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- EMDB-49668: Cryo electron microscopic analysis of the adduct of syringolin an... -

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Basic information

Entry
Database: EMDB / ID: EMD-49668
TitleCryo electron microscopic analysis of the adduct of syringolin analog with the Mtb 20S proteasome
Map dataDesigned Syringolin analog in adduct with Mtb 20S Proteasome
Sample
  • Complex: Mycobacterium tuberculosis proteasome with modified syringolin inhibitor
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome subunit alpha
  • Ligand: 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
KeywordsProteasome 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.16 Å
AuthorsGu X / Yu Z
Funding support1 items
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 PJ / Yu Z / Mohapatra A / Lun S / Jiang X / Li D / Yan NL / Detomasi TC / Pomares DFT / Chen Y / Gestwicki JE / Lin G / Bishai WR / Ernst JD / Cheng Y / Craik CS / Sello JK
History
DepositionMar 12, 2025-
Header (metadata) releaseAug 26, 2026-
Map releaseAug 26, 2026-
UpdateAug 26, 2026-
Current statusAug 26, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49668.png

Downloads & links

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Map

FileDownload / File: emd_49668.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDesigned Syringolin analog in adduct with Mtb 20S Proteasome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 384 pix.
= 353.28 Å		0.92 Å/pix.
x 384 pix.
= 353.28 Å		0.92 Å/pix.
x 384 pix.
= 353.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 8.0
Minimum - Maximum-59.854424000000002 - 103.591830000000002
Average (Standard dev.)-0.00640096 (±3.4164333)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 353.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_49668_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49668_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Mycobacterium tuberculosis proteasome with modified syringolin in...

EntireName: Mycobacterium tuberculosis proteasome with modified syringolin inhibitor
Components
  • Complex: Mycobacterium tuberculosis proteasome with modified syringolin inhibitor
    • Protein or peptide: Proteasome subunit beta
    • Protein or peptide: Proteasome subunit alpha
  • Ligand: 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

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Supramolecule #1: Mycobacterium tuberculosis proteasome with modified syringolin in...

SupramoleculeName: Mycobacterium tuberculosis proteasome with modified syringolin inhibitor
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)

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Macromolecule #1: Proteasome subunit beta

MacromoleculeName: Proteasome subunit beta / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 25.274264 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: TTIVALKYPG GVVMAGDRRS TQGNMISGRD VRKVYITDDY TATGIAGTAA VAVEFARLYA VELEHYEKLE GVPLTFAGKI NRLAIMVRG NLAAAMQGLL ALPLLAGYDI HASDPQSAGR IVSFDAAGGW NIEEEGYQAV GSGSLFAKSS MKKLYSQVTD G DSGLRVAV ...String:
TTIVALKYPG GVVMAGDRRS TQGNMISGRD VRKVYITDDY TATGIAGTAA VAVEFARLYA VELEHYEKLE GVPLTFAGKI NRLAIMVRG NLAAAMQGLL ALPLLAGYDI HASDPQSAGR IVSFDAAGGW NIEEEGYQAV GSGSLFAKSS MKKLYSQVTD G DSGLRVAV EALYDAADDD SATGGPDLVR GIFPTAVIID ADGAVDVPES RIAELARAII ESRSGADTFG SDGGEKHHHH HH

UniProtKB: Proteasome subunit beta

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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: 25.971975 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MEQAMRERSE LARKGIARAK SVVALAYAGG VLFVAENPSR SLQKISELYD RVGFAAAGKF NEFDNLRRGG IQFADTRGYA YDRRDVTGR QLANVYAQTL GTIFTEQAKP YEVELCVAEV AHYGETKRPE LYRITYDGSI ADEPHFVVMG GTTEPIANAL K ESYAENAS ...String:
MEQAMRERSE LARKGIARAK SVVALAYAGG VLFVAENPSR SLQKISELYD RVGFAAAGKF NEFDNLRRGG IQFADTRGYA YDRRDVTGR QLANVYAQTL GTIFTEQAKP YEVELCVAEV AHYGETKRPE LYRITYDGSI ADEPHFVVMG GTTEPIANAL K ESYAENAS LTDALRIAVA ALRAGSADTS GGDQPTLGVA SLEVAVLDAN RPRRAFRRIT GSALQALLVD QESPQSDGES SG

UniProtKB: Proteasome subunit alpha

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Macromolecule #3: methyl N-{[2-({(3Z,5R,8R)-5-[(1H-indol-3-yl)methyl]-2,7-dioxo-1,6...

MacromoleculeName: 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
type: ligand / ID: 3 / Number of copies: 14 / Formula: A1B0M
Molecular weightTheoretical: 554.638 Da

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3mi0

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.16 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 375837
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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