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- EMDB-77307: yeast 26S proteasome base assembly intermediate, Rpn14-Rpt6 -

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Basic information

Entry
Database: EMDB / ID: EMD-77307
Titleyeast 26S proteasome base assembly intermediate, Rpn14-Rpt6
Map data
Sample
  • Complex: yeast 26S proteasome base assembly intermediate, Hsm3-Rpt1-Rpt2 (base-Hsm3-Nas6)
    • Protein or peptide: 26S proteasome regulatory subunit RPN1
    • Protein or peptide: 26S proteasome regulatory subunit 8 homolog
    • Protein or peptide: 26S proteasome regulatory subunit 6B homolog
    • Protein or peptide: 26S proteasome regulatory subunit RPN14
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Keywordsproteasome / chaperone / base / 26S / AAA / motor / assembly / MOTOR PROTEIN
Function / homology
Function and homology information


proteasome regulatory particle assembly / proteasome-activating activity / proteasome regulatory particle, base subcomplex / regulation of protein catabolic process / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Proteasome assembly / nonfunctional rRNA decay / Ub-specific processing proteases / positive regulation of RNA polymerase II transcription preinitiation complex assembly ...proteasome regulatory particle assembly / proteasome-activating activity / proteasome regulatory particle, base subcomplex / regulation of protein catabolic process / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Proteasome assembly / nonfunctional rRNA decay / Ub-specific processing proteases / positive regulation of RNA polymerase II transcription preinitiation complex assembly / proteasome storage granule / proteasome complex / enzyme regulator activity / Neutrophil degranulation / protein folding chaperone / positive regulation of transcription elongation by RNA polymerase II / nucleotide-excision repair / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / chromatin remodeling / protein domain specific binding / ubiquitin protein ligase binding / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
: / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / RPN1, N-terminal / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / RPN1 N-terminal domain / 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / Proteasome/cyclosome repeat / Proteasome/cyclosome repeat / : / Proteasomal ATPase OB C-terminal domain ...: / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / RPN1, N-terminal / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / RPN1 N-terminal domain / 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / Proteasome/cyclosome repeat / Proteasome/cyclosome repeat / : / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Armadillo-like helical / WD domain, G-beta repeat / Armadillo-type fold / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
26S proteasome regulatory subunit 6B homolog / 26S proteasome regulatory subunit RPN1 / 26S proteasome regulatory subunit RPN14 / 26S proteasome regulatory subunit 8 homolog
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.11 Å
AuthorsHsieh HH / Martin A
Funding support United States, 2 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM094497 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionMay 26, 2026-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77307.png

Downloads & links

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Map

FileDownload / File: emd_77307.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 512 pix.
= 536.576 Å		1.05 Å/pix.
x 512 pix.
= 536.576 Å		1.05 Å/pix.
x 512 pix.
= 536.576 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.048 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.40037006 - 0.7055813
Average (Standard dev.)-0.00021395205 (±0.009021236)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 536.576 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_77307_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_77307_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : yeast 26S proteasome base assembly intermediate, Hsm3-Rpt1-Rpt2 (...

EntireName: yeast 26S proteasome base assembly intermediate, Hsm3-Rpt1-Rpt2 (base-Hsm3-Nas6)
Components
  • Complex: yeast 26S proteasome base assembly intermediate, Hsm3-Rpt1-Rpt2 (base-Hsm3-Nas6)
    • Protein or peptide: 26S proteasome regulatory subunit RPN1
    • Protein or peptide: 26S proteasome regulatory subunit 8 homolog
    • Protein or peptide: 26S proteasome regulatory subunit 6B homolog
    • Protein or peptide: 26S proteasome regulatory subunit RPN14
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: yeast 26S proteasome base assembly intermediate, Hsm3-Rpt1-Rpt2 (...

SupramoleculeName: yeast 26S proteasome base assembly intermediate, Hsm3-Rpt1-Rpt2 (base-Hsm3-Nas6)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: 26S proteasome regulatory subunit RPN1

MacromoleculeName: 26S proteasome regulatory subunit RPN1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 109.601906 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVDESDKKQQ TIDEQSQISP EKQTPNKKDK KKEEEEQLSE EDAKLKTDLE LLVERLKEDD SSLYEASLNA LKESIKNSTS SMTAVPKPL KFLRPTYPDL CSIYDKWTDP NLKSSLADVL SILAMTYSEN GKHDSLRYRL LSDVSDFEGW GHEYIRHLAL E IGEVYNDQ ...String:
MVDESDKKQQ TIDEQSQISP EKQTPNKKDK KKEEEEQLSE EDAKLKTDLE LLVERLKEDD SSLYEASLNA LKESIKNSTS SMTAVPKPL KFLRPTYPDL CSIYDKWTDP NLKSSLADVL SILAMTYSEN GKHDSLRYRL LSDVSDFEGW GHEYIRHLAL E IGEVYNDQ VEKDAEDETS SDGSKSDGSA ATSGFEFSKE DTLRLCLDIV PYFLKHNGEE DAVDLLLEIE SIDKLPQFVD EN TFQRVCQ YMVACVPLLP PPEDVAFLKT AYSIYLSQNE LTDAIALAVR LGEEDMIRSV FDATSDPVMH KQLAYILAAQ KTS FEYEGV QDIIGNGKLS EHFLYLAKEL NLTGPKVPED IYKSHLDNSK SVFSSAGLDS AQQNLASSFV NGFLNLGYCN DKLI VDNDN WVYKTKGDGM TSAVASIGSI YQWNLDGLQQ LDKYLYVDEP EVKAGALLGI GISASGVHDG EVEPALLLLQ DYVTN PDTK ISSAAILGLG IAFAGSKNDE VLGLLLPIAA STDLPIETAA MASLALAHVF VGTCNGDITT SIMDNFLERT AIELKT DWV RFLALALGIL YMGQGEQVDD VLETISAIEH PMTSAIEVLV GSCAYTGTGD VLLIQDLLHR LTPKNVKGEE DADEEET AE GQTNSISDFL GEQVNEPTKN EEAEIEVDEM EVDAEGEEVE VKAEITEKKN GESLEGEEIK SEEKKGKSSD KDATTDGK N DDEEEEKEAG IVDELAYAVL GIALIALGED IGKEMSLRHF GHLMHYGNEH IRRMVPLAMG IVSVSDPQMK VFDTLTRFS HDADLEVSMN SIFAMGLCGA GTNNARLAQL LRQLASYYSR EQDALFITRL AQGLLHLGKG TMTMDVFNDA HVLNKVTLAS ILTTAVGLV SPSFMLKHHQ LFYMLNAGIR PKFILALNDE GEPIKVNVRV GQAVETVGQA GRPKKITGWI TQSTPVLLNH G ERAELETD EYISYTSHIE GVVILKKNPD YREEE

UniProtKB: 26S proteasome regulatory subunit RPN1

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Macromolecule #2: 26S proteasome regulatory subunit 8 homolog

MacromoleculeName: 26S proteasome regulatory subunit 8 homolog / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 45.342742 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTAAVTSSNI VLETHESGIK PYFEQKIQET ELKIRSKTEN VRRLEAQRNA LNDKVRFIKD ELRLLQEPGS YVGEVIKIVS DKKVLVKVQ PEGKYIVDVA KDINVKDLKA SQRVCLRSDS YMLHKVLENK ADPLVSLMMV EKVPDSTYDM VGGLTKQIKE I KEVIELPV ...String:
MTAAVTSSNI VLETHESGIK PYFEQKIQET ELKIRSKTEN VRRLEAQRNA LNDKVRFIKD ELRLLQEPGS YVGEVIKIVS DKKVLVKVQ PEGKYIVDVA KDINVKDLKA SQRVCLRSDS YMLHKVLENK ADPLVSLMMV EKVPDSTYDM VGGLTKQIKE I KEVIELPV KHPELFESLG IAQPKGVILY GPPGTGKTLL ARAVAHHTDC KFIRVSGAEL VQKYIGEGSR MVRELFVMAR EH APSIIFM DEIDSIGSTR VEGSGGGDSE VQRTMLELLN QLDGFETSKN IKIIMATNRL DILDPALLRP GRIDRKIEFP PPS VAARAE ILRIHSRKMN LTRGINLRKV AEKMNGCSGA DVKGVCTEAG MYALRERRIH VTQEDFELAV GKVMNKNQET AISV AKLFK

UniProtKB: 26S proteasome regulatory subunit 8 homolog

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Macromolecule #3: 26S proteasome regulatory subunit 6B homolog

MacromoleculeName: 26S proteasome regulatory subunit 6B homolog / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 47.953676 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEELGIVTPV EKAVEEKPAV KSYASLLAQL NGTVNNNSAL SNVNSDIYFK LKKLEKEYEL LTLQEDYIKD EQRHLKRELK RAQEEVKRI QSVPLVIGQF LEPIDQNTGI VSSTTGMSYV VRILSTLDRE LLKPSMSVAL HRHSNALVDI LPPDSDSSIS V MGENEKPD ...String:
MEELGIVTPV EKAVEEKPAV KSYASLLAQL NGTVNNNSAL SNVNSDIYFK LKKLEKEYEL LTLQEDYIKD EQRHLKRELK RAQEEVKRI QSVPLVIGQF LEPIDQNTGI VSSTTGMSYV VRILSTLDRE LLKPSMSVAL HRHSNALVDI LPPDSDSSIS V MGENEKPD VTYADVGGLD MQKQEIREAV ELPLVQADLY EQIGIDPPRG VLLYGPPGTG KTMLVKAVAN STKAAFIRVN GS EFVHKYL GEGPRMVRDV FRLARENAPS IIFIDEVDSI ATKRFDAQTG SDREVQRILI ELLTQMDGFD QSTNVKVIMA TNR ADTLDP ALLRPGRLDR KIEFPSLRDR RERRLIFGTI ASKMSLAPEA DLDSLIIRND SLSGAVIAAI MQEAGLRAVR KNRY VILQS DLEEAYATQV KTDNTVDKFD FYK

UniProtKB: 26S proteasome regulatory subunit 6B homolog

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Macromolecule #4: 26S proteasome regulatory subunit RPN14

MacromoleculeName: 26S proteasome regulatory subunit RPN14 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 46.433684 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTKTITVAHI QYDFKAVLEE NDENDDEFYI NVDKNLNEIK EHKIVVLGNS RGVDAGKGNT FEKVGSHLYK ARLDGHDFLF NTIIRDGSK MLKRADYTAV DTAKLQMRRF ILGTTEGDIK VLDSNFNLQR EIDQAHVSEI TKLKFFPSGE ALISSSQDMQ L KIWSVKDG ...String:
MTKTITVAHI QYDFKAVLEE NDENDDEFYI NVDKNLNEIK EHKIVVLGNS RGVDAGKGNT FEKVGSHLYK ARLDGHDFLF NTIIRDGSK MLKRADYTAV DTAKLQMRRF ILGTTEGDIK VLDSNFNLQR EIDQAHVSEI TKLKFFPSGE ALISSSQDMQ L KIWSVKDG SNPRTLIGHR ATVTDIAIID RGRNVLSASL DGTIRLWECG TGTTIHTFNR KENPHDGVNS IALFVGTDRQ LH EISTSKK NNLEFGTYGK YVIAGHVSGV ITVHNVFSKE QTIQLPSKFT CSCNSLTVDG NNANYIYAGY ENGMLAQWDL RSP ECPVGE FLINEGTPIN NVYFAAGALF VSSGFDTSIK LDIISDPESE RPAIEFETPT FLVSNDDEVS QFCYVSDDES NGEV LEVGK NNFCALYNLS NP

UniProtKB: 26S proteasome regulatory subunit RPN14

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Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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

Concentration6 mg/mL
BufferpH: 7.6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 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: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.11 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 5.0) / Number images used: 208110
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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