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- PDB-9ce7: 20S Proteasome core particle open gate variant -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 9ce7
Title20S Proteasome core particle open gate variant
Components
  • Proteasome subunit alpha
  • Proteasome subunit beta
KeywordsANTIMICROBIAL PROTEIN / Proteasome / Proteolysis
Function / homology
Function and homology information


symbiont-mediated perturbation of host defenses / zymogen 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 / modification-dependent protein catabolic process ...symbiont-mediated perturbation of host defenses / zymogen 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 / modification-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
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
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsZeytuni, N. / Uday, A.B. / Vahidi, S. / Turner, M.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT451412 Canada
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN/03031-2022 Canada
CitationJournal: Nat Commun / Year: 2025
Title: Structural basis for allosteric modulation of M. tuberculosis proteasome core particle.
Authors: Madison Turner / Adwaith B Uday / Algirdas Velyvis / Enrico Rennella / Natalie Zeytuni / Siavash Vahidi /
Abstract: The Mycobacterium tuberculosis (Mtb) proteasome system selectively degrades damaged or misfolded proteins and is crucial for the pathogen's survival within the host. Targeting the 20S core particle ...The Mycobacterium tuberculosis (Mtb) proteasome system selectively degrades damaged or misfolded proteins and is crucial for the pathogen's survival within the host. Targeting the 20S core particle (CP) offers a viable strategy for developing tuberculosis treatments. The activity of Mtb 20S CP, like that of its eukaryotic counterpart, is allosterically regulated, yet the specific conformations involved have not been captured in high-resolution structures to date. Here, we use single-particle electron cryomicroscopy and H/D exchange mass spectrometry to determine the Mtb 20S CP structure in an auto-inhibited state that is distinguished from the canonical resting state by the conformation of switch helices at the α/β interface. The rearrangement of these helices collapses the S1 pocket, effectively inhibiting substrate binding. Biochemical experiments show that the Mtb 20S CP activity can be altered through allosteric sites far from the active site. Our findings underscore the potential of targeting allostery to develop antituberculosis therapeutics.
History
DepositionJun 26, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 16, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome subunit alpha
B: Proteasome subunit alpha
C: Proteasome subunit alpha
D: Proteasome subunit alpha
E: Proteasome subunit alpha
F: Proteasome subunit alpha
G: Proteasome subunit alpha
H: Proteasome subunit alpha
I: Proteasome subunit alpha
J: Proteasome subunit alpha
K: Proteasome subunit alpha
L: Proteasome subunit alpha
M: Proteasome subunit alpha
N: Proteasome subunit alpha
O: Proteasome subunit beta
P: Proteasome subunit beta
Q: Proteasome subunit beta
R: Proteasome subunit beta
S: Proteasome subunit beta
T: Proteasome subunit beta
U: Proteasome subunit beta
V: Proteasome subunit beta
W: Proteasome subunit beta
X: Proteasome subunit beta
Y: Proteasome subunit beta
Z: Proteasome subunit beta
a: Proteasome subunit beta
b: Proteasome subunit beta


Theoretical massNumber of molelcules
Total (without water)710,00628
Polymers710,00628
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "B"
d_2ens_1chain "A"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "F"
d_7ens_1chain "G"
d_8ens_1chain "H"
d_9ens_1chain "I"
d_10ens_1chain "J"
d_11ens_1chain "K"
d_12ens_1chain "L"
d_13ens_1chain "M"
d_14ens_1chain "N"
d_1ens_2chain "X"
d_2ens_2chain "P"
d_3ens_2chain "Q"
d_4ens_2chain "R"
d_5ens_2chain "S"
d_6ens_2chain "T"
d_7ens_2chain "U"
d_8ens_2chain "V"
d_9ens_2chain "W"
d_10ens_2chain "O"
d_11ens_2chain "Y"
d_12ens_2chain "Z"
d_13ens_2chain "a"
d_14ens_2chain "b"

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1SERSERLEULEUBB8 - 2343 - 229
d_2ens_1SERSERLEULEUAA8 - 2343 - 229
d_3ens_1SERSERLEULEUCC8 - 2343 - 229
d_4ens_1SERSERLEULEUDD8 - 2343 - 229
d_5ens_1SERSERLEULEUEE8 - 2343 - 229
d_6ens_1SERSERLEULEUFF8 - 2343 - 229
d_7ens_1SERSERLEULEUGG8 - 2343 - 229
d_8ens_1SERSERLEULEUHH8 - 2343 - 229
d_9ens_1SERSERLEULEUII8 - 2343 - 229
d_10ens_1SERSERLEULEUJJ8 - 2343 - 229
d_11ens_1SERSERLEULEUKK8 - 2343 - 229
d_12ens_1SERSERLEULEULL8 - 2343 - 229
d_13ens_1SERSERLEULEUMM8 - 2343 - 229
d_14ens_1SERSERLEULEUNN8 - 2343 - 229
d_1ens_2THRTHRSERSERXX1 - 2221 - 222
d_2ens_2THRTHRSERSERPP1 - 2221 - 222
d_3ens_2THRTHRSERSERQQ1 - 2221 - 222
d_4ens_2THRTHRSERSERRR1 - 2221 - 222
d_5ens_2THRTHRSERSERSS1 - 2221 - 222
d_6ens_2THRTHRSERSERTT1 - 2221 - 222
d_7ens_2THRTHRSERSERUU1 - 2221 - 222
d_8ens_2THRTHRSERSERVV1 - 2221 - 222
d_9ens_2THRTHRSERSERWW1 - 2221 - 222
d_10ens_2THRTHRSERSEROO1 - 2221 - 222
d_11ens_2THRTHRSERSERYY1 - 2221 - 222
d_12ens_2THRTHRSERSERZZ1 - 2221 - 222
d_13ens_2THRTHRSERSERaAA1 - 2221 - 222
d_14ens_2THRTHRSERSERbBA1 - 2221 - 222

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.623332269056, 0.781953920789, -0.0022244361571), (-0.781954078355, 0.623335238707, 0.000999765269968), (0.00216833981569, 0.00111622097083, 0.999997026172)-77.3170446543, 221.768913116, -0.541075399143
2given(-0.623886139502, 0.781515248862, 2.71023741063E-5), (0.781515200038, 0.623886087459, 0.000376808343215), (0.000277572671979, 0.000256266419902, -0.99999992864)161.304422201, -77.6971809777, 381.236786128
3given(-0.999999996203, 6.9167461674E-5, -5.30038068562E-5), (6.91693979272E-5, 0.999999996941, -3.65294942289E-5), (5.30012800416E-5, -3.65331603316E-5, -0.999999997928)383.035784371, -0.00607604059337, 381.327189232
4given(-0.623491032069, -0.781830478339, -0.000189922497469), (-0.781830496054, 0.62349103783, 3.44366554597E-5), (9.14913482439E-5, 0.000169958146262, -0.999999981372)460.697923665, 221.840914382, 381.285680085
5given(0.2228413415, -0.974854725712, 1.65968371906E-5), (-0.974854609875, -0.222841306652, 0.000491584351373), (-0.000475524867137, -0.000125724819565, -0.999999879035)335.557045402, 420.833990979, 381.430401865
6given(0.901141535923, -0.433524943358, -0.000236051557298), (-0.433524935431, -0.901141566508, 8.64310981276E-5), (-0.000250185907041, 2.4447583618E-5, -0.999999968405)102.011715749, 447.133478643, 381.367060855
7given(0.900698302687, 0.434445114077, 0.000101935754635), (0.434445122935, -0.900698299498, -9.18646439921E-5), (5.19032151189E-5, 0.000127027820375, -0.999999990585)-64.1946503924, 280.854234749, 381.301537679
8given(0.22247187289, 0.974939087807, -0.000202084199932), (0.974939108703, -0.22247187016, 3.61719682591E-5), (-9.69258415015E-6, -0.00020506703529, -0.999999978927)-37.7828409742, 47.3988286393, 381.368123873
9given(-0.222791694088, 0.974866073338, 9.98955098931E-6), (-0.9748659866, -0.222791678566, 0.000419680823514), (0.000411358185307, 8.3762928166E-5, 0.999999911884)47.4684018013, 420.837500597, -0.0821026807973
10given(-0.901147088902, 0.433513308341, 0.00036831478009), (-0.433513281493, -0.901147163928, 0.00015399351733), (0.000398664058672, -2.08985390875E-5, 0.999999920315)281.012832603, 447.124110634, -0.0609452177586
11given(-0.900696181189, -0.434449508213, -0.000118343196787), (0.434449520197, -0.90069617678, -0.000107399172926), (-5.99317470341E-5, -0.00014814816998, 0.99999998723)447.237002386, 280.855213519, 0.0332187453607
12given(-0.222412848512, -0.974952539043, 0.000267264793642), (0.974952572045, -0.222412862986, -2.53339843063E-5), (8.41425602526E-5, 0.000254935894364, 0.999999963964)420.806003398, 47.3949738385, -0.059060136199
13given(0.623927939069, -0.781481876052, 6.52033707097E-5), (0.781481815657, 0.62392792004, 0.000349844117976), (-0.000314079041108, -0.000167322270995, 0.999999936679)221.71052511, -77.6949271566, 0.0834487543617
14given(0.90093336802, -0.43395451696, -0.00159486616275), (-0.433954627147, -0.900934678512, 0.000294334184196), (-0.00156459788233, 0.000426924063114, -0.999998684884)102.373490524, 447.123391943, 381.483379309
15given(0.9008055785, 0.434222566472, -0.000269275206285), (0.434222517073, -0.900805614772, -0.000223743622158), (-0.000339719147585, 8.46241451349E-5, -0.999999938715)-64.1375953357, 280.923352794, 381.369289132
16given(0.222486291967, 0.974935769149, -0.000309712023289), (0.974935774119, -0.222486366332, -0.000230520998274), (-0.000293649869428, -0.000250661569052, -0.999999925469)-37.7607941714, 47.45273048, 381.434084994
17given(-0.623661074811, 0.781694865865, -2.11078951697E-5), (0.781694736227, 0.623660955359, -0.000593392928347), (-0.000450688035462, -0.000386576002025, -0.99999982372)161.252712182, -77.5396791012, 381.49094918
18given(-0.999999999873, -5.93357977524E-6, -1.4819602478E-5), (-5.93354254574E-6, 0.999999999979, -2.51222180824E-6), (1.48196173842E-5, -2.51213387518E-6, -0.999999999887)383.043626264, 0.00156171824059, 381.32831322
19given(-0.623103700603, -0.782139220919, 0.000131888161849), (-0.782139225846, 0.623103708031, 2.07696319245E-5), (-9.84247464258E-5, -9.02132702947E-5, -0.999999991087)460.649641377, 221.973083212, 381.367135115
20given(0.222622174194, -0.974904740045, 0.000339698276767), (-0.974904799219, -0.222622159189, 8.18431724836E-5), (-4.16493294782E-6, -0.000349393585308, -0.999999938953)335.545761891, 420.857679543, 381.406058134
21given(0.623701267208, -0.781662797683, -1.22786622787E-6), (0.781662643223, 0.623701144948, -0.000627678629499), (0.000491398855152, 0.000390524179457, 0.999999803009)221.777500885, -77.5369760329, -0.167906867349
22given(-0.222503912954, -0.97493174493, 0.000318508292316), (0.974931757471, -0.22250398505, -0.000211921375018), (0.000277478240246, 0.000263370514016, 0.999999926821)420.800996038, 47.4542411764, -0.104292103727
23given(0.623114588895, 0.782130550317, -0.000106619380198), (-0.782130554227, 0.623114593061, 7.70954565655E-6), (7.24659628917E-5, 7.85863445535E-5, 0.999999994286)-77.6137343255, 221.971660437, -0.0304189776752
24given(-0.222663209016, 0.974895404468, -0.000213768613389), (-0.974895424635, -0.222663184958, 0.000130727167466), (7.98469145006E-5, 0.000237510173737, 0.999999968607)47.4829400695, 420.857571558, -0.0644762121783
25given(-0.900919739311, 0.433985729309, -0.000100373509582), (-0.433985721802, -0.900919606892, 0.00050516281988), (0.000128804992011, 0.000498671826002, 0.999999867368)280.961797395, 447.089752583, -0.133328613908
26given(-0.900776477376, -0.434282931641, 0.000270355240289), (0.434282893821, -0.900776516413, -0.000188717579802), (0.000325486475351, -5.25817006407E-5, 0.999999945647)447.185680803, 280.901792837, -0.0439431540711

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Components

#1: Protein
Proteasome subunit alpha / 20S proteasome alpha subunit / Proteasome core protein PrcA


Mass: 26269.326 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Details: 20S proteasome alpha subunit lacking residues 2-6 / Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: prcA, Rv2109c / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WHU1
#2: Protein
Proteasome subunit beta / 20S proteasome beta subunit / Proteasome core protein PrcB


Mass: 24445.383 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: prcB, Rv2110c / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WHT9, proteasome endopeptidase complex
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 20S Proteasome core particle open gate variant / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMSodium chlorideNaCl1
250 mMSodium phosphate monobasicNaH2PO41
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2750 nm / Nominal defocus min: 1250 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
9PHENIXdev_5316model refinement
10cryoSPARC4initial Euler assignment
11cryoSPARC4final Euler assignment
13cryoSPARC43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D7 (2x7 fold dihedral)
3D reconstructionResolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 756031 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 32.47 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002146830
ELECTRON MICROSCOPYf_angle_d0.458263392
ELECTRON MICROSCOPYf_chiral_restr0.04057224
ELECTRON MICROSCOPYf_plane_restr0.00348358
ELECTRON MICROSCOPYf_dihedral_angle_d3.53056818
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2BBELECTRON MICROSCOPYNCS constraints3.49837574173E-13
ens_1d_3BBELECTRON MICROSCOPYNCS constraints2.80679498609E-11
ens_1d_4BBELECTRON MICROSCOPYNCS constraints1.97212712987E-11
ens_1d_5BBELECTRON MICROSCOPYNCS constraints1.17144086036E-10
ens_1d_6BBELECTRON MICROSCOPYNCS constraints3.72923603306E-11
ens_1d_7BBELECTRON MICROSCOPYNCS constraints1.4027623657E-13
ens_1d_8BBELECTRON MICROSCOPYNCS constraints8.73177937007E-13
ens_1d_9BBELECTRON MICROSCOPYNCS constraints3.65401611299E-13
ens_1d_10BBELECTRON MICROSCOPYNCS constraints7.31337022763E-11
ens_1d_11BBELECTRON MICROSCOPYNCS constraints4.37712535617E-13
ens_1d_12BBELECTRON MICROSCOPYNCS constraints4.90220760192E-13
ens_1d_13BBELECTRON MICROSCOPYNCS constraints1.18607690516E-11
ens_1d_14BBELECTRON MICROSCOPYNCS constraints1.04410401337E-11
ens_2d_2XXELECTRON MICROSCOPYNCS constraints1.83854727217E-13
ens_2d_3XXELECTRON MICROSCOPYNCS constraints4.06629016086E-13
ens_2d_4XXELECTRON MICROSCOPYNCS constraints8.78590042569E-11
ens_2d_5XXELECTRON MICROSCOPYNCS constraints7.64941164691E-13
ens_2d_6XXELECTRON MICROSCOPYNCS constraints9.11354017614E-13
ens_2d_7XXELECTRON MICROSCOPYNCS constraints2.25886344567E-13
ens_2d_8XXELECTRON MICROSCOPYNCS constraints6.4976230143E-11
ens_2d_9XXELECTRON MICROSCOPYNCS constraints6.36938080686E-11
ens_2d_10XXELECTRON MICROSCOPYNCS constraints8.61015681666E-12
ens_2d_11XXELECTRON MICROSCOPYNCS constraints9.69953742897E-11
ens_2d_12XXELECTRON MICROSCOPYNCS constraints4.98343475599E-13
ens_2d_13XXELECTRON MICROSCOPYNCS constraints1.5147756422E-11
ens_2d_14XXELECTRON MICROSCOPYNCS constraints2.75852939858E-13

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