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- EMDB-63943: Substrate-free human 26S proteasome purified by midnolin, 20S pro... -

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Basic information

Entry
Database: EMDB / ID: EMD-63943
TitleSubstrate-free human 26S proteasome purified by midnolin, 20S proteasome, RPTs and RPN11 part
Map data
Sample
  • Complex: 26S proteasome complexed with midnolin
    • Protein or peptide: x 21 types
  • Ligand: x 5 types
KeywordsMidnolin / 26S proteasome / Complex / HYDROLASE
Function / homology
Function and homology information


thyrotropin-releasing hormone receptor binding / nuclear proteasome complex / host-mediated perturbation of viral transcription / positive regulation of inclusion body assembly / proteasome accessory complex / purine ribonucleoside triphosphate binding / cytosolic proteasome complex / positive regulation of proteasomal protein catabolic process / proteasome-activating activity / Antigen processing: Ub, ATP-independent proteasomal degradation ...thyrotropin-releasing hormone receptor binding / nuclear proteasome complex / host-mediated perturbation of viral transcription / positive regulation of inclusion body assembly / proteasome accessory complex / purine ribonucleoside triphosphate binding / cytosolic proteasome complex / positive regulation of proteasomal protein catabolic process / proteasome-activating activity / Antigen processing: Ub, ATP-independent proteasomal degradation / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / sperm glycocalyx / protein K63-linked deubiquitination / negative regulation of programmed cell death / Regulation of ornithine decarboxylase (ODC) / metal-dependent deubiquitinase activity / perinuclear theca / Proteasome assembly / proteasome core complex / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / K63-linked deubiquitinase activity / transcription factor binding / proteasome binding / myofibril / proteasomal ubiquitin-independent protein catabolic process / sperm head-tail coupling apparatus / general transcription initiation factor binding / protein deubiquitination / blastocyst development / immune system process / NF-kappaB binding / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / endopeptidase activator activity / threonine-type endopeptidase activity / proteasome assembly / proteasome core complex, alpha-subunit complex / regulation of proteasomal protein catabolic process / inclusion body / ciliary tip / : / proteasome complex / TBP-class protein binding / sarcomere / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / sperm end piece / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / centriole / negative regulation of inflammatory response to antigenic stimulus / P-body / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Degradation of DVL / lipopolysaccharide binding / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of CRY and PER proteins / Degradation of AXIN / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / G2/M Checkpoints / Hedgehog ligand biogenesis / Degradation of GLI1 by the proteasome / Defective CFTR causes cystic fibrosis / Autodegradation of the E3 ubiquitin ligase COP1 / Regulation of RUNX3 expression and activity / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Negative regulation of NOTCH4 signaling / Hedgehog 'on' state / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Vif-mediated degradation of APOBEC3G / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / Degradation of CDH1 / double-strand break repair via homologous recombination / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / ABC-family proteins mediated transport / double-strand break repair via nonhomologous end joining / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / FCERI mediated NF-kB activation / response to virus / Metalloprotease DUBs / Regulation of expression of SLITs and ROBOs / nuclear matrix
Similarity search - Function
: / 26S proteasome regulatory subunit RPN11 C-terminal domain / : / 26S proteasome regulatory subunit 7, OB domain / : / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / Proteasome subunit alpha 1 / : / JAB1/Mov34/MPN/PAD-1 ubiquitin protease ...: / 26S proteasome regulatory subunit RPN11 C-terminal domain / : / 26S proteasome regulatory subunit 7, OB domain / : / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / Proteasome subunit alpha 1 / : / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha5 / Proteasome subunit alpha6 / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit A N-terminal signature / Proteasome alpha-type subunits signature. / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / Proteasome B-type subunit / Proteasome beta-type subunit profile. / : / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome subunit / Proteasome, subunit alpha/beta / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / MPN domain profile. / ATPase, AAA-type, conserved site / AAA-protein family signature. / Nucleophile aminohydrolases, N-terminal / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / 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 10B / Ubiquitin C-terminal hydrolase PSMD14 / Proteasome subunit alpha type-7 / 26S proteasome regulatory subunit 6A / Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 ...26S proteasome regulatory subunit 10B / Ubiquitin C-terminal hydrolase PSMD14 / Proteasome subunit alpha type-7 / 26S proteasome regulatory subunit 6A / Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-4 / Proteasome subunit beta type-6 / Proteasome subunit beta type-5 / 26S proteasome regulatory subunit 7 / 26S proteasome regulatory subunit 6B / Proteasome subunit beta type-3 / Proteasome subunit beta type-2 / Proteasome subunit alpha type-6 / 26S proteasome regulatory subunit 4 / 26S proteasome regulatory subunit 8 / Proteasome subunit beta type-7
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.17 Å
AuthorsZhu C / Qin L / Liang L
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32171224 China
CitationJournal: Nat Commun / Year: 2026
Title: Structural dynamics of the midnolin-proteasome during ubiquitin-independent substrate turnover
Authors: Zhu C / Qin L
History
DepositionMar 25, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63943.png

Downloads & links

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Map

FileDownload / File: emd_63943.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 600 pix.
= 510. Å		0.85 Å/pix.
x 600 pix.
= 510. Å		0.85 Å/pix.
x 600 pix.
= 510. Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.67137015 - 1.0935888
Average (Standard dev.)-0.00012271099 (±0.041883804)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 510.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63943_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Histogram (log scale)

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Half map: #1

Fileemd_63943_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : 26S proteasome complexed with midnolin

EntireName: 26S proteasome complexed with midnolin
Components
  • Complex: 26S proteasome complexed with midnolin
    • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 14
    • Protein or peptide: 26S proteasome regulatory subunit 7
    • Protein or peptide: 26S proteasome regulatory subunit 4
    • Protein or peptide: 26S proteasome regulatory subunit 8
    • Protein or peptide: 26S proteasome regulatory subunit 6B
    • Protein or peptide: Proteasome 26S subunit, ATPase 6
    • Protein or peptide: 26S proteasome regulatory subunit 6A
    • Protein or peptide: Proteasome subunit alpha type-6
    • Protein or peptide: Proteasome subunit alpha type-2
    • Protein or peptide: Proteasome subunit alpha type-4
    • Protein or peptide: Proteasome subunit alpha type-7
    • Protein or peptide: Proteasome subunit alpha type-5
    • Protein or peptide: Isoform Long of Proteasome subunit alpha type-1
    • Protein or peptide: Proteasome subunit alpha type-3
    • Protein or peptide: Proteasome subunit beta type-6
    • Protein or peptide: Proteasome subunit beta type-7
    • Protein or peptide: Proteasome subunit beta type-3
    • Protein or peptide: Proteasome subunit beta type-2
    • Protein or peptide: Proteasome subunit beta type-5
    • Protein or peptide: Proteasome subunit beta type-1
    • Protein or peptide: Proteasome subunit beta type-4
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-4-methyl-1-oxopentan-2-yl]-L-leucinamide

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Supramolecule #1: 26S proteasome complexed with midnolin

SupramoleculeName: 26S proteasome complexed with midnolin / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#21
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 26S proteasome non-ATPase regulatory subunit 14

MacromoleculeName: 26S proteasome non-ATPase regulatory subunit 14 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 34.488824 KDa
SequenceString: DRLLRLGGGM PGLGQGPPTD APAVDTAEQV YISSLALLKM LKHGRAGVPM EVMGLMLGEF VDDYTVRVID VFAMPQSGTG VSVEAVDPV FQAKMLDMLK QTGRPEMVVG WYHSHPGFGC WLSGVDINTQ QSFEALSERA VAVVVDPIQS VKGKVVIDAF R LINANMMV ...String:
DRLLRLGGGM PGLGQGPPTD APAVDTAEQV YISSLALLKM LKHGRAGVPM EVMGLMLGEF VDDYTVRVID VFAMPQSGTG VSVEAVDPV FQAKMLDMLK QTGRPEMVVG WYHSHPGFGC WLSGVDINTQ QSFEALSERA VAVVVDPIQS VKGKVVIDAF R LINANMMV LGHEPRQTTS NLGHLNKPSI QALIHGLNRH YYSITINYRK NELEQKMLLN LHKKSWMEGL TLQDYSEHCK HN ESVVKEM LELAKNYNKA VEEEDKMTPE QLAIKNVGKQ DPKRHLEEHV DVLMTSNIVQ CLAAMLDTVV FK

UniProtKB: Ubiquitin C-terminal hydrolase PSMD14

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Macromolecule #2: 26S proteasome regulatory subunit 7

MacromoleculeName: 26S proteasome regulatory subunit 7 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 48.700805 KDa
SequenceString: MPDYLGADQR KTKEDEKDDK PIRALDEGDI ALLKTYGQST YSRQIKQVED DIQQLLKKIN ELTGIKESDT GLAPPALWDL AADKQTLQS EQPLQVARCT KIINADSEDP KYIINVKQFA KFVVDLSDQV APTDIEEGMR VGVDRNKYQI HIPLPPKIDP T VTMMQVEE ...String:
MPDYLGADQR KTKEDEKDDK PIRALDEGDI ALLKTYGQST YSRQIKQVED DIQQLLKKIN ELTGIKESDT GLAPPALWDL AADKQTLQS EQPLQVARCT KIINADSEDP KYIINVKQFA KFVVDLSDQV APTDIEEGMR VGVDRNKYQI HIPLPPKIDP T VTMMQVEE KPDVTYSDVG GCKEQIEKLR EVVETPLLHP ERFVNLGIEP PKGVLLFGPP GTGKTLCARA VANRTDACFI RV IGSELVQ KYVGEGARMV RELFEMARTK KACLIFFDEI DAIGGARFDD GAGGDNEVQR TMLELINQLD GFDPRGNIKV LMA TNRPDT LDPALMRPGR LDRKIEFSLP DLEGRTHIFK IHARSMSVER DIRFELLARL CPNSTGAEIR SVCTEAGMFA IRAR RKIAT EKDFLEAVNK VIKSYAKFSA TPRYMTYN

UniProtKB: 26S proteasome regulatory subunit 7

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Macromolecule #3: 26S proteasome regulatory subunit 4

MacromoleculeName: 26S proteasome regulatory subunit 4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.260504 KDa
SequenceString: MGQSQSGGHG PGGGKKDDKD KKKKYEPPVP TRVGKKKKKT KGPDAASKLP LVTPHTQCRL KLLKLERIKD YLLMEEEFIR NQEQMKPLE EKQEEERSKV DDLRGTPMSV GTLEEIIDDN HAIVSTSVGS EHYVSILSFV DKDLLEPGCS VLLNHKVHAV I GVLMDDTD ...String:
MGQSQSGGHG PGGGKKDDKD KKKKYEPPVP TRVGKKKKKT KGPDAASKLP LVTPHTQCRL KLLKLERIKD YLLMEEEFIR NQEQMKPLE EKQEEERSKV DDLRGTPMSV GTLEEIIDDN HAIVSTSVGS EHYVSILSFV DKDLLEPGCS VLLNHKVHAV I GVLMDDTD PLVTVMKVEK APQETYADIG GLDNQIQEIK ESVELPLTHP EYYEEMGIKP PKGVILYGPP GTGKTLLAKA VA NQTSATF LRVVGSELIQ KYLGDGPKLV RELFRVAEEH APSIVFIDEI DAIGTKRYDS NSGGEREIQR TMLELLNQLD GFD SRGDVK VIMATNRIET LDPALIRPGR IDRKIEFPLP DEKTKKRIFQ IHTSRMTLAD DVTLDDLIMA KDDLSGADIK AICT EAGLM ALRERRMKVT NEDFKKSKEN VLYKKQEGTP EGLYL

UniProtKB: 26S proteasome regulatory subunit 4

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Macromolecule #4: 26S proteasome regulatory subunit 8

MacromoleculeName: 26S proteasome regulatory subunit 8 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.852121 KDa
SequenceString: MELEEGKAGS GLRQYYLSKI EELQLIVNDK SQNLRRLQAQ RNELNAKVRL LREELQLLQE QGSYVGEVVR AMDKKKVLVK VHPEGKFVV DVDKNIDIND VTPNCRVALR NDSYTLHKIL PNKVDPLVSL MMVEKVPDST YEMIGGLDKQ IKEIKEVIEL P VKHPELFE ...String:
MELEEGKAGS GLRQYYLSKI EELQLIVNDK SQNLRRLQAQ RNELNAKVRL LREELQLLQE QGSYVGEVVR AMDKKKVLVK VHPEGKFVV DVDKNIDIND VTPNCRVALR NDSYTLHKIL PNKVDPLVSL MMVEKVPDST YEMIGGLDKQ IKEIKEVIEL P VKHPELFE ALGIAQPKGV LLYGPPGTGK TLLARAVAHH TDCTFIRVSG SELVQKFIGE GARMVRELFV MAREHAPSII FM DEIDSIG SSRLEGGSGG DSEVQRTMLE LLNQLDGFEA TKNIKVIMAT NRIDILDSAL LRPGRIDRKI EFPPPNEEAR LDI LKIHSR KMNLTRGINL RKIAELMPGA SGAEVKGVCT EAGMYALRER RVHVTQEDFE MAVAKVMQKD SEKNMSIKKL WK

UniProtKB: 26S proteasome regulatory subunit 8

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Macromolecule #5: 26S proteasome regulatory subunit 6B

MacromoleculeName: 26S proteasome regulatory subunit 6B / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.426141 KDa
SequenceString: MEEIGILVEK AQDEIPALSV SRPQTGLSFL GPEPEDLEDL YSRYKKLQQE LEFLEVQEEY IKDEQKNLKK EFLHAQEEVK RIQSIPLVI GQFLEAVDQN TAIVGSTTGS NYYVRILSTI DRELLKPNAS VALHKHSNAL VDVLPPEADS SIMMLTSDQK P DVMYADIG ...String:
MEEIGILVEK AQDEIPALSV SRPQTGLSFL GPEPEDLEDL YSRYKKLQQE LEFLEVQEEY IKDEQKNLKK EFLHAQEEVK RIQSIPLVI GQFLEAVDQN TAIVGSTTGS NYYVRILSTI DRELLKPNAS VALHKHSNAL VDVLPPEADS SIMMLTSDQK P DVMYADIG GMDIQKQEVR EAVELPLTHF ELYKQIGIDP PRGVLMYGPP GCGKTMLAKA VAHHTTAAFI RVVGSEFVQK YL GEGPRMV RDVFRLAKEN APAIIFIDEI DAIATKRFDA QTGADREVQR ILLELLNQMD GFDQNVNVKV IMATNRADTL DPA LLRPGR LDRKIEFPLP DRRQKRLIFS TITSKMNLSE EVDLEDYVAR PDKISGADIN SICQESGMLA VRENRYIVLA KDFE KAYKT VIKKDEQEHE FYK

UniProtKB: 26S proteasome regulatory subunit 6B

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Macromolecule #6: Proteasome 26S subunit, ATPase 6

MacromoleculeName: Proteasome 26S subunit, ATPase 6 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.867027 KDa
SequenceString: MAIPGIPYER RLLIMADPRD KALQDYRKKL LEHKEIDGRL KELREQLKEL TKQYEKSEND LKALQSVGQI VGEVLKQLTE EKFIVKATN GPRYVVGCRR QLDKSKLKPG TRVALDMTTL TIMRYLPREV DPLVYNMSHE DPGNVSYSEI GGLSEQIREL R EVIELPLT ...String:
MAIPGIPYER RLLIMADPRD KALQDYRKKL LEHKEIDGRL KELREQLKEL TKQYEKSEND LKALQSVGQI VGEVLKQLTE EKFIVKATN GPRYVVGCRR QLDKSKLKPG TRVALDMTTL TIMRYLPREV DPLVYNMSHE DPGNVSYSEI GGLSEQIREL R EVIELPLT NPELFQRVGI IPPKGCLLYG PPGTGKTLLA RAVASQLDCN FLKVVSSSIV DKYIGESARL IREMFNYARD HQ PCIIFMD EIDAIGGRRF SEGTSADREI QRTLMELLNQ MDGFDTLHRV KMIMATNRPD TLDPALLRPG RLDRKIHIDL PNE QARLDI LKIHAGPITK HGEIDYEAIV KLSDGFNGAD LRNVCTEAGM FAIRADHDFV VQEDFMKAVR KVADSKKLES KLDY KPV

UniProtKB: 26S proteasome regulatory subunit 10B

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Macromolecule #7: 26S proteasome regulatory subunit 6A

MacromoleculeName: 26S proteasome regulatory subunit 6A / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 49.266457 KDa
SequenceString: MNLLPNIESP VTRQEKMATV WDEAEQDGIG EEVLKMSTEE IIQRTRLLDS EIKIMKSEVL RVTHELQAMK DKIKENSEKI KVNKTLPYL VSNVIELLDV DPNDQEEDGA NIDLDSQRKG KCAVIKTSTR QTYFLPVIGL VDAEKLKPGD LVGVNKDSYL I LETLPTEY ...String:
MNLLPNIESP VTRQEKMATV WDEAEQDGIG EEVLKMSTEE IIQRTRLLDS EIKIMKSEVL RVTHELQAMK DKIKENSEKI KVNKTLPYL VSNVIELLDV DPNDQEEDGA NIDLDSQRKG KCAVIKTSTR QTYFLPVIGL VDAEKLKPGD LVGVNKDSYL I LETLPTEY DSRVKAMEVD ERPTEQYSDI GGLDKQIQEL VEAIVLPMNH KEKFENLGIQ PPKGVLMYGP PGTGKTLLAR AC AAQTKAT FLKLAGPQLV QMFIGDGAKL VRDAFALAKE KAPSIIFIDE LDAIGTKRFD SEKAGDREVQ RTMLELLNQL DGF QPNTQV KVIAATNRVD ILDPALLRSG RLDRKIEFPM PNEEARARIM QIHSRKMNVS PDVNYEELAR CTDDFNGAQC KAVC VEAGM IALRRGATEL THEDYMEGIL EVQAKKKANL QYYA

UniProtKB: 26S proteasome regulatory subunit 6A

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Macromolecule #8: Proteasome subunit alpha type-6

MacromoleculeName: Proteasome subunit alpha type-6 / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.301262 KDa
SequenceString: SRGSSAGFDR HITIFSPEGR LYQVEYAFKA INQGGLTSVA VRGKDCAVIV TQKKVPDKLL DSSTVTHLFK ITENIGCVMT GMTADSRSQ VQRARYEAAN WKYKYGYEIP VDMLCKRIAD ISQVYTQNAE MRPLGCCMIL IGIDEEQGPQ VYKCDPAGYY C GFKATAAG ...String:
SRGSSAGFDR HITIFSPEGR LYQVEYAFKA INQGGLTSVA VRGKDCAVIV TQKKVPDKLL DSSTVTHLFK ITENIGCVMT GMTADSRSQ VQRARYEAAN WKYKYGYEIP VDMLCKRIAD ISQVYTQNAE MRPLGCCMIL IGIDEEQGPQ VYKCDPAGYY C GFKATAAG VKQTESTSFL EKKVKKKFDW TFEQTVETAI TCLSTVLSID FKPSEIEVGV VTVENPKFRI LTEAEIDAHL VA LAERD

UniProtKB: Proteasome subunit alpha type-6

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Macromolecule #9: Proteasome subunit alpha type-2

MacromoleculeName: Proteasome subunit alpha type-2 / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.796338 KDa
SequenceString: AERGYSFSLT TFSPSGKLVQ IEYALAAVAG GAPSVGIKAA NGVVLATEKK QKSILYDERS VHKVEPITKH IGLVYSGMGP DYRVLVHRA RKLAQQYYLV YQEPIPTAQL VQRVASVMQE YTQSGGVRPF GVSLLICGWN EGRPYLFQSD PSGAYFAWKA T AMGKNYVN ...String:
AERGYSFSLT TFSPSGKLVQ IEYALAAVAG GAPSVGIKAA NGVVLATEKK QKSILYDERS VHKVEPITKH IGLVYSGMGP DYRVLVHRA RKLAQQYYLV YQEPIPTAQL VQRVASVMQE YTQSGGVRPF GVSLLICGWN EGRPYLFQSD PSGAYFAWKA T AMGKNYVN GKTFLEKRYN EDLELEDAIH TAILTLKESF EGQMTEDNIE VGICNEAGFR RLTPTEVKDY LAAIA

UniProtKB: Proteasome subunit alpha type-2

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Macromolecule #10: Proteasome subunit alpha type-4

MacromoleculeName: Proteasome subunit alpha type-4 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.394648 KDa
SequenceString: SRRYDSRTTI FSPEGRLYQV EYAMEAIGHA GTCLGILAND GVLLAAERRN IHKLLDEVFF SEKIYKLNED MACSVAGITS DANVLTNEL RLIAQRYLLQ YQEPIPCEQL VTALCDIKQA YTQFGGKRPF GVSLLYIGWD KHYGFQLYQS DPSGNYGGWK A TCIGNNSA ...String:
SRRYDSRTTI FSPEGRLYQV EYAMEAIGHA GTCLGILAND GVLLAAERRN IHKLLDEVFF SEKIYKLNED MACSVAGITS DANVLTNEL RLIAQRYLLQ YQEPIPCEQL VTALCDIKQA YTQFGGKRPF GVSLLYIGWD KHYGFQLYQS DPSGNYGGWK A TCIGNNSA AAVSMLKQDY KEGEMTLKSA LALAIKVLNK TMDVSKLSAE KVEIATLTRE NGKTVIRVLK QKEVEQLIKK HE EEEAKAE REKKEKEQKE KDK

UniProtKB: Proteasome subunit alpha type-4

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Macromolecule #11: Proteasome subunit alpha type-7

MacromoleculeName: Proteasome subunit alpha type-7 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.798695 KDa
SequenceString: SYDRAITVFS PDGHLFQVEY AQEAVKKGST AVGVRGRDIV VLGVEKKSVA KLQDERTVRK ICALDDNVCM AFAGLTADAR IVINRARVE CQSHRLTVED PVTVEYITRY IASLKQRYTQ SNGRRPFGIS ALIVGFDFDG TPRLYQTDPS GTYHAWKANA I GRGAKSVR ...String:
SYDRAITVFS PDGHLFQVEY AQEAVKKGST AVGVRGRDIV VLGVEKKSVA KLQDERTVRK ICALDDNVCM AFAGLTADAR IVINRARVE CQSHRLTVED PVTVEYITRY IASLKQRYTQ SNGRRPFGIS ALIVGFDFDG TPRLYQTDPS GTYHAWKANA I GRGAKSVR EFLEKNYTDE AIETDDLTIK LVIKALLEVV QSGGKNIELA VMRRDQSLKI LNPEEIEKYV AEIEKEKEEN EK KKQKKAS

UniProtKB: Proteasome subunit alpha type-7

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Macromolecule #12: Proteasome subunit alpha type-5

MacromoleculeName: Proteasome subunit alpha type-5 / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.304779 KDa
SequenceString: FLTRSEYDRG VNTFSPEGRL FQVEYAIEAI KLGSTAIGIQ TSEGVCLAVE KRITSPLMEP SSIEKIVEID AHIGCAMSGL IADAKTLID KARVETQNHW FTYNETMTVE SVTQAVSNLA LQFGEEDADP GAMSRPFGVA LLFGGVDEKG PQLFHMDPSG T FVQCDARA ...String:
FLTRSEYDRG VNTFSPEGRL FQVEYAIEAI KLGSTAIGIQ TSEGVCLAVE KRITSPLMEP SSIEKIVEID AHIGCAMSGL IADAKTLID KARVETQNHW FTYNETMTVE SVTQAVSNLA LQFGEEDADP GAMSRPFGVA LLFGGVDEKG PQLFHMDPSG T FVQCDARA IGSASEGAQS SLQEVYHKSM TLKEAIKSSL IILKQVMEEK LNATNIELAT VQPGQNFHMF TKEELEEVIK DI

UniProtKB: Proteasome subunit alpha type-5

+
Macromolecule #13: Isoform Long of Proteasome subunit alpha type-1

MacromoleculeName: Isoform Long of Proteasome subunit alpha type-1 / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.150277 KDa
SequenceString: QLSKVKFRNQ YDNDVTVWSP QGRIHQIEYA MEAVKQGSAT VGLKSKTHAV LVALKRAQSE LAAHQKKILH VDNHIGISIA GLTADARLL CNFMRQECLD SRFVFDRPLP VSRLVSLIGS KTQIPTQRYG RRPYGVGLLI AGYDDMGPHI FQTCPSANYF D CRAMSIGA ...String:
QLSKVKFRNQ YDNDVTVWSP QGRIHQIEYA MEAVKQGSAT VGLKSKTHAV LVALKRAQSE LAAHQKKILH VDNHIGISIA GLTADARLL CNFMRQECLD SRFVFDRPLP VSRLVSLIGS KTQIPTQRYG RRPYGVGLLI AGYDDMGPHI FQTCPSANYF D CRAMSIGA RSQSARTYLE RHMSEFMECN LNELVKHGLR ALRETLPAEQ DLTTKNVSIG IVGKDLEFTI YDDDDVSPFL EG LEERPQR KAQPAQPADE PAEKADEPME H

UniProtKB: Proteasome subunit alpha type-1

+
Macromolecule #14: Proteasome subunit alpha type-3

MacromoleculeName: Proteasome subunit alpha type-3 / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.338057 KDa
SequenceString: SSIGTGYDLS ASTFSPDGRV FQVEYAMKAV ENSSTAIGIR CKDGVVFGVE KLVLSKLYEE GSNKRLFNVD RHVGMAVAGL LADARSLAD IAREEASNFR SNFGYNIPLK HLADRVAMYV HAYTLYSAVR PFGCSFMLGS YSVNDGAQLY MIDPSGVSYG Y WGCAIGKA ...String:
SSIGTGYDLS ASTFSPDGRV FQVEYAMKAV ENSSTAIGIR CKDGVVFGVE KLVLSKLYEE GSNKRLFNVD RHVGMAVAGL LADARSLAD IAREEASNFR SNFGYNIPLK HLADRVAMYV HAYTLYSAVR PFGCSFMLGS YSVNDGAQLY MIDPSGVSYG Y WGCAIGKA RQAAKTEIEK LQMKEMTCRD IVKEVAKIIY IVHDEVKDKA FELELSWVGE LTNGRHEIVP KDIREEAEKY AK ESLKEED ESDDDNM

UniProtKB: Proteasome subunit alpha type-3

+
Macromolecule #15: Proteasome subunit beta type-6

MacromoleculeName: Proteasome subunit beta type-6 / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.246455 KDa
SequenceString: AATLLAARGA GPAPAWGPEA FTPDWESREV STGTTIMAVQ FDGGVVLGAD SRTTTGSYIA NRVTDKLTPI HDRIFCCRSG SAADTQAVA DAVTYQLGFH SIELNEPPLV HTAASLFKEM CYRYREDLMA GIIIAGWDPQ EGGQVYSVPM GGMMVRQSFA I GGSGSSYI ...String:
AATLLAARGA GPAPAWGPEA FTPDWESREV STGTTIMAVQ FDGGVVLGAD SRTTTGSYIA NRVTDKLTPI HDRIFCCRSG SAADTQAVA DAVTYQLGFH SIELNEPPLV HTAASLFKEM CYRYREDLMA GIIIAGWDPQ EGGQVYSVPM GGMMVRQSFA I GGSGSSYI YGYVDATYRE GMTKEECLQF TANALALAME RDGSSGGVIR LAAIAESGVE RQVLLGDQIP KFAVATLPPA

UniProtKB: Proteasome subunit beta type-6

+
Macromolecule #16: Proteasome subunit beta type-7

MacromoleculeName: Proteasome subunit beta type-7 / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.869223 KDa
SequenceString: AAVSVYAPPV GGFSFDNCRR NAVLEADFAK RGYKLPKVRK TGTTIAGVVY KDGIVLGADT RATEGMVVAD KNCSKIHFIS PNIYCCGAG TAADTDMTTQ LISSNLELHS LSTGRLPRVV TANRMLKQML FRYQGYIGAA LVLGGVDVTG PHLYSIYPHG S TDKLPYVT ...String:
AAVSVYAPPV GGFSFDNCRR NAVLEADFAK RGYKLPKVRK TGTTIAGVVY KDGIVLGADT RATEGMVVAD KNCSKIHFIS PNIYCCGAG TAADTDMTTQ LISSNLELHS LSTGRLPRVV TANRMLKQML FRYQGYIGAA LVLGGVDVTG PHLYSIYPHG S TDKLPYVT MGSGSLAAMA VFEDKFRPDM EEEEAKNLVS EAIAAGIFND LGSGSNIDLC VISKNKLDFL RPYTVPNKKG TR LGRYRCE KGTTAVLTEK ITPLEIEVLE ETVQTMDTS

UniProtKB: Proteasome subunit beta type-7

+
Macromolecule #17: Proteasome subunit beta type-3

MacromoleculeName: Proteasome subunit beta type-3 / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.841701 KDa
SequenceString: SIMSYNGGAV MAMKGKNCVA IAADRRFGIQ AQMVTTDFQK IFPMGDRLYI GLAGLATDVQ TVAQRLKFRL NLYELKEGRQ IKPYTLMSM VANLLYEKRF GPYYTEPVIA GLDPKTFKPF ICSLDLIGCP MVTDDFVVSG TCAEQMYGMC ESLWEPNMDP D HLFETISQ ...String:
SIMSYNGGAV MAMKGKNCVA IAADRRFGIQ AQMVTTDFQK IFPMGDRLYI GLAGLATDVQ TVAQRLKFRL NLYELKEGRQ IKPYTLMSM VANLLYEKRF GPYYTEPVIA GLDPKTFKPF ICSLDLIGCP MVTDDFVVSG TCAEQMYGMC ESLWEPNMDP D HLFETISQ AMLNAVDRDA VSGMGVIVHI IEKDKITTRT LKARMD

UniProtKB: Proteasome subunit beta type-3

+
Macromolecule #18: Proteasome subunit beta type-2

MacromoleculeName: Proteasome subunit beta type-2 / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.864277 KDa
SequenceString: MEYLIGIQGP DYVLVASDRV AASNIVQMKD DHDKMFKMSE KILLLCVGEA GDTVQFAEYI QKNVQLYKMR NGYELSPTAA ANFTRRNLA DCLRSRTPYH VNLLLAGYDE HEGPALYYMD YLAALAKAPF AAHGYGAFLT LSILDRYYTP TISRERAVEL L RKCLEELQ ...String:
MEYLIGIQGP DYVLVASDRV AASNIVQMKD DHDKMFKMSE KILLLCVGEA GDTVQFAEYI QKNVQLYKMR NGYELSPTAA ANFTRRNLA DCLRSRTPYH VNLLLAGYDE HEGPALYYMD YLAALAKAPF AAHGYGAFLT LSILDRYYTP TISRERAVEL L RKCLEELQ KRFILNLPTF SVRIIDKNGI HDLDNISFPK QGS

UniProtKB: Proteasome subunit beta type-2

+
Macromolecule #19: Proteasome subunit beta type-5

MacromoleculeName: Proteasome subunit beta type-5 / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO / EC number: proteasome endopeptidase complex
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.379053 KDa
SequenceString: ALASVLERPL PVNQRGFFGL GGRADLLDLG PGSLSDGLSL AAPGWGVPEE PGIEMLHGTT TLAFKFRHGV IVAADSRATA GAYIASQTV KKVIEINPYL LGTMAGGAAD CSFWERLLAR QCRIYELRNK ERISVAAASK LLANMVYQYK GMGLSMGTMI C GWDKRGPG ...String:
ALASVLERPL PVNQRGFFGL GGRADLLDLG PGSLSDGLSL AAPGWGVPEE PGIEMLHGTT TLAFKFRHGV IVAADSRATA GAYIASQTV KKVIEINPYL LGTMAGGAAD CSFWERLLAR QCRIYELRNK ERISVAAASK LLANMVYQYK GMGLSMGTMI C GWDKRGPG LYYVDSEGNR ISGATFSVGS GSVYAYGVMD RGYSYDLEVE QAYDLARRAI YQATYRDAYS GGAVNLYHVR ED GWIRVSS DNVADLHEKY SGSTP

UniProtKB: Proteasome subunit beta type-5

+
Macromolecule #20: Proteasome subunit beta type-1

MacromoleculeName: Proteasome subunit beta type-1 / type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 26.391201 KDa
SequenceString: LSSTAMYSAP GRDLGMEPHR AAGPLQLRFS PYVFNGGTIL AIAGEDFAIV ASDTRLSEGF SIHTRDSPKC YKLTDKTVIG CSGFHGDCL TLTKIIEARL KMYKHSNNKA MTTGAIAAML STILYSRRFF PYYVYNIIGG LDEEGKGAVY SFDPVGSYQR D SFKAGGSA ...String:
LSSTAMYSAP GRDLGMEPHR AAGPLQLRFS PYVFNGGTIL AIAGEDFAIV ASDTRLSEGF SIHTRDSPKC YKLTDKTVIG CSGFHGDCL TLTKIIEARL KMYKHSNNKA MTTGAIAAML STILYSRRFF PYYVYNIIGG LDEEGKGAVY SFDPVGSYQR D SFKAGGSA SAMLQPLLDN QVGFKNMQNV EHVPLSLDRA MRLVKDVFIS AAERDVYTGD ALRICIVTKE GIREETVSLR KD

UniProtKB: Proteasome subunit beta type-1

+
Macromolecule #21: Proteasome subunit beta type-4

MacromoleculeName: Proteasome subunit beta type-4 / type: protein_or_peptide / ID: 21 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 29.099986 KDa
SequenceString: EAFLGSRSGL WAGGPAPGQF YRIPSTPDSF MDPASALYRG PITRTQNPMV TGTSVLGVKF EGGVVIAADM LGSYGSLARF RNISRIMRV NNSTMLGASG DYADFQYLKQ VLGQMVIDEE LLGDGHSYSP RAIHSWLTRA MYSRRSKMNP LWNTMVIGGY A DGESFLGY ...String:
EAFLGSRSGL WAGGPAPGQF YRIPSTPDSF MDPASALYRG PITRTQNPMV TGTSVLGVKF EGGVVIAADM LGSYGSLARF RNISRIMRV NNSTMLGASG DYADFQYLKQ VLGQMVIDEE LLGDGHSYSP RAIHSWLTRA MYSRRSKMNP LWNTMVIGGY A DGESFLGY VDMLGVAYEA PSLATGYGAY LAQPLLREVL EKQPVLSQTE ARDLVERCMR VLYYRDARSY NRFQIATVTE KG VEIEGPL STETNWDIAH MISGFE

UniProtKB: Proteasome subunit beta type-4

+
Macromolecule #22: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 22 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

+
Macromolecule #23: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 23 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

+
Macromolecule #24: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 24 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #25: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 25 / Number of copies: 2 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

+
Macromolecule #26: N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-4-methyl-1-oxopentan-2-y...

MacromoleculeName: N-[(benzyloxy)carbonyl]-L-leucyl-N-[(2S)-4-methyl-1-oxopentan-2-yl]-L-leucinamide
type: ligand / ID: 26 / Number of copies: 6 / Formula: LDZ
Molecular weightTheoretical: 475.621 Da
Chemical component information


ChemComp, No image

ChemComp-PRD_000907:
Unknown entry / inhibitor*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.17 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 22379
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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