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- PDB-10gx: Yeast Blm10 apo Structure -

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Basic information

Entry
Database: PDB / ID: 10gx
TitleYeast Blm10 apo Structure
ComponentsProteasome activator BLM10
KeywordsPROTEIN BINDING / Proteasome Regulator
Function / homology
Function and homology information


proteasome core complex import into nucleus / proteasome storage granule assembly / peptidase activator activity / proteasome binding / proteasomal ubiquitin-independent protein catabolic process / proteasome storage granule / proteasome assembly / regulation of proteasomal protein catabolic process / DNA repair / DNA damage response / nucleus
Similarity search - Function
Proteasome activator Blm10, N-terminal / Proteasome-substrate-size regulator, N-terminal / Proteasome activator complex subunit 4 C-terminal domain / Proteasome activator Blm10, mid region / Proteasome activator complex subunit 4 / : / Proteasome activator complex subunit 4-like, C-terminal / Proteasome activator complex subunit 4, mid HEAT repeats region / Proteasome activator complex subunit 4-like, HEAT repeat-like / Armadillo-type fold
Similarity search - Domain/homology
Proteasome activator BLM10
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWalsh Jr, R.M. / Rawson, S. / Fermin Perez, E. / Venclovaite, U. / Hanna, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM144367 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2026
Title: Blm10 and PI31 comprise a failsafe mechanism for proteasome inhibition.
Authors: Darlene Fung / Shaun Rawson / Richard M Walsh / Erignacio Fermin Perez / Urte Venclovaite / Tamayanthi Rajakumar / Benjamin Velez / John Hanna /
Abstract: Blm10 (PA200 in mammals) is an evolutionarily conserved regulator of the proteasome's core particle (CP), a barrel-shaped complex that houses six individual protease subunits. Despite decades of ...Blm10 (PA200 in mammals) is an evolutionarily conserved regulator of the proteasome's core particle (CP), a barrel-shaped complex that houses six individual protease subunits. Despite decades of study, Blm10's function has remained unresolved. Here, we provide structural, biochemical, and genetic evidence that yeast Blm10 inhibits the proteasome and that it does so in cooperation with a second proteasome inhibitor, PI31 (also known as Fub1). Both proteins are highly enriched in CPs with abnormal subunit composition, suggesting that Blm10 and PI31 may function to neutralize aberrant proteasomes. We report an unexpected proteasome configuration in which Blm10's dome-like structure completely encases PI31's N-terminal domain, which sits outside and atop the CP, while PI31's C-terminal domain is present inside the CP, simultaneously inhibiting all six active sites. These Blm10/PI31-bound CP are strongly deficient in degradation of both proteins and small peptides, and loss of both proteins results in strongly synergistic genetic phenotypes in vivo. These data suggest that Blm10 and PI31 constitute a partially redundant failsafe system for proteasome inhibition.
History
DepositionJan 19, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proteasome activator BLM10


Theoretical massNumber of molelcules
Total (without water)249,2441
Polymers249,2441
Non-polymers00
Water00
1


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

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Components

#1: Protein Proteasome activator BLM10 / Bleomycin resistance protein BLM10


Mass: 249243.672 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: First 24 residues "MHHHHHHHHHHHHTANNDDDIKSP" are part of Histdine tag and linker sequence
Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / Strain: S288C / References: UniProt: P43583
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: Apo Blm10 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightValue: 0.240 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: S288C
Buffer solutionpH: 7.5
Details: Sample was mixed with RvLEAMshort peptide to a final concentration of 1mg/ml sample and 30 micromolar RvLEAMshort immediately before preparation.
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris(hydroxymethyl)aminomethane1
2100 mMsodium chlorideNaCl1
31 mMEDTA[CH2N(CH2CO2H)2]21
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Sample was mixed with RvLEAMshort peptide to a final concentration of 1mg/ml sample and 30 micromolar RvLEAMshort immediately before preparation.
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 K
Details: wait time of 8 s, blot time of 12 s and a blot force of 8

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recording
IDImaging-IDAverage exposure time (sec.)Electron dose (e/Å2)Film or detector modelNum. of grids imagedNum. of real images
116.3250.253TFS FALCON 4i (4k x 4k)111278
2150.253FEI FALCON IV (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV
Image scans
WidthHeightIDImage recording-IDEntry-ID
409640961110GX
2210GX

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1Topaz0.3.7particle selection
2EPUimage acquisition
4CTFFIND4.1.14-c7CTF correction
7Coot0.9.8.92model fittingManual rebuilding
8ISOLDE1.10.1_c9model fittingManual rebuilding
9UCSF ChimeraX1.9_rhel9model fittingrigid Fitting/rebuilding
11PHENIX1.21.2-5419model refinement
12cryoSPARC4.7initial Euler assignment
13RELION5.0.1_cu12.2final Euler assignment
14RELION5.0.1_cu12.2classification
15RELION5.0.1_cu12.23D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2419467
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 333883 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingDetails: Model Angelo generated / Source name: Other / Type: experimental model
RefinementHighest resolution: 3.2 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00415364
ELECTRON MICROSCOPYf_angle_d0.59220814
ELECTRON MICROSCOPYf_dihedral_angle_d14.5575684
ELECTRON MICROSCOPYf_chiral_restr0.042374
ELECTRON MICROSCOPYf_plane_restr0.0072635

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