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- PDB-8jgn: Cryo-EM structure of alpha/beta hydrolase DANGEROUS MIX 3 (DM3) f... -

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Basic information

Entry
Database: PDB / ID: 8jgn
TitleCryo-EM structure of alpha/beta hydrolase DANGEROUS MIX 3 (DM3) forms compartmentalized hexamer structure
ComponentsAT3g61540/F2A19_140
KeywordsHYDROLASE / Complex / immune related alpha/beta hydrolase / PROLYL AMINOPEPTIDASE 2
Function / homology
Function and homology information


vacuole / aminopeptidase activity / proteolysis / cytosol
Similarity search - Function
: / Peptidase S33 / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsKim, G. / Song, J.J.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2020R1A2B5B03001517 Korea, Republic Of
CitationJournal: To Be Published
Title: Cryo-EM structure of alpha/beta hydrolase DANGEROUS MIX 3 (DM3) forms compartmentalized hexamer structure
Authors: Kim, G. / Song, J.J.
History
DepositionMay 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AT3g61540/F2A19_140
B: AT3g61540/F2A19_140
C: AT3g61540/F2A19_140
D: AT3g61540/F2A19_140
E: AT3g61540/F2A19_140
F: AT3g61540/F2A19_140


Theoretical massNumber of molelcules
Total (without water)302,5966
Polymers302,5966
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
AT3g61540/F2A19_140 / Alpha/beta-Hydrolases superfamily protein / Prolyl aminopeptidase-like protein


Mass: 50432.719 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: F2A19.140, At3g61540 / Variant: Columbia accession (Col-0) / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RILP / References: UniProt: Q9M314
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Homohexamer complex of DM3 from Columbia accession (Col-0)
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMsodium chlorideNaCl1
250 mMTrisamineTris1
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: After glow discharge, graphene oxide was treated onto the grid
Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 330509 / Symmetry type: POINT

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