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- EMDB-27225: Cryo-EM 3D map of the Mycobacterium tuberculosis 20S proteasome b... -

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Basic information

Entry
Database: EMDB / ID: EMD-27225
TitleCryo-EM 3D map of the Mycobacterium tuberculosis 20S proteasome bound to the ATP-bound Mpa ATPase
Map dataCryo-EM 3D map of the Mycobacterium tuberculosis 20S proteasome bound to the ATP-bound Mpa ATPase
Sample
  • Complex: binary complex of 20S proteasome with ATPase Mpa
    • Protein or peptide: AAA ATPase forming ring-shaped complexes
    • Protein or peptide: Proteasome subunit alpha
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome-associated ATPase
KeywordsMpa / proteasome / ANTIMICROBIAL PROTEIN
Function / homology
Function and homology information


proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / proteasomal protein catabolic process / proteasome complex / modification-dependent protein catabolic process / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Proteasome ATPase / Proteasomal ATPase, N-terminal OB domain / Proteasomal ATPase OB N-terminal domain / Proteasome, alpha subunit, bacterial / Proteasome subunit beta, actinobacteria / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / : / : / Proteasome alpha-type subunit ...Proteasome ATPase / Proteasomal ATPase, N-terminal OB domain / Proteasomal ATPase OB N-terminal domain / Proteasome, alpha subunit, bacterial / Proteasome subunit beta, actinobacteria / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / : / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / ATPase, AAA-type, conserved site / AAA-protein family signature. / Nucleophile aminohydrolases, N-terminal / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Proteasome subunit beta / AAA ATPase forming ring-shaped complexes / Proteasome-associated ATPase / Proteasome subunit alpha
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsXiao X / Li H
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Library of Medicine (NIH/NLM)R01 United States
CitationJournal: mSphere / Year: 2022
Title: The β-Grasp Domain of Proteasomal ATPase Mpa Makes Critical Contacts with the Mycobacterium tuberculosis 20S Core Particle to Facilitate Degradation.
Authors: Xiansha Xiao / Xiang Feng / Jin Hee Yoo / Amanda Kovach / K Heran Darwin / Huilin Li /
Abstract: Mycobacterium tuberculosis possesses a Pup-proteasome system analogous to the eukaryotic ubiquitin-proteasome pathway. We have previously shown that the hexameric mycobacterial proteasome ATPase (Mpa) ...Mycobacterium tuberculosis possesses a Pup-proteasome system analogous to the eukaryotic ubiquitin-proteasome pathway. We have previously shown that the hexameric mycobacterial proteasome ATPase (Mpa) recruits pupylated protein substrates via interactions between amino-terminal coiled-coils in Mpa monomers and the degradation tag Pup. However, it is unclear how Mpa rings interact with a proteasome due to the presence of a carboxyl-terminal β-grasp domain unique to Mpa homologues that makes the interaction highly unstable. Here, we describe newly identified critical interactions between Mpa and 20S core proteasomes. Interestingly, the Mpa C-terminal GQYL motif binds the 20S core particle activation pocket differently than the same motif of the ATP-independent proteasome accessory factor PafE. We further found that the β-hairpin of the Mpa β-grasp domain interacts variably with the H0 helix on top of the 20S core particle via a series of ionic and hydrogen-bond interactions. Individually mutating several involved residues reduced Mpa-mediated protein degradation both and . The Pup-proteasome system in Mycobacterium tuberculosis is critical for this species to cause lethal infections in mice. Investigating the molecular mechanism of how the Mpa ATPase recruits and unfolds pupylated substrates to the 20S proteasomal core particle for degradation will be essential to fully understand how degradation is regulated, and the structural information we report may be useful for the development of new tuberculosis chemotherapies.
History
DepositionJun 6, 2022-
Header (metadata) releaseAug 3, 2022-
Map releaseAug 3, 2022-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27225.png

Downloads & links

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Map

FileDownload / File: emd_27225.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM 3D map of the Mycobacterium tuberculosis 20S proteasome bound to the ATP-bound Mpa ATPase
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.59 Å/pix.
x 96 pix.
= 440.832 Å		4.59 Å/pix.
x 96 pix.
= 440.832 Å		4.59 Å/pix.
x 96 pix.
= 440.832 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.592 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.2
Minimum - Maximum-13.770946 - 25.607745999999999
Average (Standard dev.)-0.122346185 (±1.501035)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 440.832 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : binary complex of 20S proteasome with ATPase Mpa

EntireName: binary complex of 20S proteasome with ATPase Mpa
Components
  • Complex: binary complex of 20S proteasome with ATPase Mpa
    • Protein or peptide: AAA ATPase forming ring-shaped complexes
    • Protein or peptide: Proteasome subunit alpha
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome-associated ATPase

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Supramolecule #1: binary complex of 20S proteasome with ATPase Mpa

SupramoleculeName: binary complex of 20S proteasome with ATPase Mpa / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)

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Macromolecule #1: AAA ATPase forming ring-shaped complexes

MacromoleculeName: AAA ATPase forming ring-shaped complexes / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 67.48793 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGESERSEAF GIPRDSPLSS GDAAELEQLR REAAVLREQL ENAVGSHAPT RSARDIHQLE ARIDSLAARN SKLMETLKEA RQQLLALRE EVDRLGQPPS GYGVLLATHD DDTVDVFTSG RKMRLTCSPN IDAASLKKGQ TVRLNEALTV VEAGTFEAVG E ISTLREIL ...String:
MGESERSEAF GIPRDSPLSS GDAAELEQLR REAAVLREQL ENAVGSHAPT RSARDIHQLE ARIDSLAARN SKLMETLKEA RQQLLALRE EVDRLGQPPS GYGVLLATHD DDTVDVFTSG RKMRLTCSPN IDAASLKKGQ TVRLNEALTV VEAGTFEAVG E ISTLREIL ADGHRALVVG HADEERVVWL ADPLIAEDLP DGLPEALNDD TRPRKLRPGD SLLVDTKAGY AFERIPKAEV ED LVLEEVP DVSYADIGGL SRQIEQIRDA VELPFLHKEL YREYSLRPPK GVLLYGPPGC GKTLIAKAVA NSLAKKMAEV RGD DAHEAK SYFLNIKGPE LLNKFVGETE RHIRLIFQRA REKASEGTPV IVFFDEMDSI FRTRGTGVSS DVETTVVPQL LSEI DGVEG LENVIVIGAS NREDMIDPAI LRPGRLDVKI KIERPDAEAA QDIYSKYLTE FLPVHADDLA EFDGDRSACI KAMIE KVVD RMYAEIDDNR FLEVTYANGD KEVMYFKDFN SGAMIQNVVD RAKKNAIKSV LETGQPGLRI QHLLDSIVDE FAENED LPN TTNPDDWARI SGKKGERIVY IRTLVTGKSS SASRAIDTES NLGQYL

UniProtKB: AAA ATPase forming ring-shaped complexes

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Macromolecule #2: Proteasome subunit alpha

MacromoleculeName: Proteasome subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 14 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 26.911039 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSFPYFISPE QAMRERSELA RKGIARAKSV VALAYAGGVL FVAENPSRSL QKISELYDRV GFAAAGKFNE FDNLRRGGIQ FADTRGYAY DRRDVTGRQL ANVYAQTLGT IFTEQAKPYE VELCVAEVAH YGETKRPELY RITYDGSIAD EPHFVVMGGT T EPIANALK ...String:
MSFPYFISPE QAMRERSELA RKGIARAKSV VALAYAGGVL FVAENPSRSL QKISELYDRV GFAAAGKFNE FDNLRRGGIQ FADTRGYAY DRRDVTGRQL ANVYAQTLGT IFTEQAKPYE VELCVAEVAH YGETKRPELY RITYDGSIAD EPHFVVMGGT T EPIANALK ESYAENASLT DALRIAVAAL RAGSADTSGG DQPTLGVASL EVAVLDANRP RRAFRRITGS ALQALLVDQE SP QSDGESS G

UniProtKB: Proteasome subunit alpha

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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 (bacteria)
Molecular weightTheoretical: 30.332006 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTWPLPDRLS INSLSGTPAV DLSSFTDFLR RQAPELLPAS ISGGAPLAGG DAQLPHGTTI VALKYPGGVV MAGDRRSTQG NMISGRDVR KVYITDDYTA TGIAGTAAVA VEFARLYAVE LEHYEKLEGV PLTFAGKINR LAIMVRGNLA AAMQGLLALP L LAGYDIHA ...String:
MTWPLPDRLS INSLSGTPAV DLSSFTDFLR RQAPELLPAS ISGGAPLAGG DAQLPHGTTI VALKYPGGVV MAGDRRSTQG NMISGRDVR KVYITDDYTA TGIAGTAAVA VEFARLYAVE LEHYEKLEGV PLTFAGKINR LAIMVRGNLA AAMQGLLALP L LAGYDIHA SDPQSAGRIV SFDAAGGWNI EEEGYQAVGS GSLFAKSSMK KLYSQVTDGD SGLRVAVEAL YDAADDDSAT GG PDLVRGI FPTAVIIDAD GAVDVPESRI AELARAIIES RSGADTFGSD GGEK

UniProtKB: Proteasome subunit beta

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Macromolecule #4: Proteasome-associated ATPase

MacromoleculeName: Proteasome-associated ATPase / type: protein_or_peptide / ID: 4 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 479.527 Da
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GQYL

UniProtKB: Proteasome-associated ATPase

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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: 8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 6.0 sec. / Average electron dose: 1.2 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.2 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6bgo

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 213000
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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