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- EMDB-75163: Yeast Blm10 apo Structure -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-75163
TitleYeast Blm10 apo Structure
Map dataFinal Sharpened Map Blm10
Sample
  • Complex: Apo Blm10
    • Protein or peptide: Proteasome activator BLM10
KeywordsProteasome Regulator / PROTEIN BINDING
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsWalsh Jr RM / Rawson S / Fermin Perez E / Venclovaite U / Hanna J
Funding support United States, 1 items
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 RM / Fermin Perez E / Venclovaite U / Velez B / Rajakumar T / Hanna J
History
DepositionJan 19, 2026-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75163.png

Downloads & links

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Map

FileDownload / File: emd_75163.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal Sharpened Map Blm10
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.19 Å/pix.
x 320 pix.
= 380.8 Å		1.19 Å/pix.
x 320 pix.
= 380.8 Å		1.19 Å/pix.
x 320 pix.
= 380.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.19 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.0158
Minimum - Maximum-0.05004667 - 0.106315486
Average (Standard dev.)0.00003494349 (±0.0016024477)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 380.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Final Unsharpened Map Blm10

Fileemd_75163_additional_1.map
AnnotationFinal Unsharpened Map Blm10
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map1 Blm10

Fileemd_75163_half_map_1.map
AnnotationHalf Map1 Blm10
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map2 Blm10

Fileemd_75163_half_map_2.map
AnnotationHalf Map2 Blm10
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Apo Blm10

EntireName: Apo Blm10
Components
  • Complex: Apo Blm10
    • Protein or peptide: Proteasome activator BLM10

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Supramolecule #1: Apo Blm10

SupramoleculeName: Apo Blm10 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: S288C
Molecular weightTheoretical: 240 KDa

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Macromolecule #1: Proteasome activator BLM10

MacromoleculeName: Proteasome activator BLM10 / type: protein_or_peptide / ID: 1
Details: First 24 residues "MHHHHHHHHHHHHTANNDDDIKSP" are part of Histdine tag and linker sequence
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: S288C
Molecular weightTheoretical: 249.243672 KDa
SequenceString: MHHHHHHHHH HHHTANNDDD IKSPMTANND DDIKSPIPIT NKTLSQLKRF ERSPGRPSSS QGEIKRKKSR LYAADGRPHS PLRARSATP TLQDQKLFNG MDSTSLLNER LQHYTLDYVS DRAQHMKNIY DPSSRWFSRS VRPEFPIEEF LPYKTESHED Q AKYLCHVL ...String:
MHHHHHHHHH HHHTANNDDD IKSPMTANND DDIKSPIPIT NKTLSQLKRF ERSPGRPSSS QGEIKRKKSR LYAADGRPHS PLRARSATP TLQDQKLFNG MDSTSLLNER LQHYTLDYVS DRAQHMKNIY DPSSRWFSRS VRPEFPIEEF LPYKTESHED Q AKYLCHVL VNLYIAISSL DIQGLISISS KDLADLKKEV DDLALKTDLF RLSNNTAEND LLGNDIADYD DAEGLEDELD EY FDLAGPD FNATGKITAK SATIVNVNHW TNELKNCLHF DFPVALRKSL ATVYYYLSLV QGQKVYRQMH VDMFERLVSL DDD RTNFTE LLQKQGLLLD HQIMLNFLCE FLPYPDPDYA RYELSSKEDL QLFRLLLKHA HNAKPFFDKS KESLLVDTMN FLLS SLAPS TMMAVMPIVT SVVPYHYHIH SKIIDYFPFC YSIWSSVSAN VAIDTHMYDF VGSISKDVHN KILSSEHEKD VVGVE FGEF GIFTDDQMTF MFNRLQGHLR TDGQIHSYSR TVKPFVYAIN GSKKDRFFEK LVSLAKAIET FIHPSNNGFW TKPNAK FVH AFIKSYHGRV KYEEDICARG VTNGICLTSF CHEEIVEIFL NIISLGSQNK NPDIANYYIS CFAYLLELDP SNAYLIY DK ILIDLYDTLA DQFINSRHRI ISSLKQFTRV IRFIVMDKLY RVHITNVLSM LVSKLDMNDT NLTSNLINGI VSIAAFIP I QDLTGEDDYI SFESDTLPLV QQHFYHIKCG ESSKTFRVDD ELLNNAFKAS TTVFQSMLKV YVEKIFQLVD VDLEDSLVT KINQTTMILQ ESMDDKIFNY FASLLQRNFW SNDSFKEKDP NYELVTIPLA ALVRRNNGLS KELVRTLLFH IKEQIKRGAG SVRSTSEIQ QRDVKLVLYL TALNDVLRQC HESLLEYSDE LITFMKYLYD NVTNPPLDVI TSIVIHSALA TLCTTEITDC R LFPEDSKI PEKDRWGGLQ FDPRRFDKQH LSFQWHVPSS DEITLSISIL ESLSEYCINN VEELMKAPRH DSEYGDMIQK YV LVMTHTL SGSSLLFDPD FNKYRTQSNL SYREKLILLK NIRENNCDPQ ELDIDIEQIR SGKDDEDYIE SKDIEAGLNA GVS DVVQLR DEFPDELIVD EEVVSEMPSG VNTPIAGTHG TDNSAMSSDL AFRDLDIYTC NYYFGNTTEE KLQNPQYLQV HRVR ARIGH FFHKLYVFLS TNFENNTNMF QILLHGLKVW FTDLGQETVF NEDPNAFIDV DFLENVQSLS HVNEPFTRTN FAIRA NSLH QSRVLLHSTN RKASKLENLL LVDIIQLATS LYPDIYKPAQ GTLVHCMKQL VGSYGVVINK IIPSLEKAIK DHDYMK IQV ILNVLLIKKI HRKLMTDYKD IGRLIFLLIE CCRVNELEIG MYADKILTDI VIGIKIPSSV CVISDQAFLP LAPPDGT IN LQVEAVKLAK KKKREYYLSL LVDLQDKLLD KLDNEKDMGW KIRMFILRFV TQIQSNLESK PDKRAVFSII SQISTKHP E IIHLVVKSLL STCNKIISLS DYEYDITRAY KNEFNPSFVE ILDTSTTSFP KTFTEEMNNF DNPKYFIDLR AYVGWLCWG RLMYVMSPKA LKLNLRENEL EVLKTAGHLL TREFLRDVTM NLVQDNETRG VFSSGNVSFF SLVILLISSG FCELNMSDLF ELCESYYNK DDKASMIMSV EIVAGLVCGS KFMSVSDLDK RDTFIENFLA KCLDYELNHD AFEIWSTLAW WLPAVVDLRR S KTFFCHFI NADGMFDRES DAATHQTSKI YMLRSILMSM EFRAPDVGKL FDELVFDHPY DQVRQAVAKL LTTLVQNQSN PS ISDPTTL LEAERNDPDG LGLPLKSVPE KVDAYIKKQF EIIKNLEDSV VGLNPQQFIK TDYFYRTSTI FYWIKEMARG PNK VLLVPY LVDYVLPFLI GLVKHKDVCA LASLDPVRLY AGLGYMPIRK NHVAAIVDYV CSSNVALSSN QTKLQLAFIQ HFLS AELLQ LTEEEKNKIL EFVVSNLYNE QFVEVRVRAA SILSDIVHNW KEEQPLLSLI ERFAKGLDVN KYTSKERQKL SKTDI KIHG NVLGLGAIIS AFPYVFPLPP WIPKQLSNLS SWARTSGMTG QAAKNTISEF KKVRADTWKF DRASFNTEEL EDLEGV LWR SYYA

UniProtKB: Proteasome activator BLM10

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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

Concentration1 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
50.0 mMTris(hydroxymethyl)aminomethane
100.0 mMsodium chlorideNaCl
1.0 mMEDTA[CH2N(CH2CO2H)2]2

Details: Sample was mixed with RvLEAMshort peptide to a final concentration of 1mg/ml sample and 30 micromolar RvLEAMshort immediately before preparation.
GridModel: Quantifoil / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV
Details: wait time of 8 s, blot time of 12 s and a blot force of 8.
DetailsSample was mixed with RvLEAMshort peptide to a final concentration of 1mg/ml sample and 30 micromolar RvLEAMshort immediately before preparation.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris / Energy filter - Slit width: 10 eV
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: TFS FALCON 4i (4k x 4k) / #0 - Digitization - Dimensions - Width: 4096 pixel / #0 - Digitization - Dimensions - Height: 4096 pixel / #0 - Number grids imaged: 1 / #0 - Number real images: 11278 / #0 - Average exposure time: 6.32 sec. / #0 - Average electron dose: 50.253 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: FEI FALCON IV (4k x 4k) / #1 - Average electron dose: 50.253 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Image recording ID1
Particle selectionNumber selected: 2419467
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.14-c7) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0.1_cu12.2) / Number images used: 333883
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 5.0.1_cu12.2)
Final 3D classificationSoftware - Name: RELION (ver. 5.0.1_cu12.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model / Details: Model Angelo generated
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-10gx:
Yeast Blm10 apo Structure

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