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- PDB-9d4c: Proteasome core particle assembly intermediate Blm10:alpha-ring p... -

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Basic information

Entry
Database: PDB / ID: 9d4c
TitleProteasome core particle assembly intermediate Blm10:alpha-ring purified from Saccharomyces cerevisiae.
Components
  • (Proteasome subunit alpha type- ...) x 6
  • Probable proteasome subunit alpha type-7
  • Proteasome activator BLM10
  • Proteasome subunit beta type-2
KeywordsHYDROLASE / Proteasome / Cryo-EM / Assembly / assembly chaperone / Blm10 / PA200 / Blm10-13S / Pba1 / CP
Function / homology
Function and homology information


proteasome core complex import into nucleus / proteasome storage granule assembly / peptidase activator activity / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / proteasomal ubiquitin-independent protein catabolic process ...proteasome core complex import into nucleus / proteasome storage granule assembly / peptidase activator activity / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / proteasomal ubiquitin-independent protein catabolic process / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / proteasome binding / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / Ub-specific processing proteases / proteasome assembly / threonine-type endopeptidase activity / proteasome core complex, alpha-subunit complex / : / regulation of proteasomal protein catabolic process / Neutrophil degranulation / proteasome complex / endopeptidase activity / proteasome-mediated ubiquitin-dependent protein catabolic process / DNA repair / mRNA binding / DNA damage response / mitochondrion / nucleus / cytosol
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 / Proteasome beta subunit, C-terminal ...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 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit alpha5 / Proteasome subunit alpha6 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / 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 / Armadillo-type fold
Similarity search - Domain/homology
Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-2 / Proteasome subunit alpha type-5 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4 / Proteasome activator BLM10
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.75 Å
AuthorsChen, X. / Kaur, M. / Roelofs, J. / Walters, K.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1 ZIA BC011490 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM149314 United States
CitationJournal: To Be Published
Title: Structure of Blm10:13S proteasome assembly intermediate reveals parallel assembly pathways for the proteasome core particle
Authors: Kaur, M. / Chen, X. / Lee, S.Y. / Weaver, T.M. / Freudenthal, B.D. / Walters, K.J. / Roelofs, J.
History
DepositionAug 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Primary map / Data content type: Primary map / Provider: 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 subunit alpha type-1
B: Proteasome subunit alpha type-2
C: Proteasome subunit alpha type-3
D: Proteasome subunit alpha type-4
E: Proteasome subunit alpha type-5
F: Proteasome subunit alpha type-6
G: Probable proteasome subunit alpha type-7
I: Proteasome subunit beta type-2
O: Proteasome activator BLM10


Theoretical massNumber of molelcules
Total (without water)472,8929
Polymers472,8929
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable, gel filtration, native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Proteasome subunit alpha type- ... , 6 types, 6 molecules ABCDEF

#1: Protein Proteasome subunit alpha type-1 / Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component C7- ...Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component C7-alpha / Proteasome component Y8 / Proteinase YSCE subunit 7 / SCL1 suppressor protein


Mass: 28033.830 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: SCL1, PRC2, PRS2, YGL011C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P21243
#2: Protein Proteasome subunit alpha type-2 / Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteasome component Y7 / ...Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteasome component Y7 / Proteinase YSCE subunit 7


Mass: 27191.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PRE8, PRS4, YML092C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23639
#3: Protein Proteasome subunit alpha type-3 / Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteasome component Y13 ...Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteasome component Y13 / Proteinase YSCE subunit 13


Mass: 28748.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PRE9, PRS5, YGR135W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P23638
#4: Protein Proteasome subunit alpha type-4 / Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteasome component ...Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteasome component PRE6 / Proteinase YSCE subunit PRE6


Mass: 28478.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PRE6, YOL038W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40303
#5: Protein Proteasome subunit alpha type-5 / Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteasome component ...Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteasome component PUP2 / Proteinase YSCE subunit PUP2


Mass: 28649.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PUP2, DOA5, YGR253C, G9155 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P32379
#6: Protein Proteasome subunit alpha type-6 / Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteasome component ...Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteasome component PRE5 / Proteinase YSCE subunit PRE5


Mass: 25634.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PRE5, YMR314W, YM9924.06 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P40302

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Protein , 3 types, 3 molecules GIO

#7: Protein Probable proteasome subunit alpha type-7 / Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteasome component C1 / ...Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteasome component C1 / Proteinase YSCE subunit 1


Mass: 31575.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PRE10, PRC1, PRS1, YOR362C, O6650 / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P21242
#8: Protein Proteasome subunit beta type-2 / Macropain subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1 / Proteasome component ...Macropain subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1 / Proteasome component PUP1 / Proteinase YSCE subunit PUP1


Mass: 28299.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: PUP1, YOR157C / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: P25043, proteasome endopeptidase complex
#9: Protein Proteasome activator BLM10 / Bleomycin resistance protein BLM10


Mass: 246282.375 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BLM10, BLM3, YFL007W, YFL006W / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P43583

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Details

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: Proteasome assembly intermediate / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.472 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Source (recombinant)Organism: Saccharomyces cerevisiae (brewer's yeast)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMTris(hydroxymethyl)aminomethane hydrochlorideC4H12NO3Cl1
25 mMMagnesium dichlorideMgCl21
32 mMEGTAC14H24N2O101
41 mMDichlorodiphenyltrichloroethaneC14H9Cl51
SpecimenConc.: 1.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 0.42 mBar, 15mA / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 298.15 K

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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: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 900 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 5235
EM imaging opticsEnergyfilter name: GIF Bioquantum
Image scansWidth: 5760 / Height: 4092

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Processing

EM software
IDNameCategory
7EPUimage acquisition
8cryoSPARCparticle selection
12cryoSPARC3D reconstruction
18UCSF ChimeraXmodel fitting
19Cootmodel refinement
26PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4058518
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.75 Å / Num. of particles: 414121 / Symmetry type: POINT
Atomic model buildingB value: 116.1 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeChain-IDInitial refinement model-ID
14V7O

4v7o

CA4V7OCA1
24V7O

4v7o

DA4V7ODA1
34V7O

4v7o

EA4V7OEA1
47LSX

7lsx

A7LSXA2
57LSX

7lsx

B7LSXB2
67LSX

7lsx

C7LSXC2
77LSX

7lsx

D7LSXD2
87LSX

7lsx

E7LSXE2
97LSX

7lsx

F7LSXF2
107LSX

7lsx

G7LSXG2
117LSX

7lsx

I7LSXI2
RefinementHighest resolution: 2.75 Å

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