[English] 日本語
![](img/lk-miru.gif)
- EMDB-19121: CryoEM structure of the plant helper NLR NRC2 in its resting state -
+
Open data
-
Basic information
Entry | ![]() | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CryoEM structure of the plant helper NLR NRC2 in its resting state | |||||||||
![]() | Please use contour for 0.0034 for atom inclusion. This covers all the main chain atoms in the model | |||||||||
![]() |
| |||||||||
![]() | NLR protein / Helper NLRl / plant immunity / R-protein / IMMUNE SYSTEM | |||||||||
Function / homology | ![]() | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
![]() | Selvaraj M / Kamoun S / Contreras MP | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: Activation of plant immunity through conversion of a helper NLR homodimer into a resistosome Authors: Selvaraj M / Kamoun S / Contreras MP | |||||||||
History |
|
-
Structure visualization
Supplemental images |
---|
-
Downloads & links
-EMDB archive
Map data | ![]() | 8.2 MB | ![]() | |
---|---|---|---|---|
Header (meta data) | ![]() ![]() | 19.4 KB 19.4 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.2 KB | Display | ![]() |
Images | ![]() | 57.1 KB | ||
Masks | ![]() | 64 MB | ![]() | |
Filedesc metadata | ![]() | 7 KB | ||
Others | ![]() ![]() | 48.5 MB 48.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8rfhMC M: atomic model generated by this map C: citing same article ( |
---|---|
Similar structure data | Similarity search - Function & homology ![]() |
-
Links
EMDB pages | ![]() ![]() |
---|---|
Related items in Molecule of the Month |
-
Map
File | ![]() | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Please use contour for 0.0034 for atom inclusion. This covers all the main chain atoms in the model | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.828 Å | ||||||||||||||||||||
Density |
| ||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
|
-Supplemental data
-Mask #1
File | ![]() | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #2
File | emd_19121_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: #1
File | emd_19121_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-
Sample components
-Entire : NRC2 heler NLR dimer with ADP
Entire | Name: NRC2 heler NLR dimer with ADP |
---|---|
Components |
|
-Supramolecule #1: NRC2 heler NLR dimer with ADP
Supramolecule | Name: NRC2 heler NLR dimer with ADP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 Details: This is helper NLR protein NRC2 in inactive state with ADP nucleotide bound state |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 100 KDa |
-Macromolecule #1: NRC2a
Macromolecule | Name: NRC2a / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
---|---|
Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 107.522398 KDa |
Recombinant expression | Organism: ![]() ![]() |
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 IFPPDLGSG SGRGSHHHHH HDYDIPTTAS ENLYFQGELD YKDHDGDYKD HDIDYKDDDD K UniProtKB: NRC2a |
-Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ADP |
---|---|
Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ![]() ChemComp-ADP: |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
![]() | single particle reconstruction |
Aggregation state | particle |
-
Sample preparation
Concentration | 1.2 mg/mL | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.5 Component:
| ||||||||||||
Grid | Model: C-flat / Material: COPPER / Support film - Material: GRAPHENE / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Details: The grids were negatively glow discharged | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: The C-flat grids were coated with grphene oxide, in house and the sample was applied two times inside the vitrobot chamber. | ||||||||||||
Details | the particles are NRC2 purified from plant after over expression. This was suspended in buffer and cryogrids were made on graphene oxide backing |
-
Electron microscopy
Microscope | TFS KRIOS |
---|---|
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 6000 / Average exposure time: 2.6 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / 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 |
+
Image processing
-Atomic model buiding 1
Initial model | Chain - Residue range: 1-880 / Chain - Source name: AlphaFold / Chain - Initial model type: in silico model / Details: This is the full length sequence of NRC |
---|---|
Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Overall B value: 100 / Target criteria: CC |
Output model | ![]() PDB-8rfh: |