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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Streptococcus thermophilus Cas1-Cas2-DnaQ-prespacer complex | |||||||||
![]() | Streptococcus thermophilus Cas1-Cas2-DnaQ-prespacer complex, conformation1 | |||||||||
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![]() | CRISPR-Cas / adaptation / IMMUNE SYSTEM | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.92 Å | |||||||||
![]() | Chen Q / Yu Y / Luo Y | |||||||||
Funding support | 1 items
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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 | ![]() | 40.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.5 KB 14.5 KB | Display Display | ![]() |
Images | ![]() | 27 KB | ||
Others | ![]() ![]() | 39.8 MB 39.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 11.4 KB | Display | |
Data in CIF | ![]() | 13.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | Streptococcus thermophilus Cas1-Cas2-DnaQ-prespacer complex, conformation1 | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.84 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: the first half map of conformation1
File | emd_34810_half_map_1.map | ||||||||||||
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Annotation | the first half map of conformation1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: the second half map of conformation1
File | emd_34810_half_map_2.map | ||||||||||||
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Annotation | the second half map of conformation1 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Cas1-Cas2-DnaQ-prespacer complex
Entire | Name: Cas1-Cas2-DnaQ-prespacer complex |
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Components |
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-Supramolecule #1: Cas1-Cas2-DnaQ-prespacer complex
Supramolecule | Name: Cas1-Cas2-DnaQ-prespacer complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Cas1
Macromolecule | Name: Cas1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: GASGSMVEKN GAKKTSLREL PKISDRVSFI YVEHAKINRV DSAITVLDSR GTVRIPAAMI GVLLLGPGTD ISHRAVELIG DTGTSMVWVG ERGVRQYAHG RSLAHSTKFL EKQAKLVSNS RLRLAVARKM YQMRFPDEDV SAMTMQQLRG REGARVRRVY RLQSEKYQVS ...String: GASGSMVEKN GAKKTSLREL PKISDRVSFI YVEHAKINRV DSAITVLDSR GTVRIPAAMI GVLLLGPGTD ISHRAVELIG DTGTSMVWVG ERGVRQYAHG RSLAHSTKFL EKQAKLVSNS RLRLAVARKM YQMRFPDEDV SAMTMQQLRG REGARVRRVY RLQSEKYQVS WTKREYNPDD FEGGDIVNQA LSAANVALYG LVHSIVIALG ASPGLGFVHT GHDLSFIYDI ADLYKAELTI PLAFEIAANF TEIDDIGKIA RQKVRDSFVD GKLIVRIVQD IQYLFDLDDD EELLVDTLSL WDDKDMLVKH GVSYKEEL |
-Macromolecule #2: Cas2-DnaQ
Macromolecule | Name: Cas2-DnaQ / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MPFTVVTLKS VPPSLRGDLT KWMQEIAIGV YVGNFNSRIR EKLWNRIQAN VGEGEATISY YYRNEIGYQF DMINSQKSVV DFDGIPLVLI PNSKTSSENY PKLGYSNAAK SRKIKRYSSY RGPQANSLKP YVVIDIETDG LDEKKNTIIE IGAVKFNGQQ VEEFNALIKY ...String: MPFTVVTLKS VPPSLRGDLT KWMQEIAIGV YVGNFNSRIR EKLWNRIQAN VGEGEATISY YYRNEIGYQF DMINSQKSVV DFDGIPLVLI PNSKTSSENY PKLGYSNAAK SRKIKRYSSY RGPQANSLKP YVVIDIETDG LDEKKNTIIE IGAVKFNGQQ VEEFNALIKY EEKLPPTIFK LTGISKSLLD QEGRDLKEVL SEFLLFIGDL TLVGYNIHFD IQFINNKLNK FGLPLLINKT HDIMRYVKDE KLFLDNYQLQ TALKSYGIED SVPHRALKDA RLIYHLSTKV NKFLARMKEK S |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GRAPHENE OXIDE / Mesh: 300 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.1500 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 65.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.465 µm / Nominal defocus min: 1.213 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 30496 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |