+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-50637 | ||||||||||||||||||||||||
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Title | Structure of the NbNRC2 hexameric resistosome | ||||||||||||||||||||||||
Map data | NRC2 EM map (sharpened) | ||||||||||||||||||||||||
Sample |
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Keywords | Plant immunity / complex / IMMUNE SYSTEM | ||||||||||||||||||||||||
Function / homology | Function and homology information | ||||||||||||||||||||||||
Biological species | Nicotiana benthamiana (plant) | ||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | ||||||||||||||||||||||||
Authors | Webster MW / Madhuprakash J / Kamoun S | ||||||||||||||||||||||||
Funding support | United Kingdom, European Union, 7 items
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Citation | Journal: To Be Published Title: Cryo-EM structure of the NbNRC2 hexameric resistosome Authors: Webster MW / Madhuprakash J / Kamoun S | ||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_50637.map.gz | 398.5 MB | EMDB map data format | |
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Header (meta data) | emd-50637-v30.xml emd-50637.xml | 19.7 KB 19.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_50637_fsc.xml | 15.9 KB | Display | FSC data file |
Images | emd_50637.png | 94.3 KB | ||
Filedesc metadata | emd-50637.cif.gz | 6.2 KB | ||
Others | emd_50637_additional_1.map.gz emd_50637_half_map_1.map.gz emd_50637_half_map_2.map.gz | 208.9 MB 391.8 MB 391.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-50637 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-50637 | HTTPS FTP |
-Validation report
Summary document | emd_50637_validation.pdf.gz | 984.6 KB | Display | EMDB validaton report |
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Full document | emd_50637_full_validation.pdf.gz | 984.2 KB | Display | |
Data in XML | emd_50637_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | emd_50637_validation.cif.gz | 32 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50637 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-50637 | HTTPS FTP |
-Related structure data
Related structure data | 9fp6MC 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_50637.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | NRC2 EM map (sharpened) | ||||||||||||||||||||||||||||||||||||
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: NRC2 EM map (unsharpened)
File | emd_50637_additional_1.map | ||||||||||||
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Annotation | NRC2 EM map (unsharpened) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: NRC2 EM map (half map 1)
File | emd_50637_half_map_1.map | ||||||||||||
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Annotation | NRC2 EM map (half map 1) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: NRC2 EM map (half map 2)
File | emd_50637_half_map_2.map | ||||||||||||
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Annotation | NRC2 EM map (half map 2) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : NbNRC2a
Entire | Name: NbNRC2a |
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Components |
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-Supramolecule #1: NbNRC2a
Supramolecule | Name: NbNRC2a / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: The NbNRC2 was activated in planta to a hexameric resistosome using the sensor Rx and PVX coat protein. |
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Source (natural) | Organism: Nicotiana benthamiana (plant) |
Molecular weight | Theoretical: 606 KDa |
-Macromolecule #1: NRC2a
Macromolecule | Name: NRC2a / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Nicotiana benthamiana (plant) |
Molecular weight | Theoretical: 101.27 KDa |
Recombinant expression | Organism: Nicotiana benthamiana (plant) |
Sequence | String: MANVAVEFLV QNLMQLLRDN AELIVGVKDS AESLLQDLND FNAFLKQTAK SRTENDVHKE LVKKIKTVVN SAEDAIDKFV IEAKLHKDK GVGRFVDVKH YKRVYDVAGE IKTIRDKVKE IRLNNALDLQ ALQDEDQSAK GVQERKPPVV EEDDVVGFEE E ADKVINRL ...String: MANVAVEFLV QNLMQLLRDN AELIVGVKDS AESLLQDLND FNAFLKQTAK SRTENDVHKE LVKKIKTVVN SAEDAIDKFV IEAKLHKDK GVGRFVDVKH YKRVYDVAGE IKTIRDKVKE IRLNNALDLQ ALQDEDQSAK GVQERKPPVV EEDDVVGFEE E ADKVINRL LGGSSGLEVV PVVGMPGLGK TTLANKIYKH PDIGYQFFTR IWVYVSQSYR RRELFLNIIS KFTRNTKQYH DM CEEDLAD EIEDFLGKGG KYLIVLDDVW SPDAWERIRI AFPNNNKSNR ILLTTRDSKV AKQCKQCIGI PHDLKFLTED ESW ILLEKK VFHKDKCPPE LELSGKSIAK KCNGLPLAIV VIAGALIGKG KTSREWKQVD ESVGEHLINK DQPENCNKLV QLSY DRLSY DLKACFLYCG AFPGGFEIPA WKLIRLWIAE GFIQYKGHLS LECKAEDNLN DLINRNLVMV MQRTSDGQIK TCRLH DMLH EFCRQEAMKE ENLFQEIKLG AEQYFPGKRE LATYRRLCIH SSVLEFISTK PSGEHVRSFL SFSLKKIEMP SVDIPT IPK GFPLLRVFDV ESINFSRFSK EFFQLYHLRY IAFSSDTIKI IPKHIGELWN IQTLIINTQQ RSLDIQANIW NMERLRH LH TNSSAKLPVP VTPRSSKVPL VNQSLQTLST IAPESCTEEV FARTPNLKKL GIRGKIAVLL EPNKSLLKNV KKLESLEN L KLINDSSQTG KGLRLPPSYI FPTKLRKLSL VDTWLEWNDM SILGQMEHLE VLKLKENGFM GECWESVGGF CSLLVLWIE RTDLVSWKAS ADHFPRLKHL VLICCDKLKE IPIGLADIRS FQVMELQNST KTAAISARGI RDKKDKQTQE GTNNNGFKLS IFPPDL UniProtKB: NRC2a |
-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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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 2.4 mg/mL |
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Buffer | pH: 7.5 Details: 100mM Tris HCl (pH 7.5), 150 mM NaCl, 1 mM MgCl2, 3% glycerol |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 12908 / Average exposure time: 1.95 sec. / Average electron dose: 49.5 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |