[English] 日本語
Yorodumi
- EMDB-60049: pRib-ADP bound OsEDS1-PAD4-ADR1 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-60049
TitlepRib-ADP bound OsEDS1-PAD4-ADR1 complex
Map data
Sample
  • Complex: pRib-ADP bound OsEDS1-PAD4-ADR1 complex
    • Protein or peptide: RPW8 domain-containing protein
    • Protein or peptide: EDS1
    • Protein or peptide: Lipase-like PAD4
  • Ligand: [(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[(2S,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]oxy-3-oxidanyl-oxolan-2-yl]methyl phosphono hydrogen phosphate
KeywordsADR1 / EDS1 / PAD4 / plant immunity / pRib-ADP / NLR / PLANT PROTEIN
Function / homology
Function and homology information


defense response / ADP binding / lipid metabolic process / nucleus / cytoplasm
Similarity search - Function
Powdery mildew resistance protein, RPW8 domain / RPW8 domain profile. / EDS1, EP domain / EDS1-like / Enhanced disease susceptibility 1 protein EP domain / Fungal lipase-like domain / Lipase (class 3) / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain ...Powdery mildew resistance protein, RPW8 domain / RPW8 domain profile. / EDS1, EP domain / EDS1-like / Enhanced disease susceptibility 1 protein EP domain / Fungal lipase-like domain / Lipase (class 3) / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Leucine-rich repeat domain superfamily / Alpha/Beta hydrolase fold / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
RPW8 domain-containing protein / EDS1 / Lipase, putative
Similarity search - Component
Biological speciesOryza sativa subsp. japonica (Japanese rice) / Oryza sativa Japonica Group (Japanese rice)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.96 Å
AuthorsXu WY / Zhang Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Science / Year: 2024
Title: A canonical protein complex controls immune homeostasis and multipathogen resistance.
Authors: Yue Wu / Weiying Xu / Guoyan Zhao / Ziyao Lei / Kui Li / Jiyun Liu / Shijia Huang / Junli Wang / Xiangbin Zhong / Xin Yin / Yuandong Wang / Haochen Zhang / Yang He / Zian Ye / Yonggang Meng ...Authors: Yue Wu / Weiying Xu / Guoyan Zhao / Ziyao Lei / Kui Li / Jiyun Liu / Shijia Huang / Junli Wang / Xiangbin Zhong / Xin Yin / Yuandong Wang / Haochen Zhang / Yang He / Zian Ye / Yonggang Meng / Xiaoyu Chang / Hui Lin / Xin Wang / Yuanyuan Gao / Jijie Chai / Jane E Parker / Yiwen Deng / Yu Zhang / Mingjun Gao / Zuhua He /
Abstract: The calcium (Ca) sensor ROD1 (RESISTANCE OF RICE TO DISEASES1) is a master regulator of immunity in rice. By screening suppressors of mutants, we show that ROD1 governs immune homeostasis by ...The calcium (Ca) sensor ROD1 (RESISTANCE OF RICE TO DISEASES1) is a master regulator of immunity in rice. By screening suppressors of mutants, we show that ROD1 governs immune homeostasis by surveilling the activation of a canonical immune pathway. Mutations in (), (), (), and () all abolish enhanced disease resistance of plants. OsTIR catalyzes the production of second messengers 2'-(5″-phosphoribosyl)-5'-adenosine monophosphate (pRib-AMP) and diphosphate (pRib-ADP), which trigger formation of an OsEDS1-OsPAD4-OsADR1 (EPA) immune complex. ROD1 interacts with OsTIR and inhibits its enzymatic activity, whereas mutation of leads to constitutive activation of the EPA complex. Thus, we unveil an immune network that fine-tunes immune homeostasis and multipathogen resistance in rice.
History
DepositionMay 7, 2024-
Header (metadata) releaseNov 13, 2024-
Map releaseNov 13, 2024-
UpdateJan 1, 2025-
Current statusJan 1, 2025Processing site: PDBc / Status: Released

-
Structure visualization

Supplemental images

emd_60049.png

Downloads & links

-
Map

FileDownload / File: emd_60049.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.74 Å/pix.
x 300 pix.
= 222. Å		0.74 Å/pix.
x 300 pix.
= 222. Å		0.74 Å/pix.
x 300 pix.
= 222. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.2654746 - 0.75405234
Average (Standard dev.)0.0062528085 (±0.028600326)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 222.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_60049_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_60049_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : pRib-ADP bound OsEDS1-PAD4-ADR1 complex

EntireName: pRib-ADP bound OsEDS1-PAD4-ADR1 complex
Components
  • Complex: pRib-ADP bound OsEDS1-PAD4-ADR1 complex
    • Protein or peptide: RPW8 domain-containing protein
    • Protein or peptide: EDS1
    • Protein or peptide: Lipase-like PAD4
  • Ligand: [(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[(2S,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]oxy-3-oxidanyl-oxolan-2-yl]methyl phosphono hydrogen phosphate

-
Supramolecule #1: pRib-ADP bound OsEDS1-PAD4-ADR1 complex

SupramoleculeName: pRib-ADP bound OsEDS1-PAD4-ADR1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Oryza sativa subsp. japonica (Japanese rice)

-
Macromolecule #1: RPW8 domain-containing protein

MacromoleculeName: RPW8 domain-containing protein / type: protein_or_peptide / ID: 1
Details: Sequence reference for strain 'Oryza sativa Japonica Group' is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A0E0JBT6. The author ...Details: Sequence reference for strain 'Oryza sativa Japonica Group' is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt id A0A0E0JBT6. The author provided reference sequence from NCBI (id: XP_015619838.1).
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 96.140859 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MERLFEELAG EAVKELLRAV RGTFFCRSTA ERLRRNVEPL LPLVQPQAAQ GGGGWGHGRS AGELAELAAQ LREALELARR AASAPRWNV YRTAQLARRM EAADTAIARW LSRHAPAHVL DGVRRLRDEA DARIGRLERR VEEVAAAQQQ QQAAATALPP P AISLPFAL ...String:
MERLFEELAG EAVKELLRAV RGTFFCRSTA ERLRRNVEPL LPLVQPQAAQ GGGGWGHGRS AGELAELAAQ LREALELARR AASAPRWNV YRTAQLARRM EAADTAIARW LSRHAPAHVL DGVRRLRDEA DARIGRLERR VEEVAAAQQQ QQAAATALPP P AISLPFAL PPPPPPPKAM AMMAMDTPPT KGMAVGMEVE LPFPDDEEDE SMVGGGVRVG KEKVKEMVMS GGGGGWEAVG IC GMGGSGK TTLAMEIFKD HKIRGYFSDR VFFETISQSA NLDTIKMKLW EQISGNLVLG AYNQIPEWQL KLGPRDKGPV LVI LDDVWS LSQLEELIFK FPGCKTLVVS RFKFPSLVTR TYEMELLDEE AALSVFCRAA FDQESVPRTA DKKLVRQVAA ECRG LPLAL KVIGASLRDQ PPKIWLSAKN RLSRGETISD SHETKLLERM AASIECLSGK VRECFLDLGC FPEDKKIPLD VLINI WMEI HDLDEPDAFA ILVELSNKNL LTLVNDAQNK AGDLYSSYHD FSVTQHDVLR DLALHMSGRD ALNNRRRLVM PRREES LPK DWQRNKDTPF EAQIVSIHTG EMKESDWFQM SFPKAEVLIL NFASSVYYLP PFIATMQNLK ALVLINYGTI SATLDNL SA FTTLSDLRSL WLEKITLPPL PKTTIPLKNL RKISLVLCEL TNSLRGSKVD LSMTFPRLSN LTIDHCIDLK ELPSSICE I SSLESISISN CHDLTELPYE LGKLHCLSIL RVYACPALWR LPPSVCSLKR LKYLDISQCV NLTDLPEELG HLTSLEKID MRECSRLRSL PRSSSSLKSL GHVVCDEETA LLWREAEQVI PDLRVQVAEE CYNLDWLVD

UniProtKB: RPW8 domain-containing protein

-
Macromolecule #2: EDS1

MacromoleculeName: EDS1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 68.366945 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MPAAAALSDD DRLVVAHCAA LSFPPASQPP PPPTTSSSSS GAGAGASFQV HHASHPYPCA AFAFPPSWSA APGWAAAGRA AFGDAEVDP SLFPSLRSVG SGVPARANAA FLASFGALLD GSPLQSEVSR AVAEEKRIVF TGHSSGGSIA TLAAIWFLET C TRRGSVNQ ...String:
MPAAAALSDD DRLVVAHCAA LSFPPASQPP PPPTTSSSSS GAGAGASFQV HHASHPYPCA AFAFPPSWSA APGWAAAGRA AFGDAEVDP SLFPSLRSVG SGVPARANAA FLASFGALLD GSPLQSEVSR AVAEEKRIVF TGHSSGGSIA TLAAIWFLET C TRRGSVNQ AHPFCVTFGA PLVGDNTFNN AVRREGWSQC ILNFVVPVDI IPRIPLTPLA SATEGIQAVL DWLSPQTPNF SP SGMPLII SQFYENLLRS TLSIASYEAC SFMGCTSSIL GTLTSFIELS PYRPCGTYLF LTSSEQLAVL TNSDAVLQLL FYC LQLDPQ QQLRDAAERS LSAHWQYEPI KQSMMQEIVC VDYLGVVSST LPGRQMSSTI VGGLELSKEA MLSLSAAGQW EKQR ETNQA KIDGASCTKI REALKSLNEY KRTCELHEVS YYDSFKLQRE VHDFNANVSR LELAGLWDEI VEMLRRRELP DGFES RQDW VNLGTLYRRL VEPLDIANYY RHSKNEDTGS YLSKGRPRRY KYTQEWHEQS QRISFGSSLE SCFWAMAEEL QAEIAN GKT FEDVRDRVVK LESDAHGWSM SGSLGKDIFL SRSSFVIWWK TLPENHRSAS CIAKLVPW

UniProtKB: EDS1

-
Macromolecule #3: Lipase-like PAD4

MacromoleculeName: Lipase-like PAD4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Oryza sativa Japonica Group (Japanese rice)
Molecular weightTheoretical: 71.557234 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEDASRGEEE NSMFETSHVL GALLASSPLL ARAWDRCAAA ADGGASSLGF VHGGGGGGEG EPVCVAFSGV QAALSAAAGG GGGAEIFKP VGLRGDAAGR LFAPLVAAEP EDAGGEPVAV QALALQGFLR LCRSPEFQVL LNQIRGKAVV FTGHSLGGAI A ALVALHYL ...String:
MEDASRGEEE NSMFETSHVL GALLASSPLL ARAWDRCAAA ADGGASSLGF VHGGGGGGEG EPVCVAFSGV QAALSAAAGG GGGAEIFKP VGLRGDAAGR LFAPLVAAEP EDAGGEPVAV QALALQGFLR LCRSPEFQVL LNQIRGKAVV FTGHSLGGAI A ALVALHYL CTSSSSSAFA PAPPVLCVTF GSPLLGNQAL SRAILRERWA GNFCHVVSQH DVVPRLLFCP LNVIPVHIVV GM QLHQLPV RARRAAGVVA TVTARMADTN QESLRQLIQE HAGEAAIEQK LAAPEIPSGS PYRPFGAYVL CSPDGAACVD NPT AAVQML YATFAARRAP ETGAVPPEAA HSCYGDLVLS MPHHLLLKRR LGATVTAPAA SNYDVGISIA LEASGITGEA TEAA PARQW LKTSKRVGRS PSLNCASLAT RLGRITPCRA QIEWYKALFD ANTGYYDAFK QRLSPKKFSK ANMYRIKLAQ FWDGV LSML DTSQLPYDFH RRAKWVNAAH FYQLLVEPLD IADYHRNNLH RTRGSYITHG RERRYELFDK WWKQKGCTDP STGDTS ATT TARRSKFAGL TQDPCFWARV EEAREQTESA KSERDMTSLA RMLEDLHKFE RHSSELVENK EVSIDVVAPQ SSYSLWV KE WNELKLREEV RTILFQF

UniProtKB: Lipase, putative

-
Macromolecule #4: [(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[(2S,3R,4S,5R)-3,4-bis(oxi...

MacromoleculeName: [(2R,3R,4R,5R)-5-(6-aminopurin-9-yl)-4-[(2S,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]oxy-3-oxidanyl-oxolan-2-yl]methyl phosphono hydrogen phosphate
type: ligand / ID: 4 / Number of copies: 1 / Formula: A1D8A
Molecular weightTheoretical: 639.296 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration11.5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.96 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 174833
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-8zf0:
pRib-ADP bound OsEDS1-PAD4-ADR1 complex

+
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