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Yorodumi- EMDB-32293: Cryo-EM structure of plant receptor like kinase NbBAK1 in RXEG1-B... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-32293 | |||||||||
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Title | Cryo-EM structure of plant receptor like kinase NbBAK1 in RXEG1-BAK1-XEG1 complex | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Nicotiana benthamiana (plant) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.59 Å | |||||||||
Authors | Sun Y / Wang Y / Zhang XX / Chen ZD / Xia YQ / Sun YJ / Zhang MM / Xiao Y / Han ZF / Wang YC / Chai JJ | |||||||||
Funding support | Germany, 2 items
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Citation | Journal: Nature / Year: 2022 Title: Plant receptor-like protein activation by a microbial glycoside hydrolase. Authors: Yue Sun / Yan Wang / Xiaoxiao Zhang / Zhaodan Chen / Yeqiang Xia / Lei Wang / Yujing Sun / Mingmei Zhang / Yu Xiao / Zhifu Han / Yuanchao Wang / Jijie Chai / Abstract: Plants rely on cell-surface-localized pattern recognition receptors to detect pathogen- or host-derived danger signals and trigger an immune response. Receptor-like proteins (RLPs) with a leucine- ...Plants rely on cell-surface-localized pattern recognition receptors to detect pathogen- or host-derived danger signals and trigger an immune response. Receptor-like proteins (RLPs) with a leucine-rich repeat (LRR) ectodomain constitute a subgroup of pattern recognition receptors and play a critical role in plant immunity. Mechanisms underlying ligand recognition and activation of LRR-RLPs remain elusive. Here we report a crystal structure of the LRR-RLP RXEG1 from Nicotiana benthamiana that recognizes XEG1 xyloglucanase from the pathogen Phytophthora sojae. The structure reveals that specific XEG1 recognition is predominantly mediated by an amino-terminal and a carboxy-terminal loop-out region (RXEG1(ID)) of RXEG1. The two loops bind to the active-site groove of XEG1, inhibiting its enzymatic activity and suppressing Phytophthora infection of N. benthamiana. Binding of XEG1 promotes association of RXEG1(LRR) with the LRR-type co-receptor BAK1 through RXEG1(ID) and the last four conserved LRRs to trigger RXEG1-mediated immune responses. Comparison of the structures of apo-RXEG1(LRR), XEG1-RXEG1(LRR) and XEG1-BAK1-RXEG1(LRR) shows that binding of XEG1 induces conformational changes in the N-terminal region of RXEG1(ID) and enhances structural flexibility of the BAK1-associating regions of RXEG1(LRR). These changes allow fold switching of RXEG1(ID) for recruitment of BAK1(LRR). Our data reveal a conserved mechanism of ligand-induced heterodimerization of an LRR-RLP with BAK1 and suggest a dual function for the LRR-RLP in plant immunity. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_32293.map.gz | 46.4 MB | EMDB map data format | |
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Header (meta data) | emd-32293-v30.xml emd-32293.xml | 14.6 KB 14.6 KB | Display Display | EMDB header |
Images | emd_32293.png | 5.8 KB | ||
Others | emd_32293_half_map_1.map.gz emd_32293_half_map_2.map.gz | 40.8 MB 40.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-32293 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-32293 | HTTPS FTP |
-Validation report
Summary document | emd_32293_validation.pdf.gz | 619.2 KB | Display | EMDB validaton report |
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Full document | emd_32293_full_validation.pdf.gz | 618.8 KB | Display | |
Data in XML | emd_32293_validation.xml.gz | 11.5 KB | Display | |
Data in CIF | emd_32293_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32293 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-32293 | HTTPS FTP |
-Related structure data
Related structure data | 7w3tMC 7drbC 7drcC 7w3vC 7w3xC M: atomic model generated by this map C: citing same article (ref.) |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_32293.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.061 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_32293_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_32293_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : BAK1
Entire | Name: BAK1 |
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Components |
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-Supramolecule #1: BAK1
Supramolecule | Name: BAK1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Nicotiana benthamiana (plant) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
-Macromolecule #1: Brassinosteroid insensitive 1-associated receptor kinase 1
Macromolecule | Name: Brassinosteroid insensitive 1-associated receptor kinase 1 type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Nicotiana benthamiana (plant) |
Molecular weight | Theoretical: 24.514012 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MDQWILGILG FVSTFLCLIG LLLVPVSANI EGDALNALKT NLADPNNVLQ SWDPTLVNPC TWFHVTCNSE NSVTRVDLGN ANLSGQLVP QLGQLPNLQY LELYSNNISG RIPFELGNLT NLVSLDLYLN RLNGPIPDTL GKLQKLRFLR LNNNSLNGRI P MLLTTVIS ...String: MDQWILGILG FVSTFLCLIG LLLVPVSANI EGDALNALKT NLADPNNVLQ SWDPTLVNPC TWFHVTCNSE NSVTRVDLGN ANLSGQLVP QLGQLPNLQY LELYSNNISG RIPFELGNLT NLVSLDLYLN RLNGPIPDTL GKLQKLRFLR LNNNSLNGRI P MLLTTVIS LQVLDLSNNN LTGPVPVNGS FSLFTPISFA NNPLDIPPAA PPPPISPMPP SSSGVGNSAT |
-Macromolecule #3: 2-acetamido-2-deoxy-beta-D-glucopyranose
Macromolecule | Name: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 3 / Number of copies: 4 / Formula: NAG |
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Molecular weight | Theoretical: 221.208 Da |
Chemical component information | ChemComp-NAG: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36117 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |