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- EMDB-38680: Cryo-EM structure of tomato NRC2 tetramer -

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Basic information

Entry
Database: EMDB / ID: EMD-38680
TitleCryo-EM structure of tomato NRC2 tetramer
Map data
Sample
  • Complex: NRC2 tetramer
    • Protein or peptide: NRC2
  • Ligand: INOSITOL HEXAKISPHOSPHATEPhytic acid
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
Keywordstomato / helper NLR / tetramer / PLANT PROTEIN
Function / homology
Function and homology information


defense response to other organism / ADP binding
Similarity search - Function
Virus X resistance protein-like, coiled-coil domain / Rx, N-terminal / Rx N-terminal domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Leucine-rich repeat domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesSolanum lycopersicum (tomato)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsSun Y / Ma SC / Chai JJ
Funding support China, 1 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: To Be Published
Title: Cryo-EM structure of tomato NRC2 dimer
Authors: Ma SC / Chai JJ
History
DepositionJan 14, 2024-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_38680.png

Downloads & links

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Map

FileDownload / File: emd_38680.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.85 Å
Density
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.5224076 - 0.92088634
Average (Standard dev.)0.0016903076 (±0.021114731)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_38680_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_38680_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : NRC2 tetramer

EntireName: NRC2 tetramer
Components
  • Complex: NRC2 tetramer
    • Protein or peptide: NRC2
  • Ligand: INOSITOL HEXAKISPHOSPHATEPhytic acid
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: NRC2 tetramer

SupramoleculeName: NRC2 tetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Solanum lycopersicum (tomato)

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Macromolecule #1: NRC2

MacromoleculeName: 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
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 101.332078 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: 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

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Macromolecule #2: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE / Phytic acid

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 154084

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