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- EMDB-50863: The barley MLA13-AVRA13 heterodimer -

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Basic information

Entry
Database: EMDB / ID: EMD-50863
TitleThe barley MLA13-AVRA13 heterodimer
Map dataComplex of MLA13-AVRA13, contrast AI-enhanced
Sample
  • Complex: MLA13-AVRA13 heterodimer complex
    • Protein or peptide: CSEP0372 putative effector protein
    • Protein or peptide: CC-NBS-LRR resistance protein MLA13
KeywordsComplex / Apoptosis / Immune receptor / Mildew / ANTIFUNGAL 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 Winged helix domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / : / Leucine-rich repeat region ...Virus X resistance protein-like, coiled-coil domain / Rx, N-terminal / Rx N-terminal domain / Disease resistance protein Winged helix domain / Disease resistance protein, plants / Apoptotic protease-activating factors, helical domain / NB-ARC / NB-ARC domain / : / Leucine-rich repeat region / Leucine-rich repeat domain superfamily / Winged helix-like DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
CSEP0372 putative effector protein / CC-NBS-LRR resistance protein MLA13
Similarity search - Component
Biological speciesHordeum vulgare (barley) / Blumeria graminis (grass mildew)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsBehrmann E / Schulze-Lefert P / Flores-Ibarra A / Lawson AW
Funding support Germany, 2 items
OrganizationGrant numberCountry
German Research Foundation (DFG)INST 216/949-1 FUGG Germany
German Research Foundation (DFG)INST 216/512/1 FUGG Germany
CitationJournal: EMBO J / Year: 2025
Title: The barley MLA13-AVR heterodimer reveals principles for immunoreceptor recognition of RNase-like powdery mildew effectors.
Authors: Aaron W Lawson / Andrea Flores-Ibarra / Yu Cao / Chunpeng An / Ulla Neumann / Monika Gunkel / Isabel M L Saur / Jijie Chai / Elmar Behrmann / Paul Schulze-Lefert /
Abstract: Co-evolution between cereals and pathogenic grass powdery mildew fungi is exemplified by sequence diversification of an allelic series of barley resistance genes encoding Mildew Locus A (MLA) ...Co-evolution between cereals and pathogenic grass powdery mildew fungi is exemplified by sequence diversification of an allelic series of barley resistance genes encoding Mildew Locus A (MLA) nucleotide-binding leucine-rich repeat (NLR) immunoreceptors with an N-terminal coiled-coil domain (CNLs). Each immunoreceptor recognises a matching, strain-specific powdery mildew effector encoded by an avirulence gene (AVR). We present here the cryo-EM structure of barley MLA13 in complex with its cognate effector AVR-1. The effector adopts an RNase-like fold when bound to MLA13 in planta, similar to crystal structures of other RNase-like AVR effectors unbound to receptors. AVR-1 interacts via its basal loops with MLA13 C-terminal leucine-rich repeats (LRRs) and the central winged helix domain (WHD). Co-expression of structure-guided MLA13 and AVR-1 substitution variants show that the receptor-effector interface plays an essential role in mediating immunity-associated plant cell death. Furthermore, by combining structural information from the MLA13-AVR-1 heterocomplex with sequence alignments of other MLA receptors, we engineered a single amino acid substitution in MLA7 that enables expanded effector detection of AVR-1 and the virulent variant AVR-V2. In contrast to the pentameric conformation of previously reported effector-activated CNL resistosomes, MLA13 was purified and resolved as a stable heterodimer from an in planta expression system. Our study suggests a common structural principle for RNase-like effector binding to MLAs and highlights the utility of structure-guided engineering of plant immune receptors for broadening their pathogen effector recognition capabilities.
History
DepositionJul 3, 2024-
Header (metadata) releaseFeb 12, 2025-
Map releaseFeb 12, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50863.png

Downloads & links

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Map

FileDownload / File: emd_50863.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComplex of MLA13-AVRA13, contrast AI-enhanced
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 352 pix.
= 303.424 Å		0.86 Å/pix.
x 352 pix.
= 303.424 Å		0.86 Å/pix.
x 352 pix.
= 303.424 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.862 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.175
Minimum - Maximum-0.001733708 - 2.093972
Average (Standard dev.)0.0007154537 (±0.020075876)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 303.424 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Complex of MLA13-AVRA13

Fileemd_50863_additional_1.map
AnnotationComplex of MLA13-AVRA13
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map A of Complex of MLA13-AVRA13

Fileemd_50863_half_map_1.map
AnnotationHalf-map A of Complex of MLA13-AVRA13
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B of Complex of MLA13-AVRA13

Fileemd_50863_half_map_2.map
AnnotationHalf-map B of Complex of MLA13-AVRA13
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MLA13-AVRA13 heterodimer complex

EntireName: MLA13-AVRA13 heterodimer complex
Components
  • Complex: MLA13-AVRA13 heterodimer complex
    • Protein or peptide: CSEP0372 putative effector protein
    • Protein or peptide: CC-NBS-LRR resistance protein MLA13

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Supramolecule #1: MLA13-AVRA13 heterodimer complex

SupramoleculeName: MLA13-AVRA13 heterodimer complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1
Source (natural)Organism: Hordeum vulgare (barley)
Molecular weightTheoretical: 20 KDa

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Macromolecule #1: CC-NBS-LRR resistance protein MLA13

MacromoleculeName: CC-NBS-LRR resistance protein MLA13 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hordeum vulgare (barley)
Molecular weightTheoretical: 108.095391 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: MDIVTGAISN LIPKLGELLT EEFKLHKGVK KNIEDLGKEL ESMNAALIKI GEVPREQLDS QDKLWADEVR ELSYVIEDVV DKFLVQVDG IKSDDNNNEF EGLMKRTTEL LKKVKHKHGI AHAIKDIQEQ LQKVADRRDR NKVFVPHPTR TIAIDPCLRA L YAEATELV ...String:
MDIVTGAISN LIPKLGELLT EEFKLHKGVK KNIEDLGKEL ESMNAALIKI GEVPREQLDS QDKLWADEVR ELSYVIEDVV DKFLVQVDG IKSDDNNNEF EGLMKRTTEL LKKVKHKHGI AHAIKDIQEQ LQKVADRRDR NKVFVPHPTR TIAIDPCLRA L YAEATELV GIYGKRDQGL MRLLSMEGDD ASNKRLKKVS IVGFGGLGKT TLARAVYEKI KGDFDCRAFV PVGQNPDMKK VL RDILIDL GNPHSDLAML DANQLIKKLH EFLENKRYLV IIDDIWDEKL WEGINFAFSN RNNLGSRLIT TTRIVSVSNS CCS SDGDSV YQMEPLSVDD SRMLFYKRIF PDENACINEF EQVSRDILKK CGGVPLAIIT IASALAGDQK MKPKCEWDIL LRSL GSGLT EDNSLEEMRR ILSFSYSNLP SNLKTCLLYL CVYPEDSMIS RDKLIWKWVA EGFVHHENQG NSLYLLGLNY FNQLI NRSM IQPIYNYSGE AYACRVHDMV LDLICNLSNE AKFVNLLDGT GNSMSSQSNC RRLSLQKRNE DHQARPFTDI KSMSRV RSI TIFPSAIEVM PSLSRFDVLR VLDLSRCNLG ENSSMQLNLK GVGHLTHLRY LGLEGTNISK LPAEIGKLQF LEVLDLE NN HNLKELPSTV CNFRRLIYLN LVGCQVVPPV GVLQNLTSIE VLSGILVSLN IIAQELGNLK RLRELNILFN DGSLDLYE G FVKSLCNLHH IESLIIGCNS RETSSFELMD LLGERWVPPV HFREFVSSMP SQLSALRGWI KRDPSHLSNL SELILTSVK EVQQDDVVII GALSSLRRLC IKSTYQTQRL LVIPADGFRC IVGFHLDCGS ATQILFEPGA LPRAESVVIS LGVRVAKEDG NRGFDLGLQ GNLLSLRRDV FVSIYCGGAR VGEAKEAEAA VRRALDAHPS HPPIYFEMRP HIAKGAHDDD LCEERRRTDF

UniProtKB: CC-NBS-LRR resistance protein MLA13

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Macromolecule #2: CSEP0372 putative effector protein

MacromoleculeName: CSEP0372 putative effector protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Blumeria graminis (grass mildew)
Molecular weightTheoretical: 13.731284 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString:
MKTFQFASIV AGLSFLKTTI AAGDGYITLG MGSIHKNDIY RVAEHMWTID AYSVPSNNHG SYPIFGEEIN GSVTRIFPIV YNGDDWRSG DFYYSVESTE DLSYIKLRYN GARYETCMVS SPE

UniProtKB: CSEP0372 putative effector protein

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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: 7.4
Component:
ConcentrationFormulaName
50.0 mMC10H17N3O6Sreduced glutathione
50.0 mMNH2C(CH2OH)3HClTris-HCl
150.0 mMNaClsodium chloride
2.0 mMC4H10O2S2DTT
0.1 %C58H114O26polysorbate 20
GridModel: Quantifoil R2/4 / Material: GRAPHENE OXIDE / Mesh: 200 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 3 / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 96000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5t1y

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 48191
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: AB INITIO MODEL
Output model

PDB-9fyc:
The barley MLA13-AVRA13 heterodimer

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