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- EMDB-53317: CryoEM structure of the tetrahedral M42 aminopeptidase from M. ja... -

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Basic information

Entry
Database: EMDB / ID: EMD-53317
TitleCryoEM structure of the tetrahedral M42 aminopeptidase from M. jannaschii
Map dataCryoEM map fro TET enzyme from Methanocaldococcus janaschii obtained using data collected with a Talos Glacios microscope and reconstructed using Relion.
Sample
  • Cell: MjTET
    • Protein or peptide: Putative aminopeptidase MJ0555
KeywordsEnzyme / aminopepidase / archaea / dodecamer / M42 / CYTOSOLIC PROTEIN
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases / aminopeptidase activity / metallopeptidase activity / proteolysis / metal ion binding
Similarity search - Function
Peptidase M42, domain 2 / : / M42 glutamyl aminopeptidase / Peptidase M42
Similarity search - Domain/homology
Putative aminopeptidase MJ0555
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsAtalah J / Basbous H / Girard E / Effantin E / Schoehn G / Franzetti B
Funding support France, 1 items
OrganizationGrant numberCountry
Grenoble Alliance for Integrated Structural Cell Biology (GRAL) France
CitationJournal: To Be Published
Title: CryoEM structure of the tetrahedral M42 aminopeptidase from M. jannaschii
Authors: Atalah J / Basbous H / Girard E / Effantin E / Schoehn G / Franzetti B
History
DepositionApr 3, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53317.png

Downloads & links

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Map

FileDownload / File: emd_53317.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map fro TET enzyme from Methanocaldococcus janaschii obtained using data collected with a Talos Glacios microscope and reconstructed using Relion.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 200 pix.
= 183. Å		0.92 Å/pix.
x 200 pix.
= 183. Å		0.92 Å/pix.
x 200 pix.
= 183. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.915 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0451
Minimum - Maximum-0.07890198 - 0.12760946
Average (Standard dev.)0.001573201 (±0.0090089645)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 183.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_53317_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53317_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : MjTET

EntireName: MjTET
Components
  • Cell: MjTET
    • Protein or peptide: Putative aminopeptidase MJ0555

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Supramolecule #1: MjTET

SupramoleculeName: MjTET / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Enzyme obtained from genetically modified E. coli cells.
Source (natural)Organism: Methanocaldococcus jannaschii (archaea)

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Macromolecule #1: Putative aminopeptidase MJ0555

MacromoleculeName: Putative aminopeptidase MJ0555 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Aminopeptidases
Source (natural)Organism: Methanocaldococcus jannaschii (archaea)
Molecular weightTheoretical: 38.677625 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSVVEYLKKL SKLHGISGRE DSVREFMKKE LEKYCDSVEI DNFGNLIAKR GNKGKKIMIA AHMDEIGLMV KYIDDNGFLK FTKIGGIYD PTILNQKVVV HGSKGDLIGV LGSKPPHRMK EEEKTKIIKY EDMFIDIGAE SREEAIEMGV NIGTWVSFLS E VYDLGKNR ...String:
MSVVEYLKKL SKLHGISGRE DSVREFMKKE LEKYCDSVEI DNFGNLIAKR GNKGKKIMIA AHMDEIGLMV KYIDDNGFLK FTKIGGIYD PTILNQKVVV HGSKGDLIGV LGSKPPHRMK EEEKTKIIKY EDMFIDIGAE SREEAIEMGV NIGTWVSFLS E VYDLGKNR LTGKAFDDRV GCAVLLEVMK RLSEEDIDCQ VYAVGTVQEE VGLKGARVSA FKINPDVAIA LDVTIAGDHP GI KKEDAPV DLGKGPVVGI VDASGRGLIA HPKVLDMIKA VSEKYKIDVQ WEVGEGGTTD ATAIHLTREG IPTGVISVPA RYI HTPVEV IDKRDLEKTV ELVYNCIKEV NNFF

UniProtKB: Putative aminopeptidase MJ0555

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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

Concentration1 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Specialist opticsDetails: Low electron dose was applied
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 4.0 sec. / Average electron dose: 40.0 e/Å2 / Details: 40 frames
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 36000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4000
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER / Details: Angle assignment type: Euler

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Atomic model buiding 1

DetailsInitial fitting was done using Phenix.doc_in_map; consecutive refinement was done alternating automatic refinement in Phenix with manual refinement in coot.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9qr6:
CryoEM structure of the tetrahedral M42 aminopeptidase from M. jannaschii

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