[English] 日本語
Yorodumi
- PDB-10gx: Yeast Blm10 apo Structure -

+
Open data


ID or keywords:

Loading...

-
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 ...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 / 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 / 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: To Be Published
Title: Blm10 and PI31 Compromise a Failsafe Mechanism for Proteasome Inhibition
Authors: Darlene, F. / Rawson, S. / Walsh Jr., R.M. / Fermin Perez, E. / Venclovaite, U. / Velez, B. / Rajakumar, T. / Hanna, J.
History
DepositionJan 19, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

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

-
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

Read more