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- EMDB-34809: Streptococcus thermophilus Cas1-Cas2- prespacer ternary complex -
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Open data
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Basic information
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Title | Streptococcus thermophilus Cas1-Cas2- prespacer ternary complex | |||||||||||||||||||||||||||
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![]() | CRISPR / cas / adaptation / IMMUNE SYSTEM | |||||||||||||||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.09 Å | |||||||||||||||||||||||||||
![]() | Chen Q / Luo Y | |||||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: DnaQ mediates directional spacer acquisition in the CRISPR-Cas system by a time-dependent mechanism. Authors: Dongmei Tang / Tingting Jia / Yongbo Luo / Biqin Mou / Jie Cheng / Shiqian Qi / Shaohua Yao / Zhaoming Su / Yamei Yu / Qiang Chen / ![]() Abstract: In the spacer acquisition stage of CRISPR-Cas immunity, spacer orientation and protospacer adjacent motif (PAM) removal are two prerequisites for functional spacer integration. Cas4 has been ...In the spacer acquisition stage of CRISPR-Cas immunity, spacer orientation and protospacer adjacent motif (PAM) removal are two prerequisites for functional spacer integration. Cas4 has been implicated in both processing the prespacer and determining the spacer orientation. In Cas4-lacking systems, host 3'-5' DnaQ family exonucleases were recently reported to play a Cas4-like role. However, the molecular details of DnaQ functions remain elusive. Here, we characterized the spacer acquisition of the adaptation module of the type I-E system, in which a DnaQ domain naturally fuses with Cas2. We presented X-ray crystal structures and cryo-electron microscopy structures of this adaptation module. Our biochemical data showed that DnaQ trimmed PAM-containing and PAM-deficient overhangs with different efficiencies. Based on these results, we proposed a time-dependent model for DnaQ-mediated spacer acquisition to elucidate PAM removal and spacer orientation determination in Cas4-lacking CRISPR-Cas systems. | |||||||||||||||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.2 KB 18.2 KB | Display Display | ![]() |
Images | ![]() | 104.9 KB | ||
Others | ![]() ![]() | 59.5 MB 59.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 12.3 KB | Display | |
Data in CIF | ![]() | 14.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8hi1MC ![]() 8h18C ![]() 8h2fC M: atomic model generated by this map C: citing same article ( |
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Links
EMDB pages | ![]() ![]() |
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Map
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Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_34809_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34809_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Streptococcus thermophilus Cas1-Cas2- prespacer ternary complex
Entire | Name: Streptococcus thermophilus Cas1-Cas2- prespacer ternary complex |
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Components |
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-Supramolecule #1: Streptococcus thermophilus Cas1-Cas2- prespacer ternary complex
Supramolecule | Name: Streptococcus thermophilus Cas1-Cas2- prespacer ternary complex type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: CRISPR-associated endonuclease Cas1
Macromolecule | Name: CRISPR-associated endonuclease Cas1 / type: protein_or_peptide / ID: 1 / Details: WP_024704118.1 / Number of copies: 4 / Enantiomer: LEVO / EC number: Hydrolases; Acting on ester bonds |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 35.54957 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GASGSMVEKN GAKKTSLREL PKISDRVSFI YVEHAKINRV DSAITVLDSR GTVRIPAAMI GVLLLGPGTD ISHRAVELIG DTGTSMVWV GERGVRQYAH GRSLAHSTKF LEKQAKLVSN SRLRLAVARK MYQMRFPDED VSAMTMQQLR GREGARVRRV Y RLQSEKYQ ...String: GASGSMVEKN GAKKTSLREL PKISDRVSFI YVEHAKINRV DSAITVLDSR GTVRIPAAMI GVLLLGPGTD ISHRAVELIG DTGTSMVWV GERGVRQYAH GRSLAHSTKF LEKQAKLVSN SRLRLAVARK MYQMRFPDED VSAMTMQQLR GREGARVRRV Y RLQSEKYQ VSWTKREYNP DDFEGGDIVN QALSAANVAL YGLVHSIVIA LGASPGLGFV HTGHDLSFIY DIADLYKAEL TI PLAFEIA ANFTEIDDIG KIARQKVRDS FVDGKLIVRI VQDIQYLFDL DDDEELLVDT LSLWDDKDML VKHGVSYKEE L |
-Macromolecule #2: Type I-E CRISPR-associated endoribonuclease Cas2
Macromolecule | Name: Type I-E CRISPR-associated endoribonuclease Cas2 / type: protein_or_peptide / ID: 2 / Details: WP_024704117.1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 13.94086 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MPFTVVTLKS VPPSLRGDLT KWMQEIAIGV YVGNFNSRIR EKLWNRIQAN VGEGEATISY YYRNEIGYQF DMINSQKSVV DFDGIPLVL IPNSKTSSEN YPKLGYSNAA KSRKIKRYSS YRG |
-Macromolecule #3: DNA (26-MER)
Macromolecule | Name: DNA (26-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 11.741589 KDa |
Sequence | String: (DA)(DA)(DA)(DC)(DA)(DC)(DC)(DA)(DG)(DA) (DA)(DC)(DG)(DA)(DG)(DT)(DA)(DG)(DT)(DA) (DA)(DA)(DT)(DT)(DG)(DA)(DT)(DG)(DT) (DT)(DG)(DT)(DC)(DT)(DT)(DG)(DC)(DT) |
-Macromolecule #4: DNA (31-MER)
Macromolecule | Name: DNA (31-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 11.708511 KDa |
Sequence | String: (DA)(DT)(DT)(DT)(DA)(DC)(DT)(DA)(DC)(DT) (DC)(DG)(DT)(DT)(DC)(DT)(DG)(DG)(DT)(DG) (DT)(DT)(DT)(DT)(DT)(DG)(DT)(DG)(DT) (DT)(DT)(DA)(DA)(DT)(DG)(DA)(DT)(DG) |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.741 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
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Electron microscopy
Microscope | FEI TITAN |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 49.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.465 µm / Nominal defocus min: 1.213 µm |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 188628 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |