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- EMDB-77308: yeast 26S proteasome base assembly intermediate, Hsm3-Rpt1-Rpt2 (... -

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Basic information

Entry
Database: EMDB / ID: EMD-77308
Titleyeast 26S proteasome base assembly intermediate, Hsm3-Rpt1-Rpt2 (base-Hsm3-Nas6)
Map data
Sample
  • 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: DNA mismatch repair protein HSM3
    • Protein or peptide: 26S proteasome subunit RPT4
    • Protein or peptide: 26S proteasome regulatory subunit 6A
    • Protein or peptide: 26S proteasome regulatory subunit 6B homolog
    • Protein or peptide: Probable 26S proteasome regulatory subunit p28
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
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, base subcomplex / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Proteasome assembly / nonfunctional rRNA decay ...Regulation of PTEN stability and activity / proteasome regulatory particle binding / proteasome regulatory particle assembly / protein-containing complex localization / proteasome-activating activity / proteasome regulatory particle, base subcomplex / 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 / mismatch repair / ERAD pathway / Neutrophil degranulation / protein folding chaperone / 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 domain specific binding / ubiquitin protein ligase binding / ATP hydrolysis activity / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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 / : / 26S proteasome regulatory subunit 7, OB domain / : / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / AAA ATPase, AAA+ lid 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 / : / 26S proteasome regulatory subunit 7, OB domain / : / 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. / 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-type fold / 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 6A / 26S proteasome regulatory subunit 6B homolog / 26S proteasome regulatory subunit 7 homolog / DNA mismatch repair protein HSM3 / 26S proteasome regulatory subunit 4 homolog / Probable 26S proteasome regulatory subunit p28 / 26S proteasome subunit RPT4
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.31 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_77308.png

Downloads & links

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Map

FileDownload / File: emd_77308.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.048 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.11
Minimum - Maximum-0.31036225 - 0.64582175
Average (Standard dev.)-0.00017374245 (±0.008704881)
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_77308_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_77308_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

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 7 homolog
    • Protein or peptide: 26S proteasome regulatory subunit 4 homolog
    • Protein or peptide: DNA mismatch repair protein HSM3
    • Protein or peptide: 26S proteasome subunit RPT4
    • Protein or peptide: 26S proteasome regulatory subunit 6A
    • Protein or peptide: 26S proteasome regulatory subunit 6B homolog
    • Protein or peptide: Probable 26S proteasome regulatory subunit p28
  • 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-#7
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: DNA mismatch repair protein HSM3

MacromoleculeName: DNA mismatch repair protein HSM3 / type: protein_or_peptide / ID: 3 / 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 #4: 26S proteasome subunit RPT4

MacromoleculeName: 26S proteasome subunit RPT4 / type: protein_or_peptide / ID: 4 / 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 #5: 26S proteasome regulatory subunit 6A

MacromoleculeName: 26S proteasome regulatory subunit 6A / type: protein_or_peptide / ID: 5 / 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 #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: Probable 26S proteasome regulatory subunit p28

MacromoleculeName: Probable 26S proteasome regulatory subunit p28 / type: protein_or_peptide / ID: 7 / 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 #8: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 8 / Number of copies: 5 / 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: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 5.0) / Number images used: 241263
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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