[English] 日本語
Yorodumi
- EMDB-30450: Cryo-EM structure of plant NLR RPP1 tetramer in complex with ATR1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-30450
TitleCryo-EM structure of plant NLR RPP1 tetramer in complex with ATR1
Map data
Sample
  • Complex: Tetrameric complex of RPP1 and ATR1
    • Complex: RPP1
      • Protein or peptide: NAD+ hydrolase (NADase)
    • Complex: ATR1
      • Protein or peptide: Avirulence protein ATR1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
KeywordsNADase / ETI / HR / PLANT PROTEIN
Function / homology
Function and homology information


effector-mediated perturbation of host process by symbiont / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / ADP binding / defense response / host cell cytoplasm / host cell nucleus / signal transduction / extracellular region
Similarity search - Function
: / : / Avirulence protein ATR1, WY-domain / ATR1 N-terminal domain / Leucine-rich repeat 3 / Leucine Rich Repeat / C-JID domain / C-JID domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain ...: / : / Avirulence protein ATR1, WY-domain / ATR1 N-terminal domain / Leucine-rich repeat 3 / Leucine Rich Repeat / C-JID domain / C-JID domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / TIR domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine-rich repeat domain superfamily / Winged helix DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Avirulence protein ATR1 / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress) / Hyaloperonospora arabidopsidis (strain Emoy2) (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsMa SC / Lapin D
Funding support China, Germany, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31421001 for J.C. China
Alexander von Humboldt Foundation Germany
CitationJournal: Science / Year: 2020
Title: Direct pathogen-induced assembly of an NLR immune receptor complex to form a holoenzyme.
Authors: Shoucai Ma / Dmitry Lapin / Li Liu / Yue Sun / Wen Song / Xiaoxiao Zhang / Elke Logemann / Dongli Yu / Jia Wang / Jan Jirschitzka / Zhifu Han / Paul Schulze-Lefert / Jane E Parker / Jijie Chai /
Abstract: Direct or indirect recognition of pathogen-derived effectors by plant nucleotide-binding leucine-rich repeat (LRR) receptors (NLRs) initiates innate immune responses. The effector ATR1 activates the ...Direct or indirect recognition of pathogen-derived effectors by plant nucleotide-binding leucine-rich repeat (LRR) receptors (NLRs) initiates innate immune responses. The effector ATR1 activates the N-terminal Toll-interleukin-1 receptor (TIR) domain of NLR RPP1. We report a cryo-electron microscopy structure of RPP1 bound by ATR1. The structure reveals a C-terminal jelly roll/Ig-like domain (C-JID) for specific ATR1 recognition. Biochemical and functional analyses show that ATR1 binds to the C-JID and the LRRs to induce an RPP1 tetrameric assembly required for nicotinamide adenine dinucleotide hydrolase (NADase) activity. RPP1 tetramerization creates two potential active sites, each formed by an asymmetric TIR homodimer. Our data define the mechanism of direct effector recognition by a plant NLR leading to formation of a signaling-active holoenzyme.
History
DepositionAug 13, 2020-
Header (metadata) releaseDec 16, 2020-
Map releaseDec 16, 2020-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7crc
  • Surface level: 0.014
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30450.png

Downloads & links

-
Map

FileDownload / File: emd_30450.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.1 Å/pix.
x 360 pix.
= 395.244 Å		1.1 Å/pix.
x 360 pix.
= 395.244 Å		1.1 Å/pix.
x 360 pix.
= 395.244 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0979 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014 / Movie #1: 0.014
Minimum - Maximum-0.016343672 - 0.050704446
Average (Standard dev.)0.00015298909 (±0.0015571202)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 395.24402 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.09791.09791.0979
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z395.244395.244395.244
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ360360360
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0160.0510.000

-
Supplemental data

-
Sample components

-
Entire : Tetrameric complex of RPP1 and ATR1

EntireName: Tetrameric complex of RPP1 and ATR1
Components
  • Complex: Tetrameric complex of RPP1 and ATR1
    • Complex: RPP1
      • Protein or peptide: NAD+ hydrolase (NADase)
    • Complex: ATR1
      • Protein or peptide: Avirulence protein ATR1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

-
Supramolecule #1: Tetrameric complex of RPP1 and ATR1

SupramoleculeName: Tetrameric complex of RPP1 and ATR1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

-
Supramolecule #2: RPP1

SupramoleculeName: RPP1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

-
Supramolecule #3: ATR1

SupramoleculeName: ATR1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Hyaloperonospora arabidopsidis (strain Emoy2) (eukaryote)

-
Macromolecule #1: NAD+ hydrolase (NADase)

MacromoleculeName: NAD+ hydrolase (NADase) / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 139.009781 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MGSAMSLGCS KRKATNQDVD SESRKRRKIC STNDAENCRF IQDESSWKHP WSLCANSVVN DTKDTKSSAL SLPSPPTSVS RIWKHQVFP SFHGADVRKT ILSHILESFR RKGIDPFIDN NIERSKSIGH ELKEAIKGSK IAIVLLSKNY ASSSWCLDEL A EIMKCREL ...String:
MGSAMSLGCS KRKATNQDVD SESRKRRKIC STNDAENCRF IQDESSWKHP WSLCANSVVN DTKDTKSSAL SLPSPPTSVS RIWKHQVFP SFHGADVRKT ILSHILESFR RKGIDPFIDN NIERSKSIGH ELKEAIKGSK IAIVLLSKNY ASSSWCLDEL A EIMKCREL LGQIVMTIFY EVDPTDIKKQ TGEFGKAFTK TCKGKTKEYV ERWRKALEDV ATIAGYHSHK WRNEADMIEK IA TDVSNML NSFKPSRDFN GLVGMRAHMD MLEQLLRLVL DEVRMIGIWG PPGIGKTTIA RFLFNQVSDR FQLSAIMVNI KGC YPRPCF DEYSAQLQLQ NQMLSQMINH KDIMISHLGV AQERLRDKKV FLVLDEVDQL GQLDALAKET RWFGPGSRII ITTE DLGVL KAHGINHVYK VGYPSNDEAF QIFCMNAFGQ KQPHEGFDEI AREVMALAGE LPLGLKVLGS ALRGKSKPEW ERTLP RLKT SLDGKIGSII QFSYDALCDE DKYLFLYIAC LFNKESTTKV EGLLGKFLDV RQGLHILAQK SLISIEDGNI YMHTLL EQF GRETSRKQFI HHGYTKHQLL VGERDICEVL NDDTIDSRRF IGINLDLYKN VEELNISEKA LERIHDFQFV RINGKNH AL HERLQGLIYQ SPQIRSLHWK CYQNICLPST FNSEFLVELD MSFSKLQKLW EGTKQLRNLK WMDLSYSSYL KELPNLST A TNLEELKLRN CSSLVELPSS IEKLTSLQIL DLHRCSSLVE LPSFGNATKL EILNLENCSS LVKLPPSINA NNLQELSLT NCSRVVELPA IENATNLWKL NLLNCSSLIE LPLSIGTATN LKHLDFRGCS SLVKLPSSIG DMTNLEVFYL SNCSNLVELP SSIGNLRKL TLLLMRGCSK LETLPTNINL KSLHTLNLID CSRLKSFPEI STHIKYLRLI GTAIKEVPLS IMSWSPLAHF Q ISYFESLK EFPHALDIIT ELQLSKDIQE VPPWVKRMSR LRALRLNNCN NLVSLPQLPD SLAYLYADNC KSLERLDCCF NN PEIRLYF PKCFKLNQEA RDLIMHTSTR NFAMLPGTQV PACFNHRATS GDSLKIKLKE SPLPTTLTFK ACIMLVNEEM SYD LKSMSV DIVIRDEQND LKVQCTPSYH QCTEIYVLTE HIYTFELEVE EVTSTELVFE FTSVNESICK IGECGILQRE TRSL RRSSS PDLSPESSRV SSCDHC

UniProtKB: ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase

-
Macromolecule #2: Avirulence protein ATR1

MacromoleculeName: Avirulence protein ATR1 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Hyaloperonospora arabidopsidis (strain Emoy2) (eukaryote)
Molecular weightTheoretical: 35.149426 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MRVCYFVLVP SVALAVIATE SSETSGTIVH VFPLRDVADH RNDALINRAL RAQTALDDDE ERWPFGPSAV EALIETIDRH GRVSLNDEA KMKKVVRTWK KLIERDDLIG EIGKHYFEAP GPLHDTYDEA LATRLVTTYS DRGVARAILH TRPSDPLSKK A GQAHRLEE ...String:
MRVCYFVLVP SVALAVIATE SSETSGTIVH VFPLRDVADH RNDALINRAL RAQTALDDDE ERWPFGPSAV EALIETIDRH GRVSLNDEA KMKKVVRTWK KLIERDDLIG EIGKHYFEAP GPLHDTYDEA LATRLVTTYS DRGVARAILH TRPSDPLSKK A GQAHRLEE AVASLWKGRG YTSDNVVSSI ATGHDVDFFA PTAFTFLVKC VESEDDANNA IFEYFGSNPS RYFSAVLHAM EK PDADSRV LESSKKWMFQ CYAQKQFPTP VFERTLAAYQ SEDYAIRGAR NHYEKLSLSQ IEELVEEYSR IYSV

UniProtKB: Avirulence protein ATR1

-
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

-
Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 23.542 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 323232
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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