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- PDB-9nql: Cryo electron microscopic analysis of the adduct of syringolin an... -

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Basic information

Entry
Database: PDB / ID: 9nql
TitleCryo electron microscopic analysis of the adduct of syringolin analog with the Mtb 20S proteasome
Components
  • Proteasome subunit alpha
  • Proteasome subunit beta
KeywordsHYDROLASE/ANTIBIOTIC / Proteasome Inhibitor / Mycobacterium tuberculosis / HYDROLASE-ANTIBIOTIC complex
Function / homology
Function and homology information


proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / proteasomal protein catabolic process / modification-dependent protein catabolic process / 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 alpha / Proteasome subunit beta
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.16 Å
AuthorsGu, X. / Yu, Z.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Chem.Biol. / Year: 2026
Title: Substrate Mimicry by Inhibitors of the Mycobacterium tuberculosis 20S Proteasome and Their Activity against Mycobacteria In Vitro and in Macrophages
Authors: Gu, X. / Rowheder, P.J. / Yu, Z. / Mohapatra, A. / Lun, S. / Jiang, X. / Li, D. / Yan, N.L. / Detomasi, T.C. / Pomares, D.F.T. / Chen, Y. / Gestwicki, J.E. / Lin, G. / Bishai, W.R. / Ernst, ...Authors: Gu, X. / Rowheder, P.J. / Yu, Z. / Mohapatra, A. / Lun, S. / Jiang, X. / Li, D. / Yan, N.L. / Detomasi, T.C. / Pomares, D.F.T. / Chen, Y. / Gestwicki, J.E. / Lin, G. / Bishai, W.R. / Ernst, J.D. / Cheng, Y. / Craik, C.S. / Sello, J.K.
History
DepositionMar 12, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: Proteasome subunit beta
2: Proteasome subunit beta
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)725,21242
Polymers717,44728
Non-polymers7,76514
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Proteasome subunit beta / 20S proteasome beta subunit / Proteasome core protein PrcB


Mass: 25274.264 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: prcB, MRA_2125 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A5U4D6, proteasome endopeptidase complex
#2: Protein
Proteasome subunit alpha / 20S proteasome alpha subunit / Proteasome core protein PrcA


Mass: 25971.975 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: prcA, MRA_2124 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A5U4D5, proteasome endopeptidase complex
#3: Chemical
ChemComp-A1B0M / methyl N-{[2-({(3Z,5R,8R)-5-[(1H-indol-3-yl)methyl]-2,7-dioxo-1,6-diazacyclododec-3-en-8-yl}amino)-2-oxoethyl]carbamoyl}-L-valinate


Mass: 554.638 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C28H38N6O6
Has ligand of interestY
Has protein modificationY

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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: Mycobacterium tuberculosis proteasome with modified syringolin inhibitor
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 2.16 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 375837 / Symmetry type: POINT

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