[English] 日本語
Yorodumi
- EMDB-64934: Cryo-EM structure of a CARD1 ectodomain H197A/H199A/H222A mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-64934
TitleCryo-EM structure of a CARD1 ectodomain H197A/H199A/H222A mutant
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
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: 3.61 Å
AuthorsFukuda Y / Ishihama N / Laohavisit A
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Nat Commun / Year: 2026
Title: A copper-dependent redox-based hydrogen peroxide perception in plants.
Authors: Nobuaki Ishihama / Yohta Fukuda / Yumiko Shirano / Kazuhiro J Fujimoto / Kaori Takizawa / Ryoko Hiroyama / Hiroki Ito / Mayumi Nishimura / Takeshi Yanai / Tsuyoshi Inoue / Ken Shirasu / Anuphon Laohavisit /
Abstract: Redox-related molecules, such as quinones and reactive oxygen species (ROS), are important signaling molecules for all living organisms. A plant-specific leucine-rich repeat receptor-like kinase (LRR- ...Redox-related molecules, such as quinones and reactive oxygen species (ROS), are important signaling molecules for all living organisms. A plant-specific leucine-rich repeat receptor-like kinase (LRR-RLK) CANNOT RESPOND TO DMBQ 1 (CARD1), also known as HYDROGEN-PEROXIDE-INDUCED Ca INCREASES (HPCA1), perceives both quinones and ROS, but the mechanism by which it distinguishes between these two types of signals remains unclear. Here, we determine the structure of the CARD1 ectodomain and uncover its unique features. Structural studies, coupled with genetics and biochemical analysis, demonstrate that previously identified unique cysteine residues are not essential for signal perception in CARD1. Interestingly, CARD1 harbors a copper ion on the surface of the ectodomain via histidine-coordination that is crucial for hydrogen peroxide signaling. Our work reports a unique copper-dependent redox perception in plants and provides insight into interactions between receptors and non-peptide stimuli during perception.
History
DepositionJun 5, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_64934.png

Downloads & links

-
Map

FileDownload / File: emd_64934.map.gz / Format: CCP4 / Size: 178 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 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.133
Minimum - Maximum-0.4356494 - 0.6734945
Average (Standard dev.)0.0000057949273 (±0.008467154)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_64934_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #2

Fileemd_64934_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #3

Fileemd_64934_msk_3.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A

Fileemd_64934_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B

Fileemd_64934_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
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

-
Supramolecule #1: CARD1

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

-
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: 97.936039 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 LLQTKAFAFG KNKLSGNIPK ELFSSNMSLI AVLFDGNQFT 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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
20.0 mMTris-HCl
150.0 mMsodium chlorideNaCl
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..

-
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

+
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 reconstructionResolution.type: BY AUTHOR / Resolution: 3.61 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.2) / Number images used: 220439
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)

-
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-9vbv:
Cryo-EM structure of a CARD1 ectodomain H197A/H199A/H222A mutant

+
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