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- EMDB-55793: 1.80 A cryo-EM structure of Mycobacterium tuberculosis BfrB prepa... -

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Basic information

Entry
Database: EMDB / ID: EMD-55793
Title1.80 A cryo-EM structure of Mycobacterium tuberculosis BfrB prepared under isotope-depleted abundance
Map dataBfrB isotope-depleted - Map
Sample
  • Organelle or cellular component: Mycobacterium tuberculosis BfrB C13 and N15 isotope depleted
    • Protein or peptide: Ferritin BfrB
  • Ligand: water
KeywordsBfrB / Fe storage / C13 and N15 Isotope-depleted / METAL BINDING PROTEIN
Function / homology
Function and homology information


Mtb iron assimilation by chelation / response to nitrosative stress / encapsulin nanocompartment / iron ion sequestering activity / ferroxidase / ferroxidase activity / ferric iron binding / peptidoglycan-based cell wall / iron ion transport / ferrous iron binding ...Mtb iron assimilation by chelation / response to nitrosative stress / encapsulin nanocompartment / iron ion sequestering activity / ferroxidase / ferroxidase activity / ferric iron binding / peptidoglycan-based cell wall / iron ion transport / ferrous iron binding / intracellular iron ion homeostasis / response to hypoxia / extracellular region / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Ferritin, prokaryotic-type / Ferritin / Ferritin-like diiron domain / Ferritin-like diiron domain profile. / Ferritin/DPS protein domain / Ferritin-like domain / Ferritin-like / Ferritin-like superfamily
Similarity search - Domain/homology
Bacterioferritin BfrB
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.8 Å
AuthorsHakke SS / Noteborn WEM / Knoops K / Heeren RMA
Funding support Netherlands, 1 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)15575 Netherlands
CitationJournal: To Be Published
Title: Isotope Decluttering Reduces Spectral Complexity While Maintaining Protein Structure
Authors: Hakke SS / Noteborn WEM / Cabukusta B / Gao Y / Knoops K / Lopez Iglesias C / Kilgour DPA / Clarke DJ / Mathew A / Heeren RMA
History
DepositionNov 21, 2025-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55793.png

Downloads & links

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Map

FileDownload / File: emd_55793.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationBfrB isotope-depleted - Map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.51 Å/pix.
x 400 pix.
= 205.2 Å		0.51 Å/pix.
x 400 pix.
= 205.2 Å		0.51 Å/pix.
x 400 pix.
= 205.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.513 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.26170433 - 0.4938398
Average (Standard dev.)0.0002471988 (±0.019691579)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 205.20001 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55793_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: BfrB isotope-depleted - Half map B

Fileemd_55793_half_map_1.map
AnnotationBfrB isotope-depleted - Half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: BfrB isotope-depleted - Half map A

Fileemd_55793_half_map_2.map
AnnotationBfrB isotope-depleted - Half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mycobacterium tuberculosis BfrB C13 and N15 isotope depleted

EntireName: Mycobacterium tuberculosis BfrB C13 and N15 isotope depleted
Components
  • Organelle or cellular component: Mycobacterium tuberculosis BfrB C13 and N15 isotope depleted
    • Protein or peptide: Ferritin BfrB
  • Ligand: water

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Supramolecule #1: Mycobacterium tuberculosis BfrB C13 and N15 isotope depleted

SupramoleculeName: Mycobacterium tuberculosis BfrB C13 and N15 isotope depleted
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)

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Macromolecule #1: Ferritin BfrB

MacromoleculeName: Ferritin BfrB / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO / EC number: ferroxidase
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 20.463936 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MTEYEGPKTK FHALMQEQIH NEFTAAQQYV AIAVYFDSED LPQLAKHFYS QAVEERNHAM MLVQHLLDRD LRVEIPGVDT VRNQFDRPR EALALALDQE RTVTDQVGRL TAVARDEGDF LGEQFMQWFL QEQIEEVALM ATLVRVADRA GANLFELENF V AREVDVAP AASGAPHAAG GRL

UniProtKB: Bacterioferritin BfrB

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Macromolecule #2: water

MacromoleculeName: water / type: ligand / ID: 2 / Number of copies: 1833 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration50 mg/mL
BufferpH: 8
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 285 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
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 opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: O (octahedral) / Resolution.type: BY AUTHOR / Resolution: 1.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1) / Number images used: 500000
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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