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- EMDB-61320: Cryo-EM structure of the Arabidopsis EDS1-PAD4-ADR1 immune comple... -

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Basic information

Entry
Database: EMDB / ID: EMD-61320
TitleCryo-EM structure of the Arabidopsis EDS1-PAD4-ADR1 immune complex in the presence of pRib-AMP
Map data
Sample
  • Complex: EDS1-PAD4-ADR1 complex
    • Protein or peptide: Protein EDS1
    • Protein or peptide: PAD4
    • Protein or peptide: Probable disease resistance protein At5g04720
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: 5-O-phosphono-beta-D-ribofuranose
  • Ligand: water
KeywordsTIR signaling / EDS1 / PAD4 / ADR1 / pRib-AMP / cryo-EM / IMMUNE SYSTEM
Function / homology
Function and homology information


aerenchyma formation / EDS1 disease-resistance complex / leaf abscission / systemic acquired resistance, salicylic acid mediated signaling pathway / systemic acquired resistance / plant-type hypersensitive response / response to singlet oxygen / lipase activity / regulation of hydrogen peroxide metabolic process / chloroplast ...aerenchyma formation / EDS1 disease-resistance complex / leaf abscission / systemic acquired resistance, salicylic acid mediated signaling pathway / systemic acquired resistance / plant-type hypersensitive response / response to singlet oxygen / lipase activity / regulation of hydrogen peroxide metabolic process / chloroplast / defense response / ADP binding / lipid metabolic process / defense response to Gram-negative bacterium / response to hypoxia / cell surface receptor signaling pathway / defense response to bacterium / endoplasmic reticulum / protein homodimerization activity / ATP hydrolysis activity / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Arabidopsis broad-spectrum mildew resistance protein RPW8 / 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) / Adaptor protein Cbl, N-terminal domain superfamily / Apoptotic protease-activating factors, helical domain ...Arabidopsis broad-spectrum mildew resistance protein RPW8 / 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) / Adaptor protein Cbl, N-terminal domain superfamily / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / Lipases, serine active site. / : / Leucine-rich repeat region / Leucine-rich repeat domain superfamily / Alpha/Beta hydrolase fold / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PAD4 / Probable disease resistance protein At5g04720 / Protein EDS1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.3 Å
AuthorsWang H / Tan J / Cui X / Song S / Yan C / Qi T
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Switch of TIR signaling by a Ca2+ sensor activates ADR1 recognition of pRib-AMP-bound EDS1-PAD4 for stomatal immunity
Authors: Wang H / Tan J / Cui X / Song S / Yan C / Qi T
History
DepositionAug 27, 2024-
Header (metadata) releaseSep 3, 2025-
Map releaseSep 3, 2025-
UpdateSep 3, 2025-
Current statusSep 3, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_61320.png

Downloads & links

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Map

FileDownload / File: emd_61320.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.)
0.96 Å/pix.
x 300 pix.
= 288. Å		0.96 Å/pix.
x 300 pix.
= 288. Å		0.96 Å/pix.
x 300 pix.
= 288. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-2.9210842 - 4.3432317
Average (Standard dev.)-0.0013164922 (±0.09807516)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 288.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61320_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61320_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_61320_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 : EDS1-PAD4-ADR1 complex

EntireName: EDS1-PAD4-ADR1 complex
Components
  • Complex: EDS1-PAD4-ADR1 complex
    • Protein or peptide: Protein EDS1
    • Protein or peptide: PAD4
    • Protein or peptide: Probable disease resistance protein At5g04720
  • Ligand: ADENOSINE MONOPHOSPHATE
  • Ligand: 5-O-phosphono-beta-D-ribofuranose
  • Ligand: water

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Supramolecule #1: EDS1-PAD4-ADR1 complex

SupramoleculeName: EDS1-PAD4-ADR1 complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 300 KDa

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Macromolecule #1: Protein EDS1

MacromoleculeName: Protein EDS1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 71.784195 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: MAFEALTGIN GDLITRSWSA SKQAYLTERY HKEEAGAVVI FAFQPSFSEK DFFDPDNKSS FGEIKLNRVQ FPCMRKIGKG DVATVNEAF LKNLEAIIDP RTSFQASVEM AVRSRKQIVF TGHSSGGATA ILATVWYLEK YFIRNPNVYL EPRCVTFGAP L VGDSIFSH ...String:
MAFEALTGIN GDLITRSWSA SKQAYLTERY HKEEAGAVVI FAFQPSFSEK DFFDPDNKSS FGEIKLNRVQ FPCMRKIGKG DVATVNEAF LKNLEAIIDP RTSFQASVEM AVRSRKQIVF TGHSSGGATA ILATVWYLEK YFIRNPNVYL EPRCVTFGAP L VGDSIFSH ALGREKWSRF FVNFVSRFDI VPRIMLARKA SVEETLPHVL AQLDPRKSSV QESEQRITEF YTRVMRDTST VA NQAVCEL TGSAEAFLET LSSFLELSPY RPAGTFVFST EKRLVAVNNS DAILQMLFYT SQASDEQEWS LIPFRSIRDH HSY EELVQS MGKKLFNHLD GENSIESTLN DLGVSTRGRQ YVQAALEEEK KRVENQKKII QVIEQERFLK KLAWIEDEYK PKCQ AHKNG YYDSFKVSNE ENDFKANVKR AELAGVFDEV LGLMKKCQLP DEFEGDIDWI KLATRYRRLV EPLDIANYHR HLKNE DTGP YMKRGRPTRY IYAQRGYEHY ILKPNGMIAE DVFWNKVNGL NLGLQLEEIQ ETLKNSGSEC GSCFWAEVEE LKGKPY EEV EVRVKTLEGM LGEWITDGEV DDKEIFLEGS TFRKWWITLP KNHKSHSPLR DYMMDEITDT

UniProtKB: Protein EDS1

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Macromolecule #2: PAD4

MacromoleculeName: PAD4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 61.054504 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: MDDCRFETSE LQASVMISTP LFTDSWSSCN TANCNGSIKI HDIAGITYVA IPAVSMIQLG NLVGLPVTGD VLFPGLSSDE PLPMVDAAI LKLFLQLKIK EGLELELLGK KLVVITGHST GGALAAFTAL WLLSQSSPPS FRVFCITFGS PLLGNQSLST S ISRSRLAH ...String:
MDDCRFETSE LQASVMISTP LFTDSWSSCN TANCNGSIKI HDIAGITYVA IPAVSMIQLG NLVGLPVTGD VLFPGLSSDE PLPMVDAAI LKLFLQLKIK EGLELELLGK KLVVITGHST GGALAAFTAL WLLSQSSPPS FRVFCITFGS PLLGNQSLST S ISRSRLAH NFCHVVSIHD LVPRSSNEQF WPFGTYLFCS DKGGVCLDNA GSVRLMFNIL NTTATQNTEE HQRYGHYVFT LS HMFLKSR SFLGGSIPDN SYQAGVALAV EALGFSNDDT SGVLVKECIE TATRIVRAPI LRSAELANEL ASVLPARLEI QWY KDRCDA SEEQLGYYDF FKRYSLKRDF KVNMSRIRLA KFWDTVIKMV ETNELPFDFH LGKKWIYASQ FYQLLAEPLD IANF YKNRD IKTGGHYLEG NRPKRYEVID KWQKGVKVPE ECVRSRYAST TQDTCFWAKL EQAKEWLDEA RKESSDPQRR SLLRE KIVP FESYANTLVT KKEVSLDVKA KNSSYSVWEA NLKEFKCKMG YENEIEMVVD ESDAMET

UniProtKB: PAD4

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Macromolecule #3: Probable disease resistance protein At5g04720

MacromoleculeName: Probable disease resistance protein At5g04720 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 91.662953 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: MADIIGGEVV TELVRQLYAV SQKTLRCRGI AKNLATMIDG LQPTIKEIQY SGVELTPHRQ AQLRMFSETL DKCRKLTEKV LKSSRWNMV RQLLHVRKME NLQSKVSSFL NGQLLVHVLA DVHHVRADSE FRFDRIDRKV DSLNEKLGSM KLRGSESLRE A LKTAEATV ...String:
MADIIGGEVV TELVRQLYAV SQKTLRCRGI AKNLATMIDG LQPTIKEIQY SGVELTPHRQ AQLRMFSETL DKCRKLTEKV LKSSRWNMV RQLLHVRKME NLQSKVSSFL NGQLLVHVLA DVHHVRADSE FRFDRIDRKV DSLNEKLGSM KLRGSESLRE A LKTAEATV EMVTTDGADL GVGLDLGKRK VKEMLFKSID GERLIGISGM SGSGKTTLAK ELARDEEVRG HFGNKVLFLT VS QSPNLEE LRAHIWGFLT SYEAGVGATL PESRKLVILD DVWTRESLDQ LMFENIPGTT TLVVSRSKLA DSRVTYDVEL LNE HEATAL FCLSVFNQKL VPSGFSQSLV KQVVGECKGL PLSLKVIGAS LKERPEKYWE GAVERLSRGE PADETHESRV FAQI EATLE NLDPKTRDCF LVLGAFPEDK KIPLDVLINV LVELHDLEDA TAFAVIVDLA NRNLLTLVKD PRFGHMYTSY YDIFV TQHD VLRDVALRLS NHGKVNNRER LLMPKRESML PREWERNNDE PYKARVVSIH TGEMTQMDWF DMELPKAEVL ILHFSS DKY VLPPFIAKMG KLTALVIINN GMSPARLHDF SIFTNLAKLK SLWLQRVHVP ELSSSTVPLQ NLHKLSLIFC KINTSLD QT ELDIAQIFPK LSDLTIDHCD DLLELPSTIC GITSLNSISI TNCPRIKELP KNLSKLKALQ LLRLYACHEL NSLPVEIC E LPRLKYVDIS QCVSLSSLPE KIGKVKTLEK IDTRECSLSS IPNSVVLLTS LRHVICDREA LWMWEKVQKA VAGLRVEAA EKSFSRDWLD D

UniProtKB: Probable disease resistance protein At5g04720

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Macromolecule #4: ADENOSINE MONOPHOSPHATE

MacromoleculeName: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: AMP
Molecular weightTheoretical: 347.221 Da
Chemical component information

ChemComp-AMP:
ADENOSINE MONOPHOSPHATE / AMP*YM

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Macromolecule #5: 5-O-phosphono-beta-D-ribofuranose

MacromoleculeName: 5-O-phosphono-beta-D-ribofuranose / type: ligand / ID: 5 / Number of copies: 1 / Formula: RP5
Molecular weightTheoretical: 230.11 Da
Chemical component information

ChemComp-RP5:
5-O-phosphono-beta-D-ribofuranose

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 274 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1779204
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD

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