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- EMDB-45129: Apo DUF4297 tetramer -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-45129
TitleApo DUF4297 tetramer
Map dataDeepEmhancer refined map
Sample
  • Complex: DUF4297 tetramer
    • Protein or peptide: DUF4297
Keywordsanti-phage / nuclease / ATPase / tetramer / ANTIVIRAL PROTEIN
Biological speciesBacillus sp. HMF5848 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.77 Å
AuthorsRish AD / Fosuah E / Fu TM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GR128399 United States
CitationJournal: To Be Published
Title: Structure-guided characterization of a novel bacterial anti-phage system
Authors: Rish AD / Fosuah E / Fu TM
History
DepositionMay 29, 2024-
Header (metadata) releaseJun 11, 2025-
Map releaseJun 11, 2025-
UpdateJun 11, 2025-
Current statusJun 11, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_45129.png

Downloads & links

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Map

FileDownload / File: emd_45129.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEmhancer refined map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 336 pix.
= 366.24 Å		1.09 Å/pix.
x 336 pix.
= 366.24 Å		1.09 Å/pix.
x 336 pix.
= 366.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.03844393 - 2.3545675
Average (Standard dev.)0.0006696779 (±0.015890507)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 366.24002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_45129_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_45129_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DUF4297 tetramer

EntireName: DUF4297 tetramer
Components
  • Complex: DUF4297 tetramer
    • Protein or peptide: DUF4297

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Supramolecule #1: DUF4297 tetramer

SupramoleculeName: DUF4297 tetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: pre-assembly oligomer of DUF anti-phage defense protein
Source (natural)Organism: Bacillus sp. HMF5848 (bacteria)
Molecular weightTheoretical: 1.02 MDa

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Macromolecule #1: DUF4297

MacromoleculeName: DUF4297 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Bacillus sp. HMF5848 (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSREADHTIK GFLYQFNKTL NSILSSTDQD EIQIEGIIED IDIKNSNITN AIQCKYHESK VRHNLSDIYK PILQMLLHFL ENDSLNIKYA LYAYFPNEQV GVKEVTKSQI EEILSSSNFD YISKYISKIK PPKEQIIKEL LGKTSKTTED KTRIKKYYET SKLETIVDID ...String:
MSREADHTIK GFLYQFNKTL NSILSSTDQD EIQIEGIIED IDIKNSNITN AIQCKYHESK VRHNLSDIYK PILQMLLHFL ENDSLNIKYA LYAYFPNEQV GVKEVTKSQI EEILSSSNFD YISKYISKIK PPKEQIIKEL LGKTSKTTED KTRIKKYYET SKLETIVDID KFLRDHFVFE IGLSYEELMN ETKNLLMKEG FSLEDVKDLF YPNSIQYIAE LSILPEAEKR ISSKNKLIDY LKGNKKTAMS RWTSEVLTRK QLLKVRKNQL VPSLNINSRS RYFIIDPDTI DNFDDEFILF VKDYLDKYNS KIKLHTETPC FILKTDVNNL SEYHKRFVSR NIQIITGYIG DTFYFKEFNK EPKRIIKDNW VEFKARISCN SDEVIKCINY KKCDDLYIVG GVDVSLLDTA DVNIENLEIN NFRELKYLLS MLKEI

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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

Concentration1.75 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.77 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 110823
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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