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- EMDB-76918: Bacterial Proteasome Activator Bpa from Mycobacterium tuberculosi... -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-76918
TitleBacterial Proteasome Activator Bpa from Mycobacterium tuberculosis in the undecameric state
Map data
Sample
  • Complex: Bpa assembled into a undecamer
    • Protein or peptide: Bacterial proteasome activator
KeywordsProteasome / Activator / Tuberculosis / CHAPERONE
Function / homologyBacterial proteasome activator / Bacterial proteasome activator / proteasome accessory complex / positive regulation of proteasomal protein catabolic process / proteasome binding / peptidoglycan-based cell wall / protein homooligomerization / plasma membrane / Bacterial proteasome activator
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsUday AB / Zeytuni N / Davis B / Vahidi S
Funding support Canada, 2 items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT451412 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN/03031-2022 Canada
CitationJournal: J.Am.Chem.Soc. / Year: 2026
Title: Resolving Hidden Stoichiometries
Authors: Davis BTV / Uday AB / Haris A / Keszei AFA / Ujma J / Bruton D / Richardson K / Mazhab-Jafari MT / Giles K / Zeytuni N / Vahidi S
History
DepositionApr 27, 2026-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_76918.png

Downloads & links

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Map

FileDownload / File: emd_76918.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 384 pix.
= 328.32 Å		0.86 Å/pix.
x 384 pix.
= 328.32 Å		0.86 Å/pix.
x 384 pix.
= 328.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.855 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0614
Minimum - Maximum-0.05291203 - 0.25084522
Average (Standard dev.)-0.00025958498 (±0.007895499)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 328.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_76918_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_76918_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 : Bpa assembled into a undecamer

EntireName: Bpa assembled into a undecamer
Components
  • Complex: Bpa assembled into a undecamer
    • Protein or peptide: Bacterial proteasome activator

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Supramolecule #1: Bpa assembled into a undecamer

SupramoleculeName: Bpa assembled into a undecamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)

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Macromolecule #1: Bacterial proteasome activator

MacromoleculeName: Bacterial proteasome activator / type: protein_or_peptide / ID: 1 / Details: 155-166 deletion / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MVIGLSTGSD DDDVEVIGGV DPRLIAVQEN DSDESSLTDL VEQPAKVMRI GTMIKQLLEE VRAAPLDEAS RNRLRDIHAT SIRELEDGLA PELREELDRL TLPFNEDAVP SDAELRIAQA QLVGWLEGLF HGIQTALFAQ QMAARAQLQQ MRQGGHGTGQ YL

UniProtKB: Bacterial proteasome activator

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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

Concentration5 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
100.0 mMNaClSoidum Chloride
50.0 mMNaH2PO4Sodium Phosphate Monobasic
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE / Details: Ab-initio model generated in cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 99240
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4) / Details: Non-uniform refinement in cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4) / Details: Non-uniform refinement in cryoSPARC
FSC plot (resolution estimation)

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