISMLRQ GKYAGGARGG HGRDKRIKPI EQLRDKIANF RDTTNHRYSR YIV DMAIKM GCGTIQMEDL TNIRDIGSRF LQNWTYYDLQ QKIIYKAEEA GIKVIKIDPQ YTSQRCSECG NIDSGNRIGQ AIFK CRACG YEANADYNAA RNIAIPNIDK IIAESIK UniProtKB: CRISPR-associated endodeoxyribonuclease Cas12f1 |
-Macromolecule #2: DNA (38-MER)
Macromolecule | Name: DNA (38-MER) / type: dna / ID: 2 / Number of copies: 1 / Classification: DNA |
---|---|
Source (natural) | Organism: Sulfoacidibacillus thermotolerans (bacteria) |
Molecular weight | Theoretical: 11.694576 KDa |
Sequence | String: (DG)(DA)(DA)(DT)(DG)(DG)(DT)(DT)(DC)(DA) (DA)(DG)(DC)(DG)(DC)(DA)(DC)(DC)(DT)(DA) (DA)(DT)(DT)(DT)(DC)(DC)(DT)(DA)(DA) (DA)(DT)(DT)(DA)(DG)(DA)(DA)(DA)(DA) |
-Macromolecule #3: DNA (38-MER)
Macromolecule | Name: DNA (38-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
---|---|
Source (natural) | Organism: Sulfoacidibacillus thermotolerans (bacteria) |
Molecular weight | Theoretical: 11.689535 KDa |
Sequence | String: (DT)(DT)(DT)(DT)(DC)(DT)(DA)(DA)(DT)(DT) (DT)(DA)(DG)(DG)(DA)(DA)(DA)(DT)(DT)(DA) (DG)(DG)(DT)(DG)(DC)(DG)(DC)(DT)(DT) (DG)(DA)(DA)(DC)(DC)(DA)(DT)(DT)(DC) |
-Macromolecule #4: RNA (118-MER)
Macromolecule | Name: RNA (118-MER) / type: rna / ID: 4 / Number of copies: 1 |
---|---|
Source (natural) | Organism: Sulfoacidibacillus thermotolerans (bacteria) |
Molecular weight | Theoretical: 38.288805 KDa |
Sequence | String: GGAUUCGUCG GUUCAGCGAC GAUAAGCCGA GAAGUGCCAA UAAAACUGUU AAGUGGUUUG GUAACGCUCG GUAAGGUCCG AAAGGAGAA CCACUGAACG GAAAUUAGGU GCGCUUGGC |
-Macromolecule #5: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: ZN |
---|---|
Molecular weight | Theoretical: 65.409 Da |
-Macromolecule #6: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 2 / Formula: MG |
---|---|
Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
---|---|
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (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: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |