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- EMDB-19150: Cryo-EM map of the 20S proteasome in complex with the bacterial p... -

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Basic information

Entry
Database: EMDB / ID: EMD-19150
TitleCryo-EM map of the 20S proteasome in complex with the bacterial proteasome activator Bpa from M. tuberculosis
Map data
Sample
  • Complex: Complex of the 20S proteasome with bacterial proteasome activator Bpa from M. tuberculosis
    • Protein or peptide: Proteasome subunit alpha
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Bacterial proteasome activator
Keywordsprotein degradation / quality control / proteasomal activator / mycobacteria / HYDROLASE
Function / homology
Function and homology information


symbiont-mediated perturbation of host defenses / proteasome accessory complex / zymogen binding / positive regulation of proteasomal protein catabolic process / proteasome binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process ...symbiont-mediated perturbation of host defenses / proteasome accessory complex / zymogen binding / positive regulation of proteasomal protein catabolic process / proteasome binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / proteolysis involved in protein catabolic process / peptidoglycan-based cell wall / protein homooligomerization / modification-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Bacterial proteasome activator / Bacterial proteasome activator / Proteasome, alpha subunit, bacterial / Proteasome subunit beta, actinobacteria / Proteasome B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit ...Bacterial proteasome activator / Bacterial proteasome activator / Proteasome, alpha subunit, bacterial / Proteasome subunit beta, actinobacteria / Proteasome B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
Proteasome subunit beta / Proteasome subunit alpha / Bacterial proteasome activator
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsZdanowicz R / von Rosen T / Afanasyev P / Boehringer D / Glockshuber R / Weber-Ban E
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Nat Commun / Year: 2025
Title: Substrates bind to residues lining the ring of asymmetrically engaged bacterial proteasome activator Bpa.
Authors: Tatjana von Rosen / Rafal Zdanowicz / Yasser El Hadeg / Pavel Afanasyev / Daniel Boehringer / Alexander Leitner / Rudi Glockshuber / Eilika Weber-Ban /
Abstract: Mycobacteria harbor a proteasome that was acquired by Actinobacteria through horizontal gene transfer and that supports the persistence of the human pathogen Mycobacterium tuberculosis within host ...Mycobacteria harbor a proteasome that was acquired by Actinobacteria through horizontal gene transfer and that supports the persistence of the human pathogen Mycobacterium tuberculosis within host macrophages. The core particle of the proteasome (20S CP) associates with ring-shaped activator complexes to degrade protein substrates. One of these is the bacterial proteasome activator Bpa that stimulates the ATP-independent proteasomal degradation of the heat shock repressor HspR. In this study, we determine the cryogenic electron microscopy 3D reconstruction of the complex between Bpa and its natural substrate HspR at 4.1 Å global resolution. The resulting maps allow us to identify regions of Bpa that interact with HspR. Using structure-guided site-directed mutagenesis and in vitro biochemical assays, we confirm the importance of the identified residues for Bpa-mediated substrate recruitment and subsequent proteasomal degradation. Additionally, we show that the dodecameric Bpa ring associates asymmetrically with the heptameric α-rings of the 20S CP, adopting a conformation resembling a hinged lid, while still engaging all seven docking sites on the proteasome.
History
DepositionDec 14, 2023-
Header (metadata) releaseApr 2, 2025-
Map releaseApr 2, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19150.png

Downloads & links

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Map

FileDownload / File: emd_19150.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 320 pix.
= 422.4 Å		1.32 Å/pix.
x 320 pix.
= 422.4 Å		1.32 Å/pix.
x 320 pix.
= 422.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.4822462 - 1.7473694
Average (Standard dev.)0.0106013855 (±0.076975726)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 422.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_19150_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_19150_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 : Complex of the 20S proteasome with bacterial proteasome activator...

EntireName: Complex of the 20S proteasome with bacterial proteasome activator Bpa from M. tuberculosis
Components
  • Complex: Complex of the 20S proteasome with bacterial proteasome activator Bpa from M. tuberculosis
    • Protein or peptide: Proteasome subunit alpha
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Bacterial proteasome activator

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Supramolecule #1: Complex of the 20S proteasome with bacterial proteasome activator...

SupramoleculeName: Complex of the 20S proteasome with bacterial proteasome activator Bpa from M. tuberculosis
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)

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Macromolecule #1: Proteasome subunit alpha

MacromoleculeName: Proteasome subunit alpha / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MSFPYFISPE QAMRERSELA RKGIARAKSV VALAYAGGVL FVAENPSRSL QKISELYDRV GFAAAGKFNE FDNLRRGGIQ FADTRGYAYD RRDVTGRQLA NVYAQTLGTI FTEQAKPYEV ELCVAEVAHY GETKRPELYR ITYDGSIADE PHFVVMGGTT EPIANALKES ...String:
MSFPYFISPE QAMRERSELA RKGIARAKSV VALAYAGGVL FVAENPSRSL QKISELYDRV GFAAAGKFNE FDNLRRGGIQ FADTRGYAYD RRDVTGRQLA NVYAQTLGTI FTEQAKPYEV ELCVAEVAHY GETKRPELYR ITYDGSIADE PHFVVMGGTT EPIANALKES YAENASLTDA LRIAVAALRA GSADTSGGDQ PTLGVASLEV AVLDANRPRR AFRRITGSAL QALLVDQESP QSDGESSG

UniProtKB: Proteasome subunit alpha

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Macromolecule #2: Proteasome subunit beta

MacromoleculeName: Proteasome subunit beta / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MATIVALKYP GGVVMAGDRR STQGNMISGR DVRKVYITDD YTATGIAGTA AVAVEFARLY AVELEHYEKL EGVPLTFAGK INRLAIMVRG NLAAAMQGLL ALPLLAGYDI HASDPQSAGR IVSFDAAGGW NIEEEGYQAV GSGSLFAKSS MKKLYSQVTD GDSGLRVAVE ...String:
MATIVALKYP GGVVMAGDRR STQGNMISGR DVRKVYITDD YTATGIAGTA AVAVEFARLY AVELEHYEKL EGVPLTFAGK INRLAIMVRG NLAAAMQGLL ALPLLAGYDI HASDPQSAGR IVSFDAAGGW NIEEEGYQAV GSGSLFAKSS MKKLYSQVTD GDSGLRVAVE ALYDAADDDS ATGGPDLVRG IFPTAVIIDA DGAVDVPESR IAELARAIIE SRSGADTFGS DGGEKWSHPQ FEK

UniProtKB: Proteasome subunit beta

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Macromolecule #3: Bacterial proteasome activator

MacromoleculeName: Bacterial proteasome activator / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MHHHHHHMVI GLSTGSDDDD VEVIGGVDPR LIAVQENDSD ESSLTDLVEQ PAKVMRIGTM IKQLLEEVRA APLDEASRNR LRDIHATSIR ELEDGLAPEL REELDRLTLP FNEDAVPSDA ELRIAQAQLV GWLEGLFHGI QTALFAQQMA ARAQLQQMRQ GALPPGVGKS GQHGHGTGQY L

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

BufferpH: 7.5
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: cryoSPARC Ab-Initio model
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 128712
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChainDetails

5lzp

source_name: PDB, initial_model_type: experimental model20S proteasome

5lfj

source_name: PDB, initial_model_type: experimental modelBacterial proteasome activator Bpa

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