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Yorodumi- PDB-8wmm: Structure of CbCas9-PcrIIC1 complex bound to 28-bp DNA substrate ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8wmm | |||||||||
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Title | Structure of CbCas9-PcrIIC1 complex bound to 28-bp DNA substrate (20-nt complementary) | |||||||||
Components |
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Keywords | DNA BINDING PROTEIN/DNA/RNA / Cas9 complex / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA-RNA complex | |||||||||
Function / homology | DNA / DNA (> 10) / RNA / RNA (> 10) / RNA (> 100) Function and homology information | |||||||||
Biological species | Chryseobacterium (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / Resolution: 2.98 Å | |||||||||
Authors | Zhang, S. / Lin, S. / Liu, J.J.G. | |||||||||
Funding support | China, 2items
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Citation | Journal: Nature / Year: 2024 Title: Pro-CRISPR PcrIIC1-associated Cas9 system for enhanced bacterial immunity. Authors: Shouyue Zhang / Ao Sun / Jing-Mei Qian / Shuo Lin / Wenjing Xing / Yun Yang / Han-Zhou Zhu / Xin-Yi Zhou / Yan-Shuo Guo / Yun Liu / Yu Meng / Shu-Lin Jin / Wenhao Song / Cheng-Ping Li / ...Authors: Shouyue Zhang / Ao Sun / Jing-Mei Qian / Shuo Lin / Wenjing Xing / Yun Yang / Han-Zhou Zhu / Xin-Yi Zhou / Yan-Shuo Guo / Yun Liu / Yu Meng / Shu-Lin Jin / Wenhao Song / Cheng-Ping Li / Zhaofu Li / Shuai Jin / Jian-Hua Wang / Meng-Qiu Dong / Caixia Gao / Chunlai Chen / Yang Bai / Jun-Jie Gogo Liu / Abstract: The CRISPR system is an adaptive immune system found in prokaryotes that defends host cells against the invasion of foreign DNA. As part of the ongoing struggle between phages and the bacterial ...The CRISPR system is an adaptive immune system found in prokaryotes that defends host cells against the invasion of foreign DNA. As part of the ongoing struggle between phages and the bacterial immune system, the CRISPR system has evolved into various types, each with distinct functionalities. Type II Cas9 is the most extensively studied of these systems and has diverse subtypes. It remains uncertain whether members of this family can evolve additional mechanisms to counter viral invasions. Here we identify 2,062 complete Cas9 loci, predict the structures of their associated proteins and reveal three structural growth trajectories for type II-C Cas9. We found that novel associated genes (NAGs) tended to be present within the loci of larger II-C Cas9s. Further investigation revealed that CbCas9 from Chryseobacterium species contains a novel β-REC2 domain, and forms a heterotetrameric complex with an NAG-encoded CRISPR-Cas-system-promoting (pro-CRISPR) protein of II-C Cas9 (PcrIIC1). The CbCas9-PcrIIC1 complex exhibits enhanced DNA binding and cleavage activity, broader compatibility for protospacer adjacent motif sequences, increased tolerance for mismatches and improved anti-phage immunity, compared with stand-alone CbCas9. Overall, our work sheds light on the diversity and 'growth evolutionary' trajectories of II-C Cas9 proteins at the structural level, and identifies many NAGs-such as PcrIIC1, which serves as a pro-CRISPR factor to enhance CRISPR-mediated immunity. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8wmm.cif.gz | 725.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8wmm.ent.gz | 574.5 KB | Display | PDB format |
PDBx/mmJSON format | 8wmm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8wmm_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 8wmm_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8wmm_validation.xml.gz | 82.2 KB | Display | |
Data in CIF | 8wmm_validation.cif.gz | 125 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/8wmm ftp://data.pdbj.org/pub/pdb/validation_reports/wm/8wmm | HTTPS FTP |
-Related structure data
Related structure data | 37656MC 8iyqC 8wmhC 8wmnC 8wr4C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 4 molecules ABGH
#1: Protein | Mass: 170029.109 Da / Num. of mol.: 2 / Mutation: D9A; H837A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chryseobacterium (bacteria) / Production host: Escherichia coli (E. coli) #4: Protein | Mass: 15991.991 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chryseobacterium (bacteria) / Production host: Escherichia coli (E. coli) |
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-DNA chain , 2 types, 4 molecules CFSY
#2: DNA chain | Mass: 8450.413 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Chryseobacterium (bacteria) #5: DNA chain | Mass: 8762.670 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Chryseobacterium (bacteria) |
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-RNA chain / Non-polymers , 2 types, 4 molecules DO
#3: RNA chain | Mass: 40936.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Chryseobacterium (bacteria) #6: Chemical | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Structure of CbCas9-PcrIIC1 complex bound to 28-bp DNA substrate (20-nt complementary) Type: COMPLEX / Entity ID: #1-#5 / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 0.4696 MDa / Experimental value: NO |
Source (natural) | Organism: Chryseobacterium (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 Details: 150mM NaCl, 20mM Hepes (pH=7.5), 5mM MgCl2, 1mM Tcep, 0.1% Glycerol |
Buffer component | Conc.: 1 uM / Name: sodium chloride / Formula: NaCl |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: NO |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 1500 nm / Nominal defocus min: 1300 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 355919 / Symmetry type: POINT | ||||||||||||||||||||||||
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