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- PDB-9ceb: 20S Proteasome core particle beta-T1A mutant -

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Basic information

Entry
Database: PDB / ID: 9ceb
Title20S Proteasome core particle beta-T1A mutant
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: 2.5 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)718,57028
Polymers718,57028
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "F"
d_2ens_1chain "B"
d_3ens_1chain "C"
d_4ens_1chain "D"
d_5ens_1chain "E"
d_6ens_1chain "K"
d_7ens_1chain "G"
d_8ens_1chain "H"
d_9ens_1chain "I"
d_10ens_1chain "J"
d_11ens_1chain "A"
d_12ens_1chain "L"
d_13ens_1chain "M"
d_14ens_1chain "N"
d_1ens_2(chain "b" and (resid 1 through 208 or resid 210 through 222))
d_2ens_2(chain "P" and (resid 1 through 208 or resid 210 through 222))
d_3ens_2(chain "Q" and (resid 1 through 208 or resid 210 through 222))
d_4ens_2(chain "R" and (resid 1 through 208 or resid 210 through 222))
d_5ens_2(chain "S" and (resid 1 through 208 or resid 210 through 222))
d_6ens_2(chain "T" and (resid 1 through 208 or resid 210 through 222))
d_7ens_2(chain "U" and (resid 1 through 208 or resid 210 through 222))
d_8ens_2(chain "V" and (resid 1 through 208 or resid 210 through 222))
d_9ens_2(chain "W" and (resid 1 through 208 or resid 210 through 222))
d_10ens_2(chain "X" and (resid 1 through 208 or resid 210 through 222))
d_11ens_2(chain "Y" and (resid 1 through 208 or resid 210 through 222))
d_12ens_2(chain "Z" and (resid 1 through 208 or resid 210 through 222))
d_13ens_2(chain "a" and (resid 1 through 208 or resid 210 through 222))
d_14ens_2(chain "O" and (resid 1 through 208 or resid 210 through 222))

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1SERSERLEULEUFF8 - 2348 - 234
d_21ens_1SERSERLEULEUBB8 - 2348 - 234
d_31ens_1SERSERLEULEUCC8 - 2348 - 234
d_41ens_1SERSERLEULEUDD8 - 2348 - 234
d_51ens_1SERSERLEULEUEE8 - 2348 - 234
d_61ens_1SERSERLEULEUKK8 - 2348 - 234
d_71ens_1SERSERLEULEUGG8 - 2348 - 234
d_81ens_1SERSERLEULEUHH8 - 2348 - 234
d_91ens_1SERSERLEULEUII8 - 2348 - 234
d_101ens_1SERSERLEULEUJJ8 - 2348 - 234
d_111ens_1SERSERLEULEUAA8 - 2348 - 234
d_121ens_1SERSERLEULEULL8 - 2348 - 234
d_131ens_1SERSERLEULEUMM8 - 2348 - 234
d_141ens_1SERSERLEULEUNN8 - 2348 - 234
d_11ens_2ALAALASERSERbBA1 - 2081 - 208
d_12ens_2ILEILESERSERbBA210 - 222210 - 222
d_21ens_2ALAALASERSERPP1 - 2081 - 208
d_22ens_2ILEILESERSERPP210 - 222210 - 222
d_31ens_2ALAALASERSERQQ1 - 2081 - 208
d_32ens_2ILEILESERSERQQ210 - 222210 - 222
d_41ens_2ALAALASERSERRR1 - 2081 - 208
d_42ens_2ILEILESERSERRR210 - 222210 - 222
d_51ens_2ALAALASERSERSS1 - 2081 - 208
d_52ens_2ILEILESERSERSS210 - 222210 - 222
d_61ens_2ALAALASERSERTT1 - 2081 - 208
d_62ens_2ILEILESERSERTT210 - 222210 - 222
d_71ens_2ALAALASERSERUU1 - 2081 - 208
d_72ens_2ILEILESERSERUU210 - 222210 - 222
d_81ens_2ALAALASERSERVV1 - 2081 - 208
d_82ens_2ILEILESERSERVV210 - 222210 - 222
d_91ens_2ALAALASERSERWW1 - 2081 - 208
d_92ens_2ILEILESERSERWW210 - 222210 - 222
d_101ens_2ALAALASERSERXX1 - 2081 - 208
d_102ens_2ILEILESERSERXX210 - 222210 - 222
d_111ens_2ALAALASERSERYY1 - 2081 - 208
d_112ens_2ILEILESERSERYY210 - 222210 - 222
d_121ens_2ALAALASERSERZZ1 - 2081 - 208
d_122ens_2ILEILESERSERZZ210 - 222210 - 222
d_131ens_2ALAALASERSERaAA1 - 2081 - 208
d_132ens_2ILEILESERSERaAA210 - 222210 - 222
d_141ens_2ALAALASERSEROO1 - 2081 - 208
d_142ens_2ILEILESERSEROO210 - 222210 - 222

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.899765532295, -0.43637361646, -0.000231843000844), (-0.436373105473, -0.899765085375, 0.00114191097146), (-0.000706904057738, -0.000926282082808, -0.999999321144)102.920182923, 447.118922516, 383.359242071
2given(-0.900562512105, 0.434726456549, 0.00026413371616), (-0.434726415732, -0.900562548531, 0.000199118451849), (0.000324430991584, 6.44927095033E-5, 0.999999945293)280.641094223, 447.196689251, -0.0724148682914
3given(-0.221463198382, 0.975168725291, -9.47444410879E-5), (-0.975168729652, -0.221463199444, -7.41395575687E-7), (-2.17053928313E-5, 9.22276244218E-5, 0.999999995511)47.1788464975, 420.662555035, -0.0137624524397
4given(0.623795633864, 0.781587454435, 0.000241334191882), (-0.781587491417, 0.623795595693, 0.000219212503173), (2.07905363492E-5, -0.000325367587994, 0.999999946852)-77.6866331375, 221.676491527, 0.0674509128863
5given(-0.999999997269, -1.72575764291E-6, 7.38838936884E-5), (-1.72831791214E-6, 0.999999999398, -3.46525531321E-5), (-7.3883833842E-5, -3.46526807324E-5, -0.99999999667)383.020681855, 0.00861530925764, 383.063030963
6given(0.622942467783, -0.782267617304, -0.000238223568272), (0.78226762077, 0.622942500969, -9.99101884649E-5), (0.000226556090484, -0.000124116284605, 0.999999966634)222.113753419, -77.5591676984, -0.0151262541065
7given(-0.223376653845, -0.974732202982, -5.46476703411E-5), (0.974732188784, -0.223376639817, -0.000192176805987), (0.000175113908487, -9.61946551916E-5, 0.999999980041)420.997118105, 47.7007563801, -0.0100057662128
8given(-0.901076969509, -0.433659119942, -0.000250422212683), (0.433659163397, -0.901076969963, -0.000155578255867), (-0.000158181759095, -0.000248785870567, 0.999999956542)447.195767205, 281.08954427, 0.086827788821
9given(-0.623869081709, -0.781528852723, -0.000145769049949), (-0.781528858519, 0.623869038282, 0.000257633833313), (-0.000110407477169, 0.00027465250222, -0.999999956188)460.705498585, 221.639432204, 382.999883744
10given(0.22141931077, -0.975178690672, 0.00010038871175), (-0.97517869542, -0.22141931252, -6.5280036815E-6), (2.85939696232E-5, -9.6451506883E-5, -0.99999999494)335.871292257, 420.655898516, 383.053247873
11given(-0.622893808401, 0.782306385703, 0.000149481043968), (0.7823063855, 0.622893822266, -7.3404064754E-5), (-0.000150535287427, 7.12170377607E-5, -0.999999986134)160.930984426, -77.5645472151, 383.051131822
12given(0.223420680793, 0.974722113333, -3.42682027128E-5), (0.974722003681, -0.223420672105, -0.000467778515812), (-0.000463610288386, 7.11094232522E-5, -0.999999890004)-37.9414262359, 47.7827584146, 383.112334233
13given(0.901092167729, 0.433627501924, 0.000307949978126), (0.433627551586, -0.901092189082, -0.000115246361425), (0.000227517328107, 0.000237383188665, -0.999999945943)-64.1666344135, 281.088826492, 382.94200151
14given(-0.99997894199, 0.00643582984418, 0.000834068595827), (0.0064350118475, 0.99997881515, -0.000979731327113), (-0.000840356310323, -0.000974343454625, -0.999999172228)381.834602903, -1.30487412631, 383.361051613
15given(-0.623414447843, -0.781891564733, -8.4966428792E-5), (-0.781891565599, 0.623414430526, 0.000165702091086), (-7.65917694596E-5, 0.000169735611652, -0.999999982662)460.669578318, 221.847879964, 383.029268427
16given(0.222622500229, -0.974904704083, 0.000200871677577), (-0.974904724729, -0.222622497526, 3.6001346229E-5), (9.6206727524E-6, -0.000203845457243, -0.999999979177)335.548856841, 420.859670291, 383.071139983
17given(0.901035287415, -0.433745790517, 6.54635822328E-6), (-0.433745782159, -0.901035266876, 0.000210485398904), (-8.53986561111E-5, -0.000192494227166, -0.999999977827)102.018016188, 447.114958137, 383.090254117
18given(0.901148575186, 0.433510356591, -0.000127159515775), (0.4335103747, -0.901148520654, 0.0003142452456), (2.16389589493E-5, -0.000338306624662, -0.99999994254)-64.0933726653, 281.025357747, 383.08894302
19given(0.222226655878, 0.974995001472, -0.000246013660801), (0.974995032237, -0.2222266547, 3.24611539779E-5), (-2.30213299798E-5, -0.000247075830838, -0.999999969212)-37.7082020894, 47.341017912, 383.085142687
20given(-0.623524440145, 0.781803857761, -2.30884048819E-5), (0.781803855788, 0.623524435756, -9.53433723657E-5), (-6.0143631701E-5, -7.74995268365E-5, -0.999999995188)161.224428441, -77.613634588, 383.065732958
21given(-0.222625154695, 0.974904093156, -0.000222812743469), (-0.97490411847, -0.222625152817, 3.35103380132E-5), (-1.69343553722E-5, 0.00022468130544, 0.999999974616)47.4938211959, 420.861030957, -0.0330044459064
22given(-0.901038983862, 0.433738106265, 6.88105217821E-5), (-0.433738085448, -0.901038973161, 0.000205127939728), (0.000150972766009, 0.000154982526397, 0.999999976594)281.009280039, 447.114659649, -0.0593786800065
23given(-0.901145667137, -0.433516417854, 4.52799544767E-5), (0.433516409459, -0.901145616585, 0.000316922178247), (-9.65871349565E-5, 0.000305222651033, 0.999999948755)447.148520998, 281.021945291, -0.02756168188
24given(-0.222200614725, -0.975000945691, 0.000206683315767), (0.975000964751, -0.222200625281, -2.93062157889E-5), (7.44987501073E-5, 0.000195004573107, 0.999999978212)420.751189421, 47.3468032558, -0.0479298974518
25given(0.623525978066, -0.781802630322, 4.35701712192E-5), (0.781802631008, 0.623525974628, -7.15141911721E-5), (2.87428492895E-5, 7.86542304888E-5, 0.999999996494)221.81200487, -77.6169486771, -0.0185068160864
26given(0.623437626183, 0.781873084571, 7.6694601341E-5), (-0.781873080929, 0.623437603781, 0.00019877369413), (0.000107601502878, -0.000183888444257, 0.999999977303)-77.629899438, 221.834570757, 0.00486600477635

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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: 24415.357 Da / Num. of mol.: 14 / Mutation: T1A
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 beta-T1A mutant / 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: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 808626 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 29.39 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005546970
ELECTRON MICROSCOPYf_angle_d0.711563588
ELECTRON MICROSCOPYf_chiral_restr0.057224
ELECTRON MICROSCOPYf_plane_restr0.00678400
ELECTRON MICROSCOPYf_dihedral_angle_d4.34986860
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2FFELECTRON MICROSCOPYNCS constraints1.59329945633E-10
ens_1d_3FFELECTRON MICROSCOPYNCS constraints1.85622189883E-11
ens_1d_4FFELECTRON MICROSCOPYNCS constraints3.88451003079E-13
ens_1d_5FFELECTRON MICROSCOPYNCS constraints1.69723294073E-12
ens_1d_6FFELECTRON MICROSCOPYNCS constraints5.9427992669E-12
ens_1d_7FFELECTRON MICROSCOPYNCS constraints4.35341299581E-11
ens_1d_8FFELECTRON MICROSCOPYNCS constraints1.29612947363E-10
ens_1d_9FFELECTRON MICROSCOPYNCS constraints5.22447509316E-13
ens_1d_10FFELECTRON MICROSCOPYNCS constraints3.43864993771E-11
ens_1d_11FFELECTRON MICROSCOPYNCS constraints5.96419225314E-13
ens_1d_12FFELECTRON MICROSCOPYNCS constraints6.45397399078E-13
ens_1d_13FFELECTRON MICROSCOPYNCS constraints2.89979454054E-12
ens_1d_14FFELECTRON MICROSCOPYNCS constraints1.42040262074E-12
ens_2d_2BAbELECTRON MICROSCOPYNCS constraints1.27434310624E-11
ens_2d_3BAbELECTRON MICROSCOPYNCS constraints5.34787060134E-13
ens_2d_4BAbELECTRON MICROSCOPYNCS constraints2.17275851079E-10
ens_2d_5BAbELECTRON MICROSCOPYNCS constraints2.45582263531E-12
ens_2d_6BAbELECTRON MICROSCOPYNCS constraints4.11140663098E-13
ens_2d_7BAbELECTRON MICROSCOPYNCS constraints6.34740589969E-13
ens_2d_8BAbELECTRON MICROSCOPYNCS constraints4.01483006797E-12
ens_2d_9BAbELECTRON MICROSCOPYNCS constraints3.03996007332E-13
ens_2d_10BAbELECTRON MICROSCOPYNCS constraints1.94131869866E-11
ens_2d_11BAbELECTRON MICROSCOPYNCS constraints3.39246904442E-13
ens_2d_12BAbELECTRON MICROSCOPYNCS constraints1.93544486692E-10
ens_2d_13BAbELECTRON MICROSCOPYNCS constraints2.79405897984E-13
ens_2d_14BAbELECTRON MICROSCOPYNCS constraints2.94533647717E-13

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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