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- EMDB-64920: Cryo-EM structure of CARD1 ectodomain -

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Basic information

Entry
Database: EMDB / ID: EMD-64920
TitleCryo-EM structure of CARD1 ectodomain
Map datasharp map
Sample
  • Complex: CARD1
    • Protein or peptide: Leucine-rich repeat receptor protein kinase HPCA1,Maltose/maltodextrin-binding periplasmic protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: COPPER (II) ION
Keywordsleucine-rich repeat receptor-like kinase / SIGNALING PROTEIN
Function / homology
Function and homology information


detection of chemical stimulus / regulation of stomatal closure / transmembrane receptor protein serine/threonine kinase activity / plant-type vacuole / plastid / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding ...detection of chemical stimulus / regulation of stomatal closure / transmembrane receptor protein serine/threonine kinase activity / plant-type vacuole / plastid / detection of maltose stimulus / maltose transport complex / carbohydrate transport / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / kinase activity / protein autophosphorylation / outer membrane-bounded periplasmic space / periplasmic space / non-specific serine/threonine protein kinase / DNA damage response / ATP binding / membrane / plasma membrane
Similarity search - Function
Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Leucine-rich repeat profile. / Leucine-rich repeat ...Leucine-rich repeat-containing N-terminal, plant-type / Leucine rich repeat N-terminal domain / Leucine Rich Repeat / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Leucine-rich repeat receptor protein kinase HPCA1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress) / Escherichia coli K12 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsFukuda Y / Ishihama N / Laohavisit A
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: A copper-mediated, redox-based hydrogen peroxide perception in plants
Authors: Ishihama N / Fukuda Y / Takizawa K / Hiroyama R / Shirano Y / Kanno K / Mishiro E / Ito H / Nishimura M / Fujimoto KJ / Yanai T / Inoue T / Shirasu K / Laohavisit A
History
DepositionJun 4, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_64920.png

Downloads & links

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Map

FileDownload / File: emd_64920.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharp map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å		0.83 Å/pix.
x 320 pix.
= 265.6 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.29
Minimum - Maximum-1.5151951 - 2.171747
Average (Standard dev.)0.00023817793 (±0.036483243)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 265.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_64920_msk_1.map
Projections & Slices
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Mask #2

Fileemd_64920_msk_2.map
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Mask #3

Fileemd_64920_msk_3.map
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Histogram

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Half map: half map A

Fileemd_64920_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_64920_half_map_2.map
Annotationhalf map B
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Sample components

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Entire : CARD1

EntireName: CARD1
Components
  • Complex: CARD1
    • Protein or peptide: Leucine-rich repeat receptor protein kinase HPCA1,Maltose/maltodextrin-binding periplasmic protein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: COPPER (II) ION

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Supramolecule #1: CARD1

SupramoleculeName: CARD1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Leucine-rich repeat receptor protein kinase HPCA1,Maltose/maltode...

MacromoleculeName: Leucine-rich repeat receptor protein kinase HPCA1,Maltose/maltodextrin-binding periplasmic protein
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Escherichia coli K12 (bacteria)
Molecular weightTheoretical: 98.137242 KDa
Recombinant expressionOrganism: Nicotiana benthamiana (plant)
SequenceString: LTNGLDASAL NALKSEWTTP PDGWEGSDPC GTNWVGITCQ NDRVVSISLG NLDLEGKLPA DISFLSELRI LDLSYNPKLS GPLPPNIGN LGKLRNLILV GCSFSGQIPE SIGTLKELIY LSLNLNKFSG TIPPSIGLLS KLYWFDIADN QIEGELPVSN G TSAPGLDM ...String:
LTNGLDASAL NALKSEWTTP PDGWEGSDPC GTNWVGITCQ NDRVVSISLG NLDLEGKLPA DISFLSELRI LDLSYNPKLS GPLPPNIGN LGKLRNLILV GCSFSGQIPE SIGTLKELIY LSLNLNKFSG TIPPSIGLLS KLYWFDIADN QIEGELPVSN G TSAPGLDM LLQTKHFHFG KNKLSGNIPK ELFSSNMSLI HVLFDGNQFT GEIPETLSLV KTLTVLRLDR NKLIGDIPSY LN NLTNLNE LYLANNRFTG TLPNLTSLTS LYTLDVSNNT LDFSPIPSWI SSLPSLSTLR MEGIQLNGPI PISFFSPPQL QTV ILKRNS IVESLDFGTD VSSQLEFVDL QYNEITDYKP SANKVLQVIL ANNPVCLEAG NGPSYCSAIQ HNTSFSTLPT NCSP CEPGM EASPTCRCAY PFMGTLYFRS PSFSGLFNST NFSILQKAIA DFFKKFNYPV DSVGVRNIRE NPTDHQLLID LLVFP LGRE SFNQTGMSLV GFAFSNQTYK PPPIFGPYIF KADLYKQFSG SAMKIEEGKL VIWINGDKGY NGLAEVGKKF EKDTGI KVT VEHPDKLEEK FPQVAATGDG PDIIFWAHDR FGGYAQSGLL AEITPDKAFQ DKLYPFTWDA VRYNGKLIAY PIAVEAL SL IYNKDLLPNP PKTWEEIPAL DKELKAKGKS ALMFNLQEPY FTWPLIAADG GYAFKYENGK YDIKDVGVDN AGAKAGLT F LVDLIKNKHM NADTDYSIAE AAFNKGETAM TINGPWAWSN IDTSKVNYGV TVLPTFKGQP SKPFVGVLSA GINAASPNK ELAKEFLENY LLTDEGLEAV NKDKPLGAVA LKSYEEELVK DPRIAATMEN AQKGEIMPNI PQMSAFWYAV RTAVINAASG RQTVDEALK DAQT

UniProtKB: Leucine-rich repeat receptor protein kinase HPCA1, Maltose/maltodextrin-binding periplasmic protein

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Macromolecule #4: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 4 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #5: COPPER (II) ION

MacromoleculeName: COPPER (II) ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: CU
Molecular weightTheoretical: 63.546 Da
Chemical component information

ChemComp-CU:
COPPER (II) ION

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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

Concentration0.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMTris-HCl
150.0 mMsodium chlorideNaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 20 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.007 kPa / Details: 20 mA current
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV
Details: 3 microliters droplet, 5 seconds delay before blotting, 3 seconds blot, 0 second delay before plunging..

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Electron microscopy

MicroscopeJEOL CRYO ARM 200
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 1100 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm

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Image processing

Particle selectionNumber selected: 1104287
CTF correctionSoftware - Name: cryoSPARC (ver. 3.2) / Type: NONE
Startup modelType of model: INSILICO MODEL / In silico model: predicted model / Details: AlphaFold2
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 130138
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9-f1


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9vbd:
Cryo-EM structure of CARD1 ectodomain

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