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- EMDB-4128: Binding of the C-terminal GQYL motif of the bacterial proteasome ... -

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Basic information

Entry
Database: EMDB / ID: EMD-4128
TitleBinding of the C-terminal GQYL motif of the bacterial proteasome activator Bpa to the 20S proteasome
Map data
Sample
  • Complex: proteasome in complex with bacterial proteasome activator
    • Protein or peptide: Proteasome subunit alpha
    • Protein or peptide: Bacterial proteasome activator
    • Protein or peptide: Proteasome subunit beta
KeywordsProteasome / Proteasome activator / protein degradation / complex / 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: 3.5 Å
AuthorsBolten M / Delley CL
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 26, 2016-
Map releaseNov 23, 2016-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing 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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  • Surface view with fitted model
  • Atomic models: PDB-5lzp
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5lzp
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4128.png

Downloads & links

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Map

FileDownload / File: emd_4128.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.)
1.4 Å/pix.
x 384 pix.
= 537.6 Å		1.4 Å/pix.
x 384 pix.
= 537.6 Å		1.4 Å/pix.
x 384 pix.
= 537.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.045 / Movie #1: 0.05
Minimum - Maximum-0.15803975 - 0.3953664
Average (Standard dev.)0.00048098297 (±0.009622717)
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-0.1580.3950.000

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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
    • Protein or peptide: Proteasome subunit alpha
    • Protein or peptide: Bacterial proteasome activator
    • Protein or peptide: Proteasome subunit beta

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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) / Location in cell: cytoplasm
Molecular weightTheoretical: 930 KDa

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Macromolecule #1: Proteasome subunit alpha

MacromoleculeName: Proteasome subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 26.024971 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: SPEQAMRERS ELARKGIARA KSVVALAYAG GVLFVAENPS RSLQKISELY DRVGFAAAGK FNEFDNLRRG GIQFADTRGY AYDRRDVTG RQLANVYAQT LGTIFTEQAK PYEVELCVAE VAHYGETKRP ELYRITYDGS IADEPHFVVM GGTTEPIANA L KESYAENA ...String:
SPEQAMRERS ELARKGIARA KSVVALAYAG GVLFVAENPS RSLQKISELY DRVGFAAAGK FNEFDNLRRG GIQFADTRGY AYDRRDVTG RQLANVYAQT LGTIFTEQAK PYEVELCVAE VAHYGETKRP ELYRITYDGS IADEPHFVVM GGTTEPIANA L KESYAENA SLTDALRIAV AALRAGSADT SGGDQPTLGV ASLEVAVLDA NRPRRAFRRI TGSALQALLV DQESPQSDGE SS G

UniProtKB: Proteasome subunit alpha

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Macromolecule #2: Bacterial proteasome activator

MacromoleculeName: Bacterial proteasome activator / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 19.792113 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
MHHHHHHVIG LSTGSDDDDV EVIGGVDPRL IAVQENDSDE SSLTDLVEQP AKVMRIGTMI KQLLEEVRAA PLDEASRNRL RDIHATSIR ELEDGLAPEL REELDRLTLP FNEDAVPSDA ELRIAQAQLV GWLEGLFHGI QTALFAQQMA ARAQLQQMRQ G ALPPGVGK SGQHGHGTGQ YL

UniProtKB: Bacterial proteasome activator

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Macromolecule #3: Proteasome subunit beta

MacromoleculeName: Proteasome subunit beta / type: protein_or_peptide / ID: 3 / Number of copies: 14 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Mycobacterium tuberculosis H37Rv (bacteria)
Molecular weightTheoretical: 25.457504 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: ATIVALKYPG GVVMAGDRRS TQGNMISGRD VRKVYITDDY TATGIAGTAA VAVEFARLYA VELEHYEKLE GVPLTFAGKI NRLAIMVRG NLAAAMQGLL ALPLLAGYDI HASDPQSAGR IVSFDAAGGW NIEEEGYQAV GSGSLFAKSS MKKLYSQVTD G DSGLRVAV ...String:
ATIVALKYPG GVVMAGDRRS TQGNMISGRD VRKVYITDDY TATGIAGTAA VAVEFARLYA VELEHYEKLE GVPLTFAGKI NRLAIMVRG NLAAAMQGLL ALPLLAGYDI HASDPQSAGR IVSFDAAGGW NIEEEGYQAV GSGSLFAKSS MKKLYSQVTD G DSGLRVAV EALYDAADDD SATGGPDLVR GIFPTAVIID ADGAVDVPES RIAELARAII ESRSGADTFG SDGGEKWSHP QF EK

UniProtKB: Proteasome subunit beta

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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 chlorideNaCl
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 22 sec. / 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
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Number grids imaged: 1 / Average electron dose: 25.0 e/Å2
Details: Drift corrected in post-processing. 4 images per hole.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 100000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 48799
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-5lzp:
Binding of the C-terminal GQYL motif of the bacterial proteasome activator Bpa to the 20S proteasome

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