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- EMDB-77338: yeast 26S proteasome base assembly intermediate, base-Nas2-Rpn14-... -

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Basic information

Entry
Database: EMDB / ID: EMD-77338
Titleyeast 26S proteasome base assembly intermediate, base-Nas2-Rpn14-Hsm3-Nas6
Map data
Sample
  • Complex: yeast 26S proteasome base assembly intermediate, Hsm3-Rpt1-Rpt2 (base-Hsm3-Nas6)
    • Protein or peptide: x 13 types
  • Ligand: x 1 types
Keywordsproteasome / chaperone / base / 26S / AAA / motor / assembly / MOTOR PROTEIN
Function / homology
Function and homology information


Regulation of PTEN stability and activity / proteasome regulatory particle binding / proteasome regulatory particle assembly / protein-containing complex localization / proteasome-activating activity / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / regulation of protein catabolic process / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway ...Regulation of PTEN stability and activity / proteasome regulatory particle binding / proteasome regulatory particle assembly / protein-containing complex localization / proteasome-activating activity / proteasome regulatory particle, lid subcomplex / 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 / peptide catabolic process / positive regulation of RNA polymerase II transcription preinitiation complex assembly / proteasome storage granule / mismatch repair / proteasome assembly / proteasome complex / enzyme regulator activity / ERAD pathway / Neutrophil degranulation / protein folding chaperone / ubiquitin binding / positive regulation of transcription elongation by RNA polymerase II / nucleotide-excision repair / positive regulation of protein catabolic process / 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 non-ATPase regulatory subunit 9 / Nas2, N-terminal / Nas2 N_terminal domain / DNA mismatch repair protein HSM3, C-terminal domain / DNA mismatch repair protein HSM3, N-terminal domain / DNA mismatch repair protein HSM3, C terminal domain / DNA mismatch repair protein HSM3, N terminal domain / : / Proteasomal ubiquitin receptor Rpn13/ADRM1 / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily ...26S Proteasome non-ATPase regulatory subunit 9 / Nas2, N-terminal / Nas2 N_terminal domain / DNA mismatch repair protein HSM3, C-terminal domain / DNA mismatch repair protein HSM3, N-terminal domain / DNA mismatch repair protein HSM3, C terminal domain / DNA mismatch repair protein HSM3, N terminal domain / : / Proteasomal ubiquitin receptor Rpn13/ADRM1 / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily / Rpn13/ADRM1, Pru domain / Proteasome complex subunit Rpn13, Pru domain / Pru (pleckstrin-like receptor for ubiquitin) domain profile. / PDZ domain 6 / PDZ domain / : / 26S proteasome subunit RPN2, N-terminal domain / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S proteasome regulatory subunit RPN2, C-terminal / 26S proteasome regulatory subunit RPN2 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 / : / 26S proteasome regulatory subunit 7, OB domain / : / HEAT repeats / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / Ankyrin repeat / ATPase, AAA-type, conserved site / AAA-protein family signature. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Ankyrin repeat profile. / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / ATPase family associated with various cellular activities (AAA) / Ankyrin repeat-containing domain superfamily / 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 RPN13 / 26S proteasome regulatory subunit RPN2 / 26S proteasome regulatory subunit 6A / 26S proteasome regulatory subunit 6B homolog / 26S proteasome regulatory subunit 7 homolog / DNA mismatch repair protein HSM3 / 26S proteasome regulatory subunit RPN1 / 26S proteasome regulatory subunit 4 homolog / Probable 26S proteasome regulatory subunit p27 / Probable 26S proteasome regulatory subunit p28 ...26S proteasome regulatory subunit RPN13 / 26S proteasome regulatory subunit RPN2 / 26S proteasome regulatory subunit 6A / 26S proteasome regulatory subunit 6B homolog / 26S proteasome regulatory subunit 7 homolog / DNA mismatch repair protein HSM3 / 26S proteasome regulatory subunit RPN1 / 26S proteasome regulatory subunit 4 homolog / Probable 26S proteasome regulatory subunit p27 / Probable 26S proteasome regulatory subunit p28 / 26S proteasome regulatory subunit RPN14 / 26S proteasome subunit RPT4 / 26S proteasome regulatory subunit 8 homolog
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.87 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 28, 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_77338.png

Downloads & links

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Map

FileDownload / File: emd_77338.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

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.048 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.13603206 - 0.40643916
Average (Standard dev.)-0.00020272168 (±0.006659687)
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: #2

Fileemd_77338_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_77338_half_map_2.map
Projections & Slices
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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 7 homolog
    • Protein or peptide: 26S proteasome regulatory subunit 4 homolog
    • Protein or peptide: 26S proteasome regulatory subunit RPN1
    • Protein or peptide: DNA mismatch repair protein HSM3
    • Protein or peptide: 26S proteasome regulatory subunit 8 homolog
    • Protein or peptide: 26S proteasome regulatory subunit 6B homolog
    • Protein or peptide: 26S proteasome subunit RPT4
    • Protein or peptide: 26S proteasome regulatory subunit RPN13
    • Protein or peptide: 26S proteasome regulatory subunit RPN14
    • Protein or peptide: Probable 26S proteasome regulatory subunit p28
    • Protein or peptide: 26S proteasome regulatory subunit 6A
    • Protein or peptide: Probable 26S proteasome regulatory subunit p27
    • Protein or peptide: 26S proteasome regulatory subunit RPN2
  • 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-#13
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: 26S proteasome regulatory subunit 7 homolog

MacromoleculeName: 26S proteasome regulatory subunit 7 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 52.054891 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPPKEDWEKY KAPLEDDDKK PDDDKIVPLT EGDIQVLKSY GAAPYAAKLK QTENDLKDIE ARIKEKAGVK ESDTGLAPSH LWDIMGDRQ RLGEEHPLQV ARCTKIIKGN GESDETTTDN NNSGNSNSNS NQQSTDADED DEDAKYVINL KQIAKFVVGL G ERVSPTDI ...String:
MPPKEDWEKY KAPLEDDDKK PDDDKIVPLT EGDIQVLKSY GAAPYAAKLK QTENDLKDIE ARIKEKAGVK ESDTGLAPSH LWDIMGDRQ RLGEEHPLQV ARCTKIIKGN GESDETTTDN NNSGNSNSNS NQQSTDADED DEDAKYVINL KQIAKFVVGL G ERVSPTDI EEGMRVGVDR SKYNIELPLP PRIDPSVTMM TVEEKPDVTY SDVGGCKDQI EKLREVVELP LLSPERFATL GI DPPKGIL LYGPPGTGKT LCARAVANRT DATFIRVIGS ELVQKYVGEG ARMVRELFEM ARTKKACIIF FDEIDAVGGA RFD DGAGGD NEVQRTMLEL ITQLDGFDPR GNIKVMFATN RPNTLDPALL RPGRIDRKVE FSLPDLEGRA NIFRIHSKSM SVER GIRWE LISRLCPNST GAELRSVCTE AGMFAIRARR KVATEKDFLK AVDKVISGYK KFSSTSRYMQ YN

UniProtKB: 26S proteasome regulatory subunit 7 homolog

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Macromolecule #2: 26S proteasome regulatory subunit 4 homolog

MacromoleculeName: 26S proteasome regulatory subunit 4 homolog / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 48.89816 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGQGVSSGQD KKKKKGSNQK PKYEPPVQSK FGRKKRKGGP ATAEKLPNIY PSTRCKLKLL RMERIKDHLL LEEEFVSNSE ILKPFEKKQ EEEKKQLEEI RGNPLSIGTL EEIIDDDHAI VTSPTMPDYY VSILSFVDKE LLEPGCSVLL HHKTMSIVGV L QDDADPMV ...String:
MGQGVSSGQD KKKKKGSNQK PKYEPPVQSK FGRKKRKGGP ATAEKLPNIY PSTRCKLKLL RMERIKDHLL LEEEFVSNSE ILKPFEKKQ EEEKKQLEEI RGNPLSIGTL EEIIDDDHAI VTSPTMPDYY VSILSFVDKE LLEPGCSVLL HHKTMSIVGV L QDDADPMV SVMKMDKSPT ESYSDIGGLE SQIQEIKESV ELPLTHPELY EEMGIKPPKG VILYGAPGTG KTLLAKAVAN QT SATFLRI VGSELIQKYL GDGPRLCRQI FKVAGENAPS IVFIDEIDAI GTKRYDSNSG GEREIQRTML ELLNQLDGFD DRG DVKVIM ATNKIETLDP ALIRPGRIDR KILFENPDLS TKKKILGIHT SKMNLSEDVN LETLVTTKDD LSGADIQAMC TEAG LLALR ERRMQVTAED FKQAKERVMK NKVEENLEGL YL

UniProtKB: 26S proteasome regulatory subunit 4 homolog

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Macromolecule #3: 26S proteasome regulatory subunit RPN1

MacromoleculeName: 26S proteasome regulatory subunit RPN1 / type: protein_or_peptide / ID: 3 / 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 #4: DNA mismatch repair protein HSM3

MacromoleculeName: DNA mismatch repair protein HSM3 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 55.6015 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSEKETNYVE NLLTQLENEL NEDNLPEDIN TLLRKCSLNL VTVVSLPDMD VKPLLATIKR FLTSNVSYDS LNYDYLLDVV DKLVPMADF DDVLEVYSAE DLVKALRSEI DPLKVAACRV IENSQPKGLF ATSNIIDILL DILFDEKVEN DKLITAIEKA L ERLSTDEL ...String:
MSEKETNYVE NLLTQLENEL NEDNLPEDIN TLLRKCSLNL VTVVSLPDMD VKPLLATIKR FLTSNVSYDS LNYDYLLDVV DKLVPMADF DDVLEVYSAE DLVKALRSEI DPLKVAACRV IENSQPKGLF ATSNIIDILL DILFDEKVEN DKLITAIEKA L ERLSTDEL IRRRLFDNNL PYLVSVKGRM ETVSFVRLID FLTIEFQFIS GPEFKDIIFC FTKEEILKSV EDILVFIELV NY YTKFLLE IRNQDKYWAL RHVKKILPVF AQLFEDTENY PDVRAFSTNC LLQLFAEVSR IEEDEYSLFK TMDKDSLKIG SEA KLITEW LELINPQYLV KYHKDVVENY FHVSGYSIGM LRNLSADEEC FNAIRNKFSA EIVLRLPYLE QMQVVETLTR YEYT SKFLL NEMPKVMGSL IGDGSAGAII DLETVHYRNS ALRNLLDKGE EKLSVWYEPL LREYSKAVNG KNYSTGSETK IADCR

UniProtKB: DNA mismatch repair protein HSM3

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Macromolecule #5: 26S proteasome regulatory subunit 8 homolog

MacromoleculeName: 26S proteasome regulatory subunit 8 homolog / type: protein_or_peptide / ID: 5 / 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 #6: 26S proteasome regulatory subunit 6B homolog

MacromoleculeName: 26S proteasome regulatory subunit 6B homolog / type: protein_or_peptide / ID: 6 / 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 #7: 26S proteasome subunit RPT4

MacromoleculeName: 26S proteasome subunit RPT4 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 49.479152 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSEEQDPLLA GLGETSGDNH TQQSHEQQPE QPQETEEHHE EEPSRVDPEQ EAHNKALNQF KRKLLEHRRY DDQLKQRRQN IRDLEKLYD KTENDIKALQ SIGQLIGEVM KELSEEKYIV KASSGPRYIV GVRNSVDRSK LKKGVRVTLD ITTLTIMRIL P RETDPLVY ...String:
MSEEQDPLLA GLGETSGDNH TQQSHEQQPE QPQETEEHHE EEPSRVDPEQ EAHNKALNQF KRKLLEHRRY DDQLKQRRQN IRDLEKLYD KTENDIKALQ SIGQLIGEVM KELSEEKYIV KASSGPRYIV GVRNSVDRSK LKKGVRVTLD ITTLTIMRIL P RETDPLVY NMTSFEQGEI TFDGIGGLTE QIRELREVIE LPLKNPEIFQ RVGIKPPKGV LLYGPPGTGK TLLAKAVAAT IG ANFIFSP ASGIVDKYIG ESARIIREMF AYAKEHEPCI IFMDQVDAIG GRRFSEGTSA DREIQRTLME LLTQMDGFDN LGQ TKIIMA TNRPDTLDPA LLRPGRLDRK VEIPLPNEAG RLEIFKIHTA KVKKTGEFDF EAAVKMSDGF NGADIRNCAT EAGF FAIRD DRDHINPDDL MKAVRKVAEV KKLEGTIEYQ KL

UniProtKB: 26S proteasome subunit RPT4

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Macromolecule #8: 26S proteasome regulatory subunit RPN13

MacromoleculeName: 26S proteasome regulatory subunit RPN13 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 17.919002 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSMSSTVIKF RAGVCEYNED SRLCTPIPVQ GEIEIKPNEE EELGFWDFEW RPTEKPVGRE LDPISLILIP GETMWVPIKS SKSGRIFAL VFSSNERYFF WLQEKNSGNL PLNELSAKDK EIYNKMIGVL NNSSESDEEE SNDEKQKAQD VDVSMQD

UniProtKB: 26S proteasome regulatory subunit RPN13

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Macromolecule #9: 26S proteasome regulatory subunit RPN14

MacromoleculeName: 26S proteasome regulatory subunit RPN14 / type: protein_or_peptide / ID: 9 / 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 #10: Probable 26S proteasome regulatory subunit p28

MacromoleculeName: Probable 26S proteasome regulatory subunit p28 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 25.648268 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSNYPLHQAC MENEFFKVQE LLHSKPSLLL QKDQDGRIPL HWSVSFQAHE ITSFLLSKME NVNLDDYPDD SGWTPFHIAC SVGNLEVVK SLYDRPLKPD LNKITNQGVT CLHLAVGKKW FEVSQFLIEN GASVRIKDKF NQIPLHRAAS VGSLKLIELL C GLGKSAVN ...String:
MSNYPLHQAC MENEFFKVQE LLHSKPSLLL QKDQDGRIPL HWSVSFQAHE ITSFLLSKME NVNLDDYPDD SGWTPFHIAC SVGNLEVVK SLYDRPLKPD LNKITNQGVT CLHLAVGKKW FEVSQFLIEN GASVRIKDKF NQIPLHRAAS VGSLKLIELL C GLGKSAVN WQDKQGWTPL FHALAEGHGD AAVLLVEKYG AEYDLVDNKG AKAEDVALNE QVKKFFLNNV

UniProtKB: Probable 26S proteasome regulatory subunit p28

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Macromolecule #11: 26S proteasome regulatory subunit 6A

MacromoleculeName: 26S proteasome regulatory subunit 6A / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 48.315727 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MATLEELDAQ TLPGDDELDQ EILNLSTQEL QTRAKLLDNE IRIFRSELQR LSHENNVMLE KIKDNKEKIK NNRQLPYLVA NVVEVMDMN EIEDKENSES TTQGGNVNLD NTAVGKAAVV KTSSRQTVFL PMVGLVDPDK LKPNDLVGVN KDSYLILDTL P SEFDSRVK ...String:
MATLEELDAQ TLPGDDELDQ EILNLSTQEL QTRAKLLDNE IRIFRSELQR LSHENNVMLE KIKDNKEKIK NNRQLPYLVA NVVEVMDMN EIEDKENSES TTQGGNVNLD NTAVGKAAVV KTSSRQTVFL PMVGLVDPDK LKPNDLVGVN KDSYLILDTL P SEFDSRVK AMEVDEKPTE TYSDVGGLDK QIEELVEAIV LPMKRADKFK DMGIRAPKGA LMYGPPGTGK TLLARACAAQ TN ATFLKLA APQLVQMYIG EGAKLVRDAF ALAKEKAPTI IFIDELDAIG TKRFDSEKSG DREVQRTMLE LLNQLDGFSS DDR VKVLAA TNRVDVLDPA LLRSGRLDRK IEFPLPSEDS RAQILQIHSR KMTTDDDINW QELARSTDEF NGAQLKAVTV EAGM IALRN GQSSVKHEDF VEGISEVQAR KSKSVSFYA

UniProtKB: 26S proteasome regulatory subunit 6A

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Macromolecule #12: Probable 26S proteasome regulatory subunit p27

MacromoleculeName: Probable 26S proteasome regulatory subunit p27 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 24.87541 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEEEELSKLL ANVKIDPSLT SRISQIDSFK LSELMVLKTD IETQLEAYFS VLEQQGIGMD SALVTPDGYP RSDVDVLQVT MIRKNVNML KNDLNHLLQR SHVLLNQHFD NMNVKSNQDA RRNNDDQAIQ YTIPFAFISE VVPGSPSDKA DIKVDDKLIS I GNVHAANH ...String:
MEEEELSKLL ANVKIDPSLT SRISQIDSFK LSELMVLKTD IETQLEAYFS VLEQQGIGMD SALVTPDGYP RSDVDVLQVT MIRKNVNML KNDLNHLLQR SHVLLNQHFD NMNVKSNQDA RRNNDDQAIQ YTIPFAFISE VVPGSPSDKA DIKVDDKLIS I GNVHAANH SKLQNIQMVV MKNEDRPLPV LLLREGQILK TSLTPSRNWN GRGLLGCRIQ EL

UniProtKB: Probable 26S proteasome regulatory subunit p27

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Macromolecule #13: 26S proteasome regulatory subunit RPN2

MacromoleculeName: 26S proteasome regulatory subunit RPN2 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 104.351883 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSLTTAAPLL ALLRENQDSV KTYALESINN VVDQLWSEIS NELPDIEALY DDDTFSDREM AALIASKVYY NLGEYESAVK YALAAKDRF DIDEKSQFVE TIVSKSIEMY VQEASKQYTK DEQFYTKDII DPKLTSIFER MIEKCLKASE LKLALGIALE G YRLDIIES ...String:
MSLTTAAPLL ALLRENQDSV KTYALESINN VVDQLWSEIS NELPDIEALY DDDTFSDREM AALIASKVYY NLGEYESAVK YALAAKDRF DIDEKSQFVE TIVSKSIEMY VQEASKQYTK DEQFYTKDII DPKLTSIFER MIEKCLKASE LKLALGIALE G YRLDIIES ALKSKLDQDS TSENVKIINY LLTLAITTVT NSKFRSSILR KSFDFLMNMP NCDYLTLNKV VVNLNDAGLA LQ LFKKLKE ENDEGLSAQI AFDLVSSASQ QLLEILVTEL TAQGYDPALL NILSGLPTCD YYNTFLLNNK NIDIGLLNKS KSS LDGKFS LFHTAVSVAN GFMHAGTTDN SFIKANLPWL GKAQNWAKFT ATASLGVIHK GNLLEGKKVM APYLPGSRAS SRFI KGGSL YGLGLIYAGF GRDTTDYLKN IIVENSGTSG DEDVDVLLHG ASLGIGLAAM GSANIEVYEA LKEVLYNDSA TSGEA AALG MGLCMLGTGK PEAIHDMFTY SQETQHGNIT RGLAVGLALI NYGRQELADD LITKMLASDE SLLRYGGAFT IALAYA GTG NNSAVKRLLH VAVSDSNDDV RRAAVIALGF VLLRDYTTVP RIVQLLSKSH NAHVRCGTAF ALGIACAGKG LQSAIDV LD PLTKDPVDFV RQAAMIALSM ILIQQTEKLN PQVADINKNF LSVITNKHQE GLAKFGACVA QGIMNAGGRN VTIQLENA D TGTLDTKSVV GLVMFSQFWY WFPLAHFLSL SFTPTTVIGI RGSDQAIPKF QMNCYAKEDA FSYPRMYEEA SGKEVEKVA TAVLSTTARA KARAKKTKKE KGPNEEEKKK EHEEKEKERE TNKKGIKETK ENDEEFYKNK YSSKPYKVDN MTRILPQQSR YISFIKDDR FVPVRKFKGN NGVVVLRDRE PKEPVALIET VRQMKDVNAP LPTPFKVDDN VDFPSA

UniProtKB: 26S proteasome regulatory subunit RPN2

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Macromolecule #14: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 14 / Number of copies: 6 / 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

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 5.0) / Number images used: 154122
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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