+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38680 | |||||||||
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Title | Cryo-EM structure of tomato NRC2 tetramer | |||||||||
Map data | ||||||||||
Sample |
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Keywords | tomato / helper NLR / tetramer / PLANT PROTEIN | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Solanum lycopersicum (tomato) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.17 Å | |||||||||
Authors | Sun Y / Ma SC / Chai JJ | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nature / Year: 2024 Title: Oligomerization-mediated autoinhibition and cofactor binding of a plant NLR. Authors: Shoucai Ma / Chunpeng An / Aaron W Lawson / Yu Cao / Yue Sun / Eddie Yong Jun Tan / Jinheng Pan / Jan Jirschitzka / Florian Kümmel / Nitika Mukhi / Zhifu Han / Shan Feng / Bin Wu / Paul ...Authors: Shoucai Ma / Chunpeng An / Aaron W Lawson / Yu Cao / Yue Sun / Eddie Yong Jun Tan / Jinheng Pan / Jan Jirschitzka / Florian Kümmel / Nitika Mukhi / Zhifu Han / Shan Feng / Bin Wu / Paul Schulze-Lefert / Jijie Chai / Abstract: Nucleotide-binding leucine-rich repeat (NLR) proteins have a pivotal role in plant immunity by recognizing pathogen effectors. Maintaining a balanced immune response is crucial, as excessive NLR ...Nucleotide-binding leucine-rich repeat (NLR) proteins have a pivotal role in plant immunity by recognizing pathogen effectors. Maintaining a balanced immune response is crucial, as excessive NLR expression can lead to unintended autoimmunity. Unlike most NLRs, plant NLR required for cell death 2 (NRC2) belongs to a small NLR group characterized by constitutively high expression without self-activation. The mechanisms underlying NRC2 autoinhibition and activation are not yet understood. Here we show that Solanum lycopersicum (tomato) NRC2 (SlNRC2) forms dimers and tetramers, and higher-order oligomers at elevated concentrations. Cryo-electron microscopy (cryo-EM) reveals an inactive conformation of SlNRC2 within these oligomers. Dimerization and oligomerization not only stabilize the inactive state but also sequester SlNRC2 from assembling into an active form. Mutations at the dimeric or inter-dimeric interfaces enhance pathogen-induced cell death and immunity in Nicotiana (N.) benthamiana. The cryo-EM structures unexpectedly reveal inositol hexakisphosphate (IP) or pentakisphosphate (IP) bound to the inner surface of SlNRC2's C-terminal LRR domain as confirmed by mass spectrometry. Mutations at the IP-binding site impair inositol phosphate binding of SlNRC2 and pathogen-induced SlNRC2-mediated cell death in N. benthamiana. Together, our study unveils a novel negative regulatory mechanism of NLR activation and suggests inositol phosphates as cofactors of NRCs. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38680.map.gz | 15.9 MB | EMDB map data format | |
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Header (meta data) | emd-38680-v30.xml emd-38680.xml | 15.2 KB 15.2 KB | Display Display | EMDB header |
Images | emd_38680.png | 28 KB | ||
Filedesc metadata | emd-38680.cif.gz | 6.2 KB | ||
Others | emd_38680_half_map_1.map.gz emd_38680_half_map_2.map.gz | 115.9 MB 115.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38680 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38680 | HTTPS FTP |
-Validation report
Summary document | emd_38680_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_38680_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_38680_validation.xml.gz | 14 KB | Display | |
Data in CIF | emd_38680_validation.cif.gz | 16.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38680 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38680 | HTTPS FTP |
-Related structure data
Related structure data | 8xuqMC 8xuoC 8xuvC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_38680.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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: #2
File | emd_38680_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_38680_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : NRC2 tetramer
Entire | Name: NRC2 tetramer |
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Components |
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-Supramolecule #1: NRC2 tetramer
Supramolecule | Name: NRC2 tetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Solanum lycopersicum (tomato) |
-Macromolecule #1: NRC2
Macromolecule | Name: NRC2 / type: protein_or_peptide / ID: 1 Details: Sequence reference for NRC2 is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A3Q7IF17. Regarding SlNRC2 with the accession number ...Details: Sequence reference for NRC2 is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A3Q7IF17. Regarding SlNRC2 with the accession number Solyc10g047320 in the SGN database, here is the link: https://solgenomics.net/locus/36701/view. The source article for SlNRC2 is "Helper NLR proteins NRC2a/b and NRC3 but not NRC1 are required for Pto-mediated cell death and resistance in Nicotiana benthamiana" by Wu, Chih-Hang et al. The article was published in The New Phytologist, volume 209, issue 4, in 2016. The DOI is 10.1111/nph.13764. Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Solanum lycopersicum (tomato) |
Molecular weight | Theoretical: 101.332078 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MANVAVEFLV ENLMQLLRDN VELISGVKEA AESLLQDLND FNAFLKQAAK CHINENEVLR ELVKKIRTVV NSAEDAIDKF VIEAKLHKD KGVTRVLDLP HYKRVKEVAG EIKAIRNKVR EIRQTDAIGL QALQDDDLSA RGSEERKPPV VEEDDVVGFD E EADIVINR ...String: MANVAVEFLV ENLMQLLRDN VELISGVKEA AESLLQDLND FNAFLKQAAK CHINENEVLR ELVKKIRTVV NSAEDAIDKF VIEAKLHKD KGVTRVLDLP HYKRVKEVAG EIKAIRNKVR EIRQTDAIGL QALQDDDLSA RGSEERKPPV VEEDDVVGFD E EADIVINR LLGESNHLEV VPVVGMPGLG KTTLANKIYK HPKIGYEFFT RIWVYVSQSY RRRELFLNII SKFTRNTKQY HG MCEEDLA DEIQEFLGKG GKYLVVLDDV WSDEAWERIK IAFPNNNKPN RVLLTTRDSK VAKQCNPIPH DLKFLTEDES WIL LEKKVF HKDKCPPELV LSGKSIAKKC KGLPLAIVVI AGALIGKGKT PREWKQVDDS VSEHLINRDH PENCNKLVQM SYDR LPYDL KACFLYCSAF PGGFQIPAWK LIRLWIAEGF IQYKGHLSLE CKGEDNLNDL INRNLVMVME RTSDGQIKTC RLHDM LHEF CRQEAMKEEN LFQEIKLGSE QYFPGKRELS TYRRLCIHSS VLDFFSTKPS AEHVRSFLSF SSKKIEMPSA DIPTIP KGF PLLRVLDVES INFSRFSREF YQLYHLRYVA FSSDSIKILP KLMGELWNIQ TIIINTQQRT LDIQANIWNM ERLRHLH TN SSAKLPVPVA PKNSKVTLVN QSLQTLSTIA PESCTEEVFA RTPNLKKLGI RGKISVLLDN KSAASLKNVK RLEYLENL K LINDSSIQTS KLRLPPAYIF PTKLRKLTLL DTWLEWKDMS ILGQLEHLEV LKMKENGFSG ESWESTGGFC SLLVLWIER TNLVSWKASA DDFPRLKHLV LICCDNLKEV PIALADIRSF QVMMLQNSTK TAAISARQIQ AKKDNQTQQG TKNIAFKLSI FPPDL UniProtKB: NRC1 |
-Macromolecule #2: INOSITOL HEXAKISPHOSPHATE
Macromolecule | Name: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: IHP |
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Molecular weight | Theoretical: 660.035 Da |
Chemical component information | ChemComp-IHP: |
-Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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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 K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 154084 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |