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- PDB-9ce5: 20S Proteasome core particle -

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Basic information

Entry
Database: PDB / ID: 9ce5
Title20S Proteasome core particle
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: 2.66 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)718,99028
Polymers718,99028
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 "H"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "A"
d_7ens_1chain "G"
d_8ens_1chain "F"
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 "a"
d_2ens_2chain "P"
d_3ens_2chain "T"
d_4ens_2chain "R"
d_5ens_2chain "S"
d_6ens_2chain "O"
d_7ens_2chain "U"
d_8ens_2chain "V"
d_9ens_2chain "W"
d_10ens_2chain "X"
d_11ens_2chain "Y"
d_12ens_2chain "Z"
d_13ens_2chain "Q"
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_1SERSERLEULEUHH8 - 2348 - 234
d_2ens_1SERSERLEULEUBB8 - 2348 - 234
d_3ens_1SERSERLEULEUCC8 - 2348 - 234
d_4ens_1SERSERLEULEUDD8 - 2348 - 234
d_5ens_1SERSERLEULEUEE8 - 2348 - 234
d_6ens_1SERSERLEULEUAA8 - 2348 - 234
d_7ens_1SERSERLEULEUGG8 - 2348 - 234
d_8ens_1SERSERLEULEUFF8 - 2348 - 234
d_9ens_1SERSERLEULEUII8 - 2348 - 234
d_10ens_1SERSERLEULEUJJ8 - 2348 - 234
d_11ens_1SERSERLEULEUKK8 - 2348 - 234
d_12ens_1SERSERLEULEULL8 - 2348 - 234
d_13ens_1SERSERLEULEUMM8 - 2348 - 234
d_14ens_1SERSERLEULEUNN8 - 2348 - 234
d_1ens_2THRTHRSERSERaAA1 - 2221 - 222
d_2ens_2THRTHRSERSERPP1 - 2221 - 222
d_3ens_2THRTHRSERSERTT1 - 2221 - 222
d_4ens_2THRTHRSERSERRR1 - 2221 - 222
d_5ens_2THRTHRSERSERSS1 - 2221 - 222
d_6ens_2THRTHRSERSEROO1 - 2221 - 222
d_7ens_2THRTHRSERSERUU1 - 2221 - 222
d_8ens_2THRTHRSERSERVV1 - 2221 - 222
d_9ens_2THRTHRSERSERWW1 - 2221 - 222
d_10ens_2THRTHRSERSERXX1 - 2221 - 222
d_11ens_2THRTHRSERSERYY1 - 2221 - 222
d_12ens_2THRTHRSERSERZZ1 - 2221 - 222
d_13ens_2THRTHRSERSERQQ1 - 2221 - 222
d_14ens_2THRTHRSERSERbBA1 - 2221 - 222

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.900190034818, -0.435497010185, 0.000505306815633), (-0.435496819809, -0.900190158417, -0.000445674016042), (0.000648961923917, 0.000181131796783, -0.99999977302)102.402631775, 447.389436178, 381.167981327
2given(-0.222785674984, -0.974867402436, 0.000301147547086), (0.974867423497, -0.222785729128, -0.000159692549377), (0.000222770436652, 0.000258001720918, 0.999999941904)420.812485889, 47.5244897894, -0.0918114968987
3given(-0.90092099076, -0.433982950033, 0.000409253443283), (0.433982944161, -0.900921080108, -0.000107673348915), (0.000415433451763, 8.06038340413E-5, 0.999999910459)447.083389377, 280.972457106, -0.0892405939432
4given(-0.900997622439, 0.433823898171, 0.000331261851997), (-0.433823708873, -0.900997625256, 0.000518558658961), (0.000523429280848, 0.000323510873577, 0.999999810681)280.915673189, 447.039788056, -0.155728842379
5given(0.222383273712, -0.974959035343, 0.000747646738196), (-0.974959320524, -0.222383250312, 0.000115339283247), (5.3813035394E-5, -0.00075457468326, -0.999999713861)335.474184799, 420.807114765, 381.479613333
6given(0.623416093046, 0.781890243684, 0.0001475222249), (-0.781890221334, 0.62341599557, 0.000422196234913), (0.000238143402294, -0.000378550112347, 0.999999899994)-77.6629497538, 221.769235824, 0.0406066477689
7given(-0.222628861294, 0.974903070938, -0.000626413606743), (-0.974903244389, -0.22262865555, 0.000381848525066), (0.000232807680633, 0.000695703159865, 0.999999730899)47.5915314445, 420.78613226, -0.184345979755
8given(0.623281892286, -0.781997117739, 0.00043657265102), (0.781997166441, 0.623281495345, -0.000780537522516), (0.00033827043814, 0.000827893480077, 0.999999600083)221.80793396, -77.4221101694, -0.229257400338
9given(-0.624088681684, -0.781352913842, 0.000970270163008), (-0.781353490407, 0.624088499375, -0.000517665584162), (-0.000201054937439, -0.00108119321048, -0.999999395299)460.427205748, 221.760994056, 381.588227869
10given(-0.999999364711, 0.00111567575018, -0.000160767243573), (0.00111590041518, 0.999998391482, -0.00140420809581), (0.000159200344055, -0.00140438660396, -0.999999001176)382.840373909, 0.154860252274, 381.598456744
11given(-0.623132916054, 0.782115839326, -0.000427557812308), (0.782115904962, 0.623132584263, -0.000702591498735), (-0.000283082735231, -0.000772207654699, -0.99999966178)161.179897008, -77.4289709027, 381.538835065
12given(0.223312247014, 0.9747463749, -0.00107002457177), (0.974746950257, -0.223312281625, 8.85473010642E-5), (-0.000152638467798, -0.0010627768848, -0.999999423603)-37.6489385842, 47.597677882, 381.577423749
13given(0.901108355191, 0.433593608575, -0.000561077958481), (0.433593896961, -0.901108204891, 0.000579306601507), (-0.000254408312152, -0.000765297997352, -0.999999674798)-63.9543571361, 280.912088908, 381.536970654
14given(-0.623818713132, 0.781569066634, -8.50095412293E-5), (0.781568893292, 0.623818640797, 0.000606986443719), (0.000527432364741, 0.000312208689152, -0.99999981217)161.322780262, -77.7286601372, 381.164694136
15given(0.901070599864, -0.433672407873, 0.000129270187418), (-0.433672311651, -0.901070537415, -0.000461204445301), (0.000316493199564, 0.000359516865182, -0.99999988529)101.987751657, 447.220110148, 381.203611085
16given(-0.623057897471, -0.782175691846, -0.000208526310829), (-0.782175701611, 0.623057918211, -4.86211427746E-5), (0.000167954245106, 0.000132810426487, -0.999999977076)460.66350775, 222.000455332, 381.270246347
17given(0.222645385773, -0.974899468929, -0.000240159266576), (-0.974899483612, -0.22264541868, 0.000119973327731), (-0.000170432293948, 0.000207419637134, -0.999999963965)335.628289131, 420.845818884, 381.334270067
18given(-0.222666316043, 0.974894267616, -0.000937373893114), (-0.974894194627, -0.222667090083, -0.000822360742456), (-0.00101043709083, 0.000730728329611, 0.999999222526)47.6259534386, 421.018803, 0.122009227619
19given(0.900761119053, 0.43431481594, 0.000216928466187), (0.434314800551, -0.900761145114, 0.000116079919289), (0.000245815962391, -1.03450344725E-5, -0.999999969734)-64.1852529796, 280.832282522, 381.278942563
20given(0.222303102307, 0.97497755453, 0.00031443220736), (0.974977599973, -0.222303123045, 3.21734333038E-5), (0.000101267637005, 0.000299412104851, -0.999999950049)-37.8303837327, 47.3688653339, 381.260709998
21given(-0.901062494136, 0.433689232519, -0.000176799099511), (-0.433689119212, -0.90106244729, -0.000462557865368), (-0.000359913394911, -0.000340117698107, 0.999999877391)281.056534221, 447.222704326, 0.132627307768
22given(-0.900757782541, -0.434321727032, -0.000233707161075), (0.434321707379, -0.900757812695, 0.000131787564005), (-0.000267751753621, 1.72045806948E-5, 0.999999964006)447.228429065, 280.827405827, 0.0552139141316
23given(-0.222291049339, -0.974980319001, -0.000258735487383), (0.974980350484, -0.222291061147, 1.74458855999E-5), (-7.45239811542E-5, -0.000248383951955, 0.999999966376)420.858801165, 47.3696225507, 0.0551229107667
24given(0.623933611173, -0.781477349885, 2.15678983476E-5), (0.781477197916, 0.623933506593, 0.000607031967383), (-0.000487838667612, -0.000361892826741, 0.999999815523)221.687038536, -77.7269334071, 0.166246202067
25given(-0.999999999434, 3.31780498558E-5, -5.55467110772E-6), (3.31779691774E-5, 0.999999999344, 1.45238731241E-5), (5.55515297786E-6, 1.45236888232E-5, -0.999999999879)383.035250719, -0.0101427529041, 381.326690537
26given(0.622984441859, 0.782234165592, 0.000308841005992), (-0.782234203833, 0.622984470376, 4.91187118964E-6), (-0.000188560917087, -0.000244646017765, 0.999999952297)-77.6331564453, 222.015421311, 0.0822015499847

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Components

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


Mass: 26911.039 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
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 / 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
9cryoSPARC4initial Euler assignment
10cryoSPARC4final Euler assignment
12cryoSPARC43D reconstruction
13PHENIXdev_5316model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D7 (2x7 fold dihedral)
3D reconstructionResolution: 2.66 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 282632 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 42.42 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001646830
ELECTRON MICROSCOPYf_angle_d0.422763392
ELECTRON MICROSCOPYf_chiral_restr0.03987224
ELECTRON MICROSCOPYf_plane_restr0.00328358
ELECTRON MICROSCOPYf_dihedral_angle_d2.92526818
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2HHELECTRON MICROSCOPYNCS constraints5.01323752011E-13
ens_1d_3HHELECTRON MICROSCOPYNCS constraints8.15060553764E-11
ens_1d_4HHELECTRON MICROSCOPYNCS constraints6.3155750523E-13
ens_1d_5HHELECTRON MICROSCOPYNCS constraints6.03000284934E-11
ens_1d_6HHELECTRON MICROSCOPYNCS constraints2.85096412797E-13
ens_1d_7HHELECTRON MICROSCOPYNCS constraints3.41638813796E-12
ens_1d_8HHELECTRON MICROSCOPYNCS constraints2.95057624234E-13
ens_1d_9HHELECTRON MICROSCOPYNCS constraints4.92214223703E-11
ens_1d_10HHELECTRON MICROSCOPYNCS constraints7.51105194063E-12
ens_1d_11HHELECTRON MICROSCOPYNCS constraints1.19789705717E-11
ens_1d_12HHELECTRON MICROSCOPYNCS constraints3.62263526125E-11
ens_1d_13HHELECTRON MICROSCOPYNCS constraints3.80036949468E-12
ens_1d_14HHELECTRON MICROSCOPYNCS constraints5.37909823732E-13
ens_2d_2AAaELECTRON MICROSCOPYNCS constraints2.31639977158E-10
ens_2d_3AAaELECTRON MICROSCOPYNCS constraints1.03505396215E-10
ens_2d_4AAaELECTRON MICROSCOPYNCS constraints6.21748454162E-13
ens_2d_5AAaELECTRON MICROSCOPYNCS constraints6.49085270496E-13
ens_2d_6AAaELECTRON MICROSCOPYNCS constraints4.21689569795E-13
ens_2d_7AAaELECTRON MICROSCOPYNCS constraints1.53556384632E-12
ens_2d_8AAaELECTRON MICROSCOPYNCS constraints2.44929693212E-10
ens_2d_9AAaELECTRON MICROSCOPYNCS constraints4.14083891422E-11
ens_2d_10AAaELECTRON MICROSCOPYNCS constraints6.99396524521E-13
ens_2d_11AAaELECTRON MICROSCOPYNCS constraints3.44111404854E-12
ens_2d_12AAaELECTRON MICROSCOPYNCS constraints6.20187574394E-11
ens_2d_13AAaELECTRON MICROSCOPYNCS constraints5.91703406442E-13
ens_2d_14AAaELECTRON MICROSCOPYNCS constraints1.37146961266E-10

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