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s2 cryo em image processing  (Thermo Fisher)


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    Thermo Fisher s2 cryo em image processing
    ( A ) Co-immunoprecipitation assays to test self-association of NRC2 and ZAR1 from N. benthamiana . C-terminally 3xFLAG-tagged NbNRC2 and NbZAR1 proteins were coexpressed with C-terminally 4xMyc tagged NbNRC2 or NbZAR1. Immunoprecipitations were performed with agarose beads conjugated to FLAG antibodies (FLAG IP). Total protein extracts were immunoblotted with the antisera labelled on the left. Approximate molecular weights (in kDa) of the proteins are shown on the right. Protein loading control was carried out using Ponceau stain (PS). The experiment was performed three times with similar results. ( B ) 2D classifications from negative staining transmission electron microscopy images of affinity-purified NbNRC2. NRC2 appears as a dimer, with a maximum dimension of approximately 150 Å at its widest point. Scale bar = 230 Å. ( C ) <t>Cryo-EM</t> structure of resting state of NRC2 dimers. Atomic model corresponding to NRC2 homodimer shown in two orthogonal views, with resolved NB domain (NBD), HD1-WHD and LRR domains. Notably, the N-terminal CC domain of NRC2 was absent from the Cryo-EM density. Inset shows details of interfaces between the two NRC2 protomers, highlighting amino acid stretches corresponding to three contact interfaces. ( D ) Color coding of the domains is shown in the schematic representation of the domain architecture and boundaries of NRC2, which includes the exact boundaries of the amino acid stretches at the dimerization interfaces. A schematic representation of the pipeline used for Cryo-EM imaging, data processing and model building can be found in Fig. <t>S2</t> . Additional views of the structure and dimerization interface can be found in Fig. S3, Fig. S4 and Movie S1 . Additional information on image processing and model building can be found in Table S1 .
    S2 Cryo Em Image Processing, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 99/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/cryo+em+image+processing/SUCROSE+EP%2FBP%2FNF+12KG/bio_rxiv__2023__12__17__572070-278-20-21
    Average 99 stars, based on 1 article reviews
    s2 cryo em image processing - by Bioz Stars, 2026-09
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    Images

    1) Product Images from "Activation of plant immunity through conversion of a helper NLR homodimer into a resistosome"

    Article Title: Activation of plant immunity through conversion of a helper NLR homodimer into a resistosome

    Journal: bioRxiv

    doi: 10.1101/2023.12.17.572070

    ( A ) Co-immunoprecipitation assays to test self-association of NRC2 and ZAR1 from N. benthamiana . C-terminally 3xFLAG-tagged NbNRC2 and NbZAR1 proteins were coexpressed with C-terminally 4xMyc tagged NbNRC2 or NbZAR1. Immunoprecipitations were performed with agarose beads conjugated to FLAG antibodies (FLAG IP). Total protein extracts were immunoblotted with the antisera labelled on the left. Approximate molecular weights (in kDa) of the proteins are shown on the right. Protein loading control was carried out using Ponceau stain (PS). The experiment was performed three times with similar results. ( B ) 2D classifications from negative staining transmission electron microscopy images of affinity-purified NbNRC2. NRC2 appears as a dimer, with a maximum dimension of approximately 150 Å at its widest point. Scale bar = 230 Å. ( C ) Cryo-EM structure of resting state of NRC2 dimers. Atomic model corresponding to NRC2 homodimer shown in two orthogonal views, with resolved NB domain (NBD), HD1-WHD and LRR domains. Notably, the N-terminal CC domain of NRC2 was absent from the Cryo-EM density. Inset shows details of interfaces between the two NRC2 protomers, highlighting amino acid stretches corresponding to three contact interfaces. ( D ) Color coding of the domains is shown in the schematic representation of the domain architecture and boundaries of NRC2, which includes the exact boundaries of the amino acid stretches at the dimerization interfaces. A schematic representation of the pipeline used for Cryo-EM imaging, data processing and model building can be found in Fig. S2 . Additional views of the structure and dimerization interface can be found in Fig. S3, Fig. S4 and Movie S1 . Additional information on image processing and model building can be found in Table S1 .
    Figure Legend Snippet: ( A ) Co-immunoprecipitation assays to test self-association of NRC2 and ZAR1 from N. benthamiana . C-terminally 3xFLAG-tagged NbNRC2 and NbZAR1 proteins were coexpressed with C-terminally 4xMyc tagged NbNRC2 or NbZAR1. Immunoprecipitations were performed with agarose beads conjugated to FLAG antibodies (FLAG IP). Total protein extracts were immunoblotted with the antisera labelled on the left. Approximate molecular weights (in kDa) of the proteins are shown on the right. Protein loading control was carried out using Ponceau stain (PS). The experiment was performed three times with similar results. ( B ) 2D classifications from negative staining transmission electron microscopy images of affinity-purified NbNRC2. NRC2 appears as a dimer, with a maximum dimension of approximately 150 Å at its widest point. Scale bar = 230 Å. ( C ) Cryo-EM structure of resting state of NRC2 dimers. Atomic model corresponding to NRC2 homodimer shown in two orthogonal views, with resolved NB domain (NBD), HD1-WHD and LRR domains. Notably, the N-terminal CC domain of NRC2 was absent from the Cryo-EM density. Inset shows details of interfaces between the two NRC2 protomers, highlighting amino acid stretches corresponding to three contact interfaces. ( D ) Color coding of the domains is shown in the schematic representation of the domain architecture and boundaries of NRC2, which includes the exact boundaries of the amino acid stretches at the dimerization interfaces. A schematic representation of the pipeline used for Cryo-EM imaging, data processing and model building can be found in Fig. S2 . Additional views of the structure and dimerization interface can be found in Fig. S3, Fig. S4 and Movie S1 . Additional information on image processing and model building can be found in Table S1 .

    Techniques Used: Immunoprecipitation, Staining, Negative Staining, Transmission Assay, Electron Microscopy, Affinity Purification, Cryo-EM Sample Prep, Imaging


    Figure Legend Snippet:

    Techniques Used:

    Related Articles

    other:

    Article Title: Insights into the dual functions of AcrIF14 during the inhibition of type I-F CRISPR–Cas surveillance complex
    Article Snippet: Figure S6 Cryo-EM image processing for the Csy-AcrIF14-dsDNASP complex (A) A representative raw cryo-EM micrograph of the Csy-AcrIF14-dsDNASP complex. (B) Representative processing pipeline includes 2D class averages, 3D classification and refinement of cryo-EM particles. (C) Local resolution estimation and Euler angle distribution of the map. (D) Plot of the global FSC indicates an average resolution of 3.11 Å.

    Article Title: Inhibitory mechanism of CRISPR-Cas9 by AcrIIC4.
    Article Snippet: Details of the cryo-EM image processing is summarized in Supplementary Table S2.

    Article Title: Cryo-electron microscopy structure and potential enzymatic function of human six-transmembrane epithelial antigen of the prostate 1 (STEAP1)
    Article Snippet: A B D F 616,302 particles 3D classification (C1 sym) 7.7 Å 42% 12.3 Å 26% 10.3 Å 25% 10.0 Å 5% 11.9 Å 2% C 262,939 particles 1) CTF refinement (Relion 3.0) 2) Bayesian Polishing (Relion 3.0) 3) 3D Classification without image alignment (C1 sym, tau2fudge 8) 4.4 Å 66% 5.3 Å 22% 7.0 Å 13% 172,724 particles 1) 2nd CTF refinement (Relion3.0) 2) 2D Classification 172,293 particles 3D Auto-Refinement (C3 sym) Unmasked: 3.80 Å Masked: 3.47 Å 1) CTF refinement (Relion 3.1b) 2) Bayesian Polishing (Relion 3.1b) Repeat 3x 3) 3D Classification without image alignment (C1) 169,426 particles 3D Auto-Refinement (C3 sym) Unmasked: 3.32 Å Masked: 2.97 Å 0.0 0.1 0.2 0.3 0.4 0.5 0.0 0.2 0.4 0.6 0.8 1.0 2.97 Å 0.143 Unmasked Corrected, masked Phase randomized 1/resolution (Å) F o u ri e r S h e ll C o rr e la ti o n E Figure S2: Cryo-EM image processing. (A) Micrograph depicting STEAP1-Fab120.545 particles distributed in vitreous ice.

    Article Title: Insights into the dual functions of AcrIF14 during the inhibition of type I-F CRISPR–Cas surveillance complex
    Article Snippet: Figure S2 Cryo-EM image processing for the Csy-AcrIF14 complex (A) A representative raw cryo-EM micrograph of the Csy-AcrIF14 complex. (B) Representative processing pipeline includes 2D class averages, 3D classification and refinement of cryo-EM particles. (C) Local resolution estimation and Euler angle distribution of the map. (D) Plot of the global FSC indicates an average resolution of 3.43 Å.

    Generated:

    Article Title: Structure of the human ClC-1 chloride channel.
    Article Snippet: .. CLC, chloride channelGUV, giant unilamellar vesicle; 9-AC, 9-anthracene-carboxylic acid. (TIF) PLOS Biology | https://doi.org/10.1371/journal.pbio.3000218 April 25, 2019 13 / 20 S2 Fig. Cryo-EM image processing for the pH 7.5 and 6.2 data sets. (a) The 4 maps (Maps 0–3, respectively) generated using the pH 7.5. ..



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    ( A ) Co-immunoprecipitation assays to test self-association of NRC2 and ZAR1 from N. benthamiana . C-terminally 3xFLAG-tagged NbNRC2 and NbZAR1 proteins were coexpressed with C-terminally 4xMyc tagged NbNRC2 or NbZAR1. Immunoprecipitations were performed with agarose beads conjugated to FLAG antibodies (FLAG IP). Total protein extracts were immunoblotted with the antisera labelled on the left. Approximate molecular weights (in kDa) of the proteins are shown on the right. Protein loading control was carried out using Ponceau stain (PS). The experiment was performed three times with similar results. ( B ) 2D classifications from negative staining transmission electron microscopy images of affinity-purified NbNRC2. NRC2 appears as a dimer, with a maximum dimension of approximately 150 Å at its widest point. Scale bar = 230 Å. ( C ) <t>Cryo-EM</t> structure of resting state of NRC2 dimers. Atomic model corresponding to NRC2 homodimer shown in two orthogonal views, with resolved NB domain (NBD), HD1-WHD and LRR domains. Notably, the N-terminal CC domain of NRC2 was absent from the Cryo-EM density. Inset shows details of interfaces between the two NRC2 protomers, highlighting amino acid stretches corresponding to three contact interfaces. ( D ) Color coding of the domains is shown in the schematic representation of the domain architecture and boundaries of NRC2, which includes the exact boundaries of the amino acid stretches at the dimerization interfaces. A schematic representation of the pipeline used for Cryo-EM imaging, data processing and model building can be found in Fig. <t>S2</t> . Additional views of the structure and dimerization interface can be found in Fig. S3, Fig. S4 and Movie S1 . Additional information on image processing and model building can be found in Table S1 .
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    Image Search Results


    ( A ) Co-immunoprecipitation assays to test self-association of NRC2 and ZAR1 from N. benthamiana . C-terminally 3xFLAG-tagged NbNRC2 and NbZAR1 proteins were coexpressed with C-terminally 4xMyc tagged NbNRC2 or NbZAR1. Immunoprecipitations were performed with agarose beads conjugated to FLAG antibodies (FLAG IP). Total protein extracts were immunoblotted with the antisera labelled on the left. Approximate molecular weights (in kDa) of the proteins are shown on the right. Protein loading control was carried out using Ponceau stain (PS). The experiment was performed three times with similar results. ( B ) 2D classifications from negative staining transmission electron microscopy images of affinity-purified NbNRC2. NRC2 appears as a dimer, with a maximum dimension of approximately 150 Å at its widest point. Scale bar = 230 Å. ( C ) Cryo-EM structure of resting state of NRC2 dimers. Atomic model corresponding to NRC2 homodimer shown in two orthogonal views, with resolved NB domain (NBD), HD1-WHD and LRR domains. Notably, the N-terminal CC domain of NRC2 was absent from the Cryo-EM density. Inset shows details of interfaces between the two NRC2 protomers, highlighting amino acid stretches corresponding to three contact interfaces. ( D ) Color coding of the domains is shown in the schematic representation of the domain architecture and boundaries of NRC2, which includes the exact boundaries of the amino acid stretches at the dimerization interfaces. A schematic representation of the pipeline used for Cryo-EM imaging, data processing and model building can be found in Fig. S2 . Additional views of the structure and dimerization interface can be found in Fig. S3, Fig. S4 and Movie S1 . Additional information on image processing and model building can be found in Table S1 .

    Journal: bioRxiv

    Article Title: Activation of plant immunity through conversion of a helper NLR homodimer into a resistosome

    doi: 10.1101/2023.12.17.572070

    Figure Lengend Snippet: ( A ) Co-immunoprecipitation assays to test self-association of NRC2 and ZAR1 from N. benthamiana . C-terminally 3xFLAG-tagged NbNRC2 and NbZAR1 proteins were coexpressed with C-terminally 4xMyc tagged NbNRC2 or NbZAR1. Immunoprecipitations were performed with agarose beads conjugated to FLAG antibodies (FLAG IP). Total protein extracts were immunoblotted with the antisera labelled on the left. Approximate molecular weights (in kDa) of the proteins are shown on the right. Protein loading control was carried out using Ponceau stain (PS). The experiment was performed three times with similar results. ( B ) 2D classifications from negative staining transmission electron microscopy images of affinity-purified NbNRC2. NRC2 appears as a dimer, with a maximum dimension of approximately 150 Å at its widest point. Scale bar = 230 Å. ( C ) Cryo-EM structure of resting state of NRC2 dimers. Atomic model corresponding to NRC2 homodimer shown in two orthogonal views, with resolved NB domain (NBD), HD1-WHD and LRR domains. Notably, the N-terminal CC domain of NRC2 was absent from the Cryo-EM density. Inset shows details of interfaces between the two NRC2 protomers, highlighting amino acid stretches corresponding to three contact interfaces. ( D ) Color coding of the domains is shown in the schematic representation of the domain architecture and boundaries of NRC2, which includes the exact boundaries of the amino acid stretches at the dimerization interfaces. A schematic representation of the pipeline used for Cryo-EM imaging, data processing and model building can be found in Fig. S2 . Additional views of the structure and dimerization interface can be found in Fig. S3, Fig. S4 and Movie S1 . Additional information on image processing and model building can be found in Table S1 .

    Article Snippet: Approximate molecular weights (kDa) of the proteins are shown on the left of the green panel. biorxiv;2023.12.17.572070v1/FIGS2 F7 figs2 Fig. S2: Cryo-EM image processing and 3D-reconstruction of NRC2 homodimers.

    Techniques: Immunoprecipitation, Staining, Negative Staining, Transmission Assay, Electron Microscopy, Affinity Purification, Cryo-EM Sample Prep, Imaging

    Journal: bioRxiv

    Article Title: Activation of plant immunity through conversion of a helper NLR homodimer into a resistosome

    doi: 10.1101/2023.12.17.572070

    Figure Lengend Snippet:

    Article Snippet: Approximate molecular weights (kDa) of the proteins are shown on the left of the green panel. biorxiv;2023.12.17.572070v1/FIGS2 F7 figs2 Fig. S2: Cryo-EM image processing and 3D-reconstruction of NRC2 homodimers.

    Techniques: