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Open data
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Basic information
Entry | ![]() | |||||||||||||||
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Title | Cryo-EM structure of the tomato NRC3 hexameric resistosome | |||||||||||||||
![]() | unsharpened consensus map | |||||||||||||||
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![]() | Plant Immunity / NLR / Resistosome / IMMUNE SYSTEM | |||||||||||||||
Function / homology | ![]() | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.85 Å | |||||||||||||||
![]() | Seager BA / Kamoun S / Madhuprakash J | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structure of the tomato NRC3 hexameric resistosome Authors: Seager BA / Kamoun S / Madhuprakash J | |||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 237.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 22.8 KB 22.8 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 22.8 KB | Display | ![]() |
Images | ![]() | 81.3 KB | ||
Filedesc metadata | ![]() | 6.9 KB | ||
Others | ![]() ![]() ![]() | 450.5 MB 441.8 MB 441.8 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 815 KB | Display | ![]() |
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Full document | ![]() | 814.4 KB | Display | |
Data in XML | ![]() | 25.1 KB | Display | |
Data in CIF | ![]() | 34 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9ri9MC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | unsharpened consensus map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.828 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: sharpened consensus map
File | emd_53990_additional_1.map | ||||||||||||
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Annotation | sharpened consensus map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map B
File | emd_53990_half_map_1.map | ||||||||||||
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Annotation | half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map A
File | emd_53990_half_map_2.map | ||||||||||||
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Annotation | half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : hexameric assembly of SlNRC3
Entire | Name: hexameric assembly of SlNRC3 |
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Components |
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-Supramolecule #1: hexameric assembly of SlNRC3
Supramolecule | Name: hexameric assembly of SlNRC3 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: hexameric resistosome formed by activation with Rx and CP |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: SlNRC3
Macromolecule | Name: SlNRC3 / type: protein_or_peptide / ID: 1 Details: This is a fusion protein. The first 18 residues were not modelled. The protein contains a single amino acid linker followed by a 3x FLAG tag Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 104.763977 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MADVAVKFEL ENETQLEIDN ADLILGIQGE VENLLTDLNY FNAFLKEAAK SRRENEVLKE LVKKIRKVVN DAEDSIDKFV VEAKRHDDK NKFAQWFHIT HVARAKGVAD EIKSIRERVK EIRDNDAYGL QAITLDDNFN RGDEERKAPV VEEDDVVGFD D EAKTVIDR ...String: MADVAVKFEL ENETQLEIDN ADLILGIQGE VENLLTDLNY FNAFLKEAAK SRRENEVLKE LVKKIRKVVN DAEDSIDKFV VEAKRHDDK NKFAQWFHIT HVARAKGVAD EIKSIRERVK EIRDNDAYGL QAITLDDNFN RGDEERKAPV VEEDDVVGFD D EAKTVIDR LIGGSDYVEV VPVVGMPGLG KTTLAYKIYK DPKVEYEFFT RVWVYVSQTF KRREIFLNII SKFTRNTKQY DD TPEDDLA NEVKELLGKG GKYLIVLDDV WTMEAWDRIK IAFPNNGKRN RVLMTTRQSN VAKRCNDKPH DLKFLTKDES WEL LEKKVF HKEKCPPELE LPGISIAEKC MGLPLAIVVI AGALIGKGKT TREWELVAAS VGEHLINRDP ENCKKLVQMS YDRL PYDLK ACFLYCGAFP GGSQIPAKKL IRLWIAEGFI QYQGPLALED VAEDHLNDLV NRNLVMVTQR SCSGQIKTCR VHDML HEFC RHEAMMEENL FQEIKQGQER SFPGKQELAT YRRLCIQSLI PEFLSMKPSG EHVRSFLCVG SKKIDMPPNE IPSIPK AFP LLRVLDAESI KFSRFSREFF KLFHLRYIAL STDKIKTIPA DFGNLWNIQT LIVETQQATL DIKADIWNMT RLRHVCT NA SATLPSTKRP KSSKDNLVNR CLQTLSTIAP ECCTAEVFTR TPNLKKLGVR GKIDALLESS KDGSGSGLFS NIGKLGCL E YLKLVNDTRL SSKPLHLPPA YIFPQKLKKL SLVDTWFEWK DMSILGLLPE LEVLKLKENA FKGQSWEQED GGFPRLQVL WIERTDLTSW KASSGNFPRL KHLALISCDK LEELPAELAD VKNLQLIELQ SSSESAARSA RAILKRNQEK EQDGDKGTGF KLSIFPHDL GLSDYKDHDG DYKDHDLDAA AADYKDDDDK UniProtKB: Uncharacterized protein |
-Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 6 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ![]() ChemComp-ATP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.3 mg/mL | |||||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR | |||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: LEICA EM GP |
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Electron microscopy
Microscope | TFS KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6150 / Average electron dose: 50.84 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model | Chain - Source name: AlphaFold / Chain - Initial model type: in silico model |
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Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | ![]() PDB-9ri9: |