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- EMDB-4127: Cryo-EM reconstruction of the Bacterial proteasome interactor (Bp... -

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Basic information

Entry
Database: EMDB / ID: EMD-4127
TitleCryo-EM reconstruction of the Bacterial proteasome interactor (Bpa) bound to the 20S proteasome of M. tuberculosis.
Map databacterial proteasome activator bound to bacterial proteasome reconstructed without applied symmetry
Sample
  • Complex: proteasome in complex with bacterial proteasome activator
Function / homology
Function and homology information


symbiont-mediated perturbation of host defenses / proteasome accessory complex / positive regulation of proteasomal protein catabolic process / zymogen binding / proteasome binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process ...symbiont-mediated perturbation of host defenses / proteasome accessory complex / positive regulation of proteasomal protein catabolic process / zymogen binding / proteasome binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteolysis involved in protein catabolic process / peptidoglycan-based cell wall / proteasomal protein catabolic process / modification-dependent protein catabolic process / protein homooligomerization / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Bacterial proteasome activator / Bacterial proteasome activator / Proteasome, alpha subunit, bacterial / Proteasome subunit beta, actinobacteria / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-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: 4.6 Å
AuthorsBolten M / Delley CL / Leibundgut M / Boehringer D / Ban N / Weber-Ban E
CitationJournal: Structure / Year: 2016
Title: Structural Analysis of the Bacterial Proteasome Activator Bpa in Complex with the 20S Proteasome.
Authors: Marcel Bolten / Cyrille L Delley / Marc Leibundgut / Daniel Boehringer / Nenad Ban / Eilika Weber-Ban /
Abstract: Mycobacterium tuberculosis harbors proteasomes that recruit substrates for degradation through an ubiquitin-like modification pathway. Recently, a non-ATPase activator termed Bpa (bacterial ...Mycobacterium tuberculosis harbors proteasomes that recruit substrates for degradation through an ubiquitin-like modification pathway. Recently, a non-ATPase activator termed Bpa (bacterial proteasome activator) was shown to support an alternate proteasomal degradation pathway. Here, we present the cryo-electron microscopy (cryo-EM) structure of Bpa in complex with the 20S core particle (CP). For docking into the cryo-EM density, we solved the X-ray structure of Bpa, showing that it forms tight four-helix bundles arranged into a 12-membered ring with a 40 Å wide central pore and the C-terminal helix of each protomer protruding from the ring. The Bpa model was fitted into the cryo-EM map of the Bpa-CP complex, revealing its architecture and striking symmetry mismatch. The Bpa-CP interface was resolved to 3.5 Å, showing the interactions between the C-terminal GQYL motif of Bpa and the proteasome α-rings. This docking mode is related to the one observed for eukaryotic activators with features specific to the bacterial complex.
History
DepositionSep 30, 2016-
Header (metadata) releaseOct 12, 2016-
Map releaseNov 23, 2016-
UpdateAug 2, 2017-
Current statusAug 2, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4127.png

Downloads & links

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Map

FileDownload / File: emd_4127.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationbacterial proteasome activator bound to bacterial proteasome reconstructed without applied symmetry
Voxel sizeX=Y=Z: 1.4 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.068901986 - 0.21896023
Average (Standard dev.)0.000502153 (±0.008364692)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 537.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z537.600537.600537.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0690.2190.001

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Supplemental data

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Sample components

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Entire : proteasome in complex with bacterial proteasome activator

EntireName: proteasome in complex with bacterial proteasome activator
Components
  • Complex: proteasome in complex with bacterial proteasome activator

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Supramolecule #1: proteasome in complex with bacterial proteasome activator

SupramoleculeName: proteasome in complex with bacterial proteasome activator
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
Molecular weightTheoretical: 930 KDa

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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

Concentration0.102 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
50.0 mMHEPES
150.0 mMSodium chlorideNaClSodium chloride
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: OTHER
Details: Quantifoil R 2/2 with an additional thin carbon layer
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 280.5 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 100000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.6 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Sampling interval: 14.0 µm / Number grids imaged: 1 / Average electron dose: 25.0 e/Å2
Details: Drift corrected in post-processing. 4 images per hole.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.0.17)
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 33652
FSC plot (resolution estimation)

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