[English] 日本語
Yorodumi
- EMDB-38679: Cryo-EM structure of tomato NRC2 dimer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-38679
TitleCryo-EM structure of tomato NRC2 dimer
Map data
Sample
  • Complex: NRC2 dimer
    • Protein or peptide: NRC2
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: INOSITOL HEXAKISPHOSPHATEPhytic acid
Keywordstomato / helper NLR / dimer / 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: 2.84 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 13, 2024-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_38679.png

Downloads & links

-
Map

FileDownload / File: emd_38679.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: 0.15
Minimum - Maximum-1.2201469 - 1.6737925
Average (Standard dev.)-0.00021555432 (±0.027167948)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: #2

Fileemd_38679_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_38679_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : NRC2 dimer

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

-
Supramolecule #1: NRC2 dimer

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

-
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: 2 / Enantiomer: LEVO
Source (natural)Organism: Solanum lycopersicum (tomato)
Molecular weightTheoretical: 86.267594 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: DDDLSARGSE ERKPPVVEED DVVGFDEEAD IVINRLLGES NHLEVVPVVG MPGLGKTTLA NKIYKHPKIG YEFFTRIWVY VSQSYRRRE LFLNIISKFT RNTKQYHGMC EEDLADEIQE FLGKGGKYLV VLDDVWSDEA WERIKIAFPN NNKPNRVLLT T RDSKVAKQ ...String:
DDDLSARGSE ERKPPVVEED DVVGFDEEAD IVINRLLGES NHLEVVPVVG MPGLGKTTLA NKIYKHPKIG YEFFTRIWVY VSQSYRRRE LFLNIISKFT RNTKQYHGMC EEDLADEIQE FLGKGGKYLV VLDDVWSDEA WERIKIAFPN NNKPNRVLLT T RDSKVAKQ CNPIPHDLKF LTEDESWILL EKKVFHKDKC PPELVLSGKS IAKKCKGLPL AIVVIAGALI GKGKTPREWK QV DDSVSEH LINRDHPENC NKLVQMSYDR LPYDLKACFL YCSAFPGGFQ IPAWKLIRLW IAEGFIQYKG HLSLECKGED NLN DLINRN LVMVMERTSD GQIKTCRLHD MLHEFCRQEA MKEENLFQEI KLGSEQYFPG KRELSTYRRL CIHSSVLDFF STKP SAEHV RSFLSFSSKK IEMPSADIPT IPKGFPLLRV LDVESINFSR FSREFYQLYH LRYVAFSSDS IKILPKLMGE LWNIQ TIII NTQQRTLDIQ ANIWNMERLR HLHTNSSAKL PVPVAPKNSK VTLVNQSLQT LSTIAPESCT EEVFARTPNL KKLGIR GKI SVLLDNKSAA SLKNVKRLEY LENLKLINDS SIQTSKLRLP PAYIFPTKLR KLTLLDTWLE WKDMSILGQL EHLEVLK MK ENGFSGESWE STGGFCSLLV LWIERTNLVS WKASADDFPR LKHLVLICCD NLKEVPIALA DIRSFQVMML QNSTKTAA I SARQIQAKKD NQTQQGTKNI AFKLSIFPPD L

UniProtKB: NRC1

-
Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

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

-
Macromolecule #3: INOSITOL HEXAKISPHOSPHATE

MacromoleculeName: INOSITOL HEXAKISPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: IHP
Molecular weightTheoretical: 660.035 Da
Chemical component information

ChemComp-IHP:
INOSITOL HEXAKISPHOSPHATE / Phytic acid

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
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

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 560935

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more