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- PDB-9ub0: effector of a plant pathogen -

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Basic information

Entry
Database: PDB / ID: 9ub0
Titleeffector of a plant pathogen
ComponentsEC88 protein
KeywordsTOXIN / pathogen / effector / plant
Function / homologyKnottin, scorpion toxin-like superfamily / EC88 protein
Function and homology information
Biological speciesColletotrichum higginsianum (fungus)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsOhki, S. / Mori, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20K06049 Japan
Japan Society for the Promotion of Science (JSPS)21H05032 Japan
CitationJournal: Plants (Basel) / Year: 2025
Title: Necrosis-Suppressing Effector Protein ChEC88 Adopts a Novel Structural Motif Conserved Among Genus-Spanning Hemibiotrophic Phytopathogens.
Authors: Ohki, S. / Takahara, H. / Imamura, T. / Sakane, K. / Bai, A. / Sasaki, K. / Nishiuchi, T. / Mori, M.
History
DepositionApr 2, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: EC88 protein


Theoretical massNumber of molelcules
Total (without water)8,2091
Polymers8,2091
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein EC88 protein


Mass: 8209.192 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Colletotrichum higginsianum (fungus) / Gene: EC88, CH35J_011169 / Plasmid: pET32b(+) / Production host: Escherichia coli (E. coli) / References: UniProt: K7N7H0
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC
131isotropic13D C(CO)NH
141isotropic13D CBCA(CO)NH
151isotropic13D H(CCO)NH
1141isotropic13D HNCA
1131isotropic13D HN(CA)CB
1121isotropic13D (H)CCH-TOCSY
1111isotropic13D 1H-13C NOESY
1101isotropic13D 1H-15N NOESY
191isotropic13D 1H-15N TOCSY

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Sample preparation

DetailsType: solution / Contents: 0.6 mM 13C,15N ChEC88, 90% H2O/10% D2O / Label: 13C,15N / Solvent system: 90% H2O/10% D2O
SampleConc.: 0.6 mM / Component: ChEC88 / Isotopic labeling: 13C,15N
Sample conditionsIonic strength: 50 mM / Label: 13C,15N / pH: 6.5 Not defined / Pressure: 1 atm / Temperature: 288 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE III / Manufacturer: Bruker / Model: AVANCE III / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2Guntert, Mumenthaler and Wuthrichstructure calculation
X-PLOR NIH3.1Schwieters, Kuszewski, Tjandra and Clorerefinement
NMRFAM-SPARKYLee W, Tonelli M, Markley JLchemical shift assignment
NMRFAM-SPARKYLee W, Tonelli M, Markley JLpeak picking
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 2
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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