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- EMDB-8684: Conformational Landscape of the p28-Bound Human Proteasome Regula... -

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Basic information

Entry
Database: EMDB / ID: EMD-8684
TitleConformational Landscape of the p28-Bound Human Proteasome Regulatory Particle
Map datap28-Bound Human Proteasome Regulatory Particle
Sample
  • Complex: Proteasome regulatory particle
    • Protein or peptide: x 17 types
  • Protein or peptide: x 1 types
  • Ligand: x 1 types
Keywordsp28 / 26S proteasome / regulatory particle / 19S / gankyrin / HYDROLASE
Function / homology
Function and homology information


positive regulation of inclusion body assembly / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / meiosis I / positive regulation of proteasomal protein catabolic process / metal-dependent deubiquitinase activity ...positive regulation of inclusion body assembly / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / thyrotropin-releasing hormone receptor binding / modulation by host of viral transcription / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / meiosis I / positive regulation of proteasomal protein catabolic process / metal-dependent deubiquitinase activity / proteasome regulatory particle / cytosolic proteasome complex / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / protein K63-linked deubiquitination / negative regulation of programmed cell death / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Regulation of ornithine decarboxylase (ODC) / Resolution of D-loop Structures through Holliday Junction Intermediates / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / Impaired BRCA2 binding to RAD51 / K63-linked deubiquitinase activity / proteasome binding / regulation of protein catabolic process / Presynaptic phase of homologous DNA pairing and strand exchange / proteasome storage granule / blastocyst development / transcription factor binding / polyubiquitin modification-dependent protein binding / general transcription initiation factor binding / endopeptidase activator activity / proteasome assembly / positive regulation of RNA polymerase II transcription preinitiation complex assembly / regulation of proteasomal protein catabolic process / enzyme regulator activity / mRNA export from nucleus / : / inclusion body / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Degradation of DVL / P-body / stem cell differentiation / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Degradation of AXIN / Defective CFTR causes cystic fibrosis / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Negative regulation of NOTCH4 signaling / double-strand break repair via homologous recombination / G2/M Checkpoints / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Vif-mediated degradation of APOBEC3G / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / ABC-family proteins mediated transport / Degradation of beta-catenin by the destruction complex / HDR through Homologous Recombination (HRR) / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / cytoplasmic ribonucleoprotein granule / Metalloprotease DUBs / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / osteoblast differentiation / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / double-strand break repair via nonhomologous end joining / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs
Similarity search - Function
: / : / Ubiquitin interaction motif / 26S proteasome regulatory subunit RPN7/PSMD6 C-terminal helix / 26S proteasome non-ATPase regulatory subunit Rpn12 / 26S proteasome regulatory subunit, C-terminal / Proteasome regulatory subunit C-terminal / DSS1/SEM1 / 26S proteasome regulatory subunit RPN5, C-terminal domain / : ...: / : / Ubiquitin interaction motif / 26S proteasome regulatory subunit RPN7/PSMD6 C-terminal helix / 26S proteasome non-ATPase regulatory subunit Rpn12 / 26S proteasome regulatory subunit, C-terminal / Proteasome regulatory subunit C-terminal / DSS1/SEM1 / 26S proteasome regulatory subunit RPN5, C-terminal domain / : / DSS1/SEM1 family / 26S proteasome regulatory subunit RPN5 C-terminal domain / 26S proteasome subunit RPN2, N-terminal domain / DSS1_SEM1 / 26S proteasome regulatory subunit Rpn6, N-terminal / 6S proteasome subunit Rpn6, C-terminal helix domain / 26S proteasome regulatory subunit RPN6 N-terminal domain / 26S proteasome subunit RPN6 C-terminal helix domain / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S Proteasome non-ATPase regulatory subunit 13 / 26S proteasome regulatory subunit RPN2, C-terminal / 26S proteasome regulatory subunit RPN2 C-terminal domain / 26S Proteasome non-ATPase regulatory subunit 7/8 / : / 26S proteasome regulatory subunit 7, OB 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 / 26S proteasome regulatory subunit Rpn7, N-terminal / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome subunit RPN7 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / Proteasome/cyclosome repeat / Proteasome/cyclosome repeat / Ubiquitin-interacting motif. / PCI/PINT associated module / von Willebrand factor type A domain / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / HEAT repeats / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / von Willebrand factor A-like domain superfamily / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Armadillo-type fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome non-ATPase regulatory subunit 12 / 26S proteasome non-ATPase regulatory subunit 14 / 26S proteasome non-ATPase regulatory subunit 3 / 26S proteasome regulatory subunit 6A / 26S proteasome regulatory subunit 7 / 26S proteasome regulatory subunit 6B / 26S proteasome non-ATPase regulatory subunit 8 / 26S proteasome non-ATPase regulatory subunit 7 / 26S proteasome non-ATPase regulatory subunit 4 ...26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome non-ATPase regulatory subunit 12 / 26S proteasome non-ATPase regulatory subunit 14 / 26S proteasome non-ATPase regulatory subunit 3 / 26S proteasome regulatory subunit 6A / 26S proteasome regulatory subunit 7 / 26S proteasome regulatory subunit 6B / 26S proteasome non-ATPase regulatory subunit 8 / 26S proteasome non-ATPase regulatory subunit 7 / 26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome complex subunit SEM1 / 26S proteasome regulatory subunit 4 / 26S proteasome regulatory subunit 8 / 26S proteasome regulatory subunit 10B / 26S proteasome non-ATPase regulatory subunit 2 / 26S proteasome non-ATPase regulatory subunit 6 / 26S proteasome non-ATPase regulatory subunit 1 / 26S proteasome non-ATPase regulatory subunit 13
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.8 Å
AuthorsLu Y / Wu J
CitationJournal: Mol Cell / Year: 2017
Title: Conformational Landscape of the p28-Bound Human Proteasome Regulatory Particle.
Authors: Ying Lu / Jiayi Wu / Yuanchen Dong / Shuobing Chen / Shuangwu Sun / Yong-Bei Ma / Qi Ouyang / Daniel Finley / Marc W Kirschner / Youdong Mao /
Abstract: The proteasome holoenzyme is activated by its regulatory particle (RP) consisting of two subcomplexes, the lid and the base. A key event in base assembly is the formation of a heterohexameric ring of ...The proteasome holoenzyme is activated by its regulatory particle (RP) consisting of two subcomplexes, the lid and the base. A key event in base assembly is the formation of a heterohexameric ring of AAA-ATPases, which is guided by at least four RP assembly chaperones in mammals: PAAF1, p28/gankyrin, p27/PSMD9, and S5b. Using cryogenic electron microscopy, we analyzed the non-AAA structure of the p28-bound human RP at 4.5 Å resolution and determined seven distinct conformations of the Rpn1-p28-AAA subcomplex within the p28-bound RP at subnanometer resolutions. Remarkably, the p28-bound AAA ring does not form a channel in the free RP and spontaneously samples multiple "open" and "closed" topologies at the Rpt2-Rpt6 and Rpt3-Rpt4 interfaces. Our analysis suggests that p28 assists the proteolytic core particle to select a specific conformation of the ATPase ring for RP engagement and is released in a shoehorn-like fashion in the last step of the chaperone-mediated proteasome assembly.
History
DepositionApr 13, 2017-
Header (metadata) releaseAug 23, 2017-
Map releaseAug 23, 2017-
UpdateAug 16, 2023-
Current statusAug 16, 2023Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.003
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.003
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5vhs
  • Surface level: 0.003
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8684.png

Downloads & links

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Map

FileDownload / File: emd_8684.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationp28-Bound Human Proteasome Regulatory Particle
Voxel sizeX=Y=Z: 0.86 Å
Density
Contour LevelBy AUTHOR: 0.004 / Movie #1: 0.003
Minimum - Maximum-0.003160499 - 0.009280332
Average (Standard dev.)0.00009587084 (±0.0009812362)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 258.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z258.000258.000258.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-36
NX/NY/NZ528549
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0030.0090.000

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Supplemental data

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Sample components

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Entire : Proteasome regulatory particle

EntireName: Proteasome regulatory particle
Components
  • Complex: Proteasome regulatory particle
    • 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: 26S proteasome regulatory subunit 10B
    • Protein or peptide: 26S proteasome regulatory subunit 6A
    • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 1
    • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 3
    • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 12
    • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 11
    • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 6
    • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 7
    • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 13
    • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 4
    • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 14
    • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 8
    • Protein or peptide: 26S proteasome complex subunit SEM1Proteasome
  • Protein or peptide: 26S proteasome non-ATPase regulatory subunit 2
  • Ligand: ZINC ION

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Supramolecule #1: Proteasome regulatory particle

SupramoleculeName: Proteasome regulatory particle / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: 26S proteasome regulatory subunit 7

MacromoleculeName: 26S proteasome regulatory subunit 7 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.395434 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: APPALWDLAA DKQTLQSEQP LQVARCTKII NADSEDPKYI INVKQFAKFV VDLSDQVAPT DIEEGMRVGV DRNKYQIHIP LPPKIDPTV TMMQVEEKPD VTYSDVGGCK EQIEKLREVV ETPLLHPERF VNLGIEPPKG VLLFGPPGTG KTLCARAVAN R TDACFIRV ...String:
APPALWDLAA DKQTLQSEQP LQVARCTKII NADSEDPKYI INVKQFAKFV VDLSDQVAPT DIEEGMRVGV DRNKYQIHIP LPPKIDPTV TMMQVEEKPD VTYSDVGGCK EQIEKLREVV ETPLLHPERF VNLGIEPPKG VLLFGPPGTG KTLCARAVAN R TDACFIRV IGSELVQKYV GEGARMVREL FEMARTKKAC LIFFDEIDAI GGARFDDGAG GDNEVQRTML ELINQLDGFD PR GNIKVLM ATNRPDTLDP ALMRPGRLDR KIEFSLPDLE GRTHIFKIHA RSMSVERDIR FELLARLCPN STGAEIRSVC TEA GMFAIR ARRKIATEKD FLEAVNKVIK SYAKFS

UniProtKB: 26S proteasome regulatory subunit 7

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Macromolecule #2: 26S proteasome regulatory subunit 4

MacromoleculeName: 26S proteasome regulatory subunit 4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 38.025398 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EEERSKVDDL RGTPMSVGTL EEIIDDNHAI VSTSVGSEHY VSILSFVDKD LLEPGCSVLL NHKVHAVIGV LMDDTDPLVT VMKVEKAPQ ETYADIGGLD NQIQEIKESV ELPLTHPEYY EEMGIKPPKG VILYGPPGTG KTLLAKAVAN QTSATFLRVV G SELIQKYL ...String:
EEERSKVDDL RGTPMSVGTL EEIIDDNHAI VSTSVGSEHY VSILSFVDKD LLEPGCSVLL NHKVHAVIGV LMDDTDPLVT VMKVEKAPQ ETYADIGGLD NQIQEIKESV ELPLTHPEYY EEMGIKPPKG VILYGPPGTG KTLLAKAVAN QTSATFLRVV G SELIQKYL GDGPKLVREL FRVAEEHAPS IVFIDEIDAI GTKRYDSNSG GEREIQRTML ELLNQLDGFD SRGDVKVIMA TN RIETLDP ALIRPGRIDR KIEFPLPDEK TKKRIFQIHT SRMTLADDVT LDDLIMAKDD LSGADIKAIC TEAGLMALRE RRM KVTNED FKKSKENVLY KKQEG

UniProtKB: 26S proteasome regulatory subunit 4

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Macromolecule #3: 26S proteasome regulatory subunit 8

MacromoleculeName: 26S proteasome regulatory subunit 8 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.201078 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LEEGKAGSGL RQYYLSKIEE LQLIVNDKSQ NLRRLQAQRN ELNAKVRLLR EELQLLQEQG SYVGEVVRAM DKKKVLVKVH PEGKFVVDV DKNIDINDVT PNCRVALRND SYTLHKILPN KVDPLVSLMM VEKVPDSTYE MIGGLDKQIK EIKEVIELPV K HPELFEAL ...String:
LEEGKAGSGL RQYYLSKIEE LQLIVNDKSQ NLRRLQAQRN ELNAKVRLLR EELQLLQEQG SYVGEVVRAM DKKKVLVKVH PEGKFVVDV DKNIDINDVT PNCRVALRND SYTLHKILPN KVDPLVSLMM VEKVPDSTYE MIGGLDKQIK EIKEVIELPV K HPELFEAL GIAQPKGVLL YGPPGTGKTL LARAVAHHTD CTFIRVSGSE LVQKFIGEGA RMVRELFVMA REHAPSIIFM DE IDSIGSS RLEGGSGGDS EVQRTMLELL NQLDGFEATK NIKVIMATNR IDILDSALLR PGRIDRKIEF PPPNEEARLD ILK IHSRKM NLTRGINLRK IAELMPGASG AEVKGVCTEA GMYALRERRV HVTQEDFEMA VAKVMQKDS

UniProtKB: 26S proteasome regulatory subunit 8

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Macromolecule #4: 26S proteasome regulatory subunit 6B

MacromoleculeName: 26S proteasome regulatory subunit 6B / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.723801 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DLYSRYKKLQ QELEFLEVQE EYIKDEQKNL KKEFLHAQEE VKRIQSIPLV IGQFLEAVDQ NTAIVGSTTG SNYYVRILST IDRELLKPN ASVALHKHSN ALVDVLPPEA DSSIMMLTSD QKPDVMYADI GGMDIQKQEV REAVELPLTH FELYKQIGID P PRGVLMYG ...String:
DLYSRYKKLQ QELEFLEVQE EYIKDEQKNL KKEFLHAQEE VKRIQSIPLV IGQFLEAVDQ NTAIVGSTTG SNYYVRILST IDRELLKPN ASVALHKHSN ALVDVLPPEA DSSIMMLTSD QKPDVMYADI GGMDIQKQEV REAVELPLTH FELYKQIGID P PRGVLMYG PPGCGKTMLA KAVAHHTTAA FIRVVGSEFV QKYLGEGPRM VRDVFRLAKE NAPAIIFIDE IDAIATKRFD AQ TGADREV QRILLELLNQ MDGFDQNVNV KVIMATNRAD TLDPALLRPG RLDRKIEFPL PDRRQKRLIF STITSKMNLS EEV DLEDYV ARPDKISGAD INSICQESGM LAVRENRYIV LAKDFEKAYK TV

UniProtKB: 26S proteasome regulatory subunit 6B

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Macromolecule #5: 26S proteasome regulatory subunit 10B

MacromoleculeName: 26S proteasome regulatory subunit 10B / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.112707 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYRKKLLEHK EIDGRLKELR EQLKELTKQY EKSENDLKAL QSVGQIVGEV LKQLTEEKFI VKATNGPRYV VGCRRQLDKS KLKPGTRVA LDMTTLTIMR YLPREVDPLV YNMSHEDPGN VSYSEIGGLS EQIRELREVI ELPLTNPELF QRVGIIPPKG C LLYGPPGT ...String:
DYRKKLLEHK EIDGRLKELR EQLKELTKQY EKSENDLKAL QSVGQIVGEV LKQLTEEKFI VKATNGPRYV VGCRRQLDKS KLKPGTRVA LDMTTLTIMR YLPREVDPLV YNMSHEDPGN VSYSEIGGLS EQIRELREVI ELPLTNPELF QRVGIIPPKG C LLYGPPGT GKTLLARAVA SQLDCNFLKV VSSSIVDKYI GESARLIREM FNYARDHQPC IIFMDEIDAI GGRRFSEGTS AD REIQRTL MELLNQMDGF DTLHRVKMIM ATNRPDTLDP ALLRPGRLDR KIHIDLPNEQ ARLDILKIHA GPITKHGEID YEA IVKLSD GFNGADLRNV CTEAGMFAIR ADHDFVVQED FMKAVRKVAD SKKLESKLDY KPV

UniProtKB: 26S proteasome regulatory subunit 10B

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Macromolecule #6: 26S proteasome regulatory subunit 6A

MacromoleculeName: 26S proteasome regulatory subunit 6A / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.467867 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: KIMKSEVLRV THELQAMKDK IKENSEKIKV NKTLPYLVSN VIELLDVDPN DQEEDGANID LDSQRKGKCA VIKTSTRQTY FLPVIGLVD AEKLKPGDLV GVNKDSYLIL ETLPTEYDSR VKAMEVDERP TEQYSDIGGL DKQIQELVEA IVLPMNHKEK F ENLGIQPP ...String:
KIMKSEVLRV THELQAMKDK IKENSEKIKV NKTLPYLVSN VIELLDVDPN DQEEDGANID LDSQRKGKCA VIKTSTRQTY FLPVIGLVD AEKLKPGDLV GVNKDSYLIL ETLPTEYDSR VKAMEVDERP TEQYSDIGGL DKQIQELVEA IVLPMNHKEK F ENLGIQPP KGVLMYGPPG TGKTLLARAC AAQTKATFLK LAGPQLVQMF IGDGAKLVRD AFALAKEKAP SIIFIDELDA IG TKRFDSE KAGDREVQRT MLELLNQLDG FQPNTQVKVI AATNRVDILD PALLRSGRLD RKIEFPMPNE EARARIMQIH SRK MNVSPD VNYEELARCT DDFNGAQCKA VCVEAGMIAL RRGATELTHE DYMEGILEVQ AKKK

UniProtKB: 26S proteasome regulatory subunit 6A

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Macromolecule #7: 26S proteasome non-ATPase regulatory subunit 1

MacromoleculeName: 26S proteasome non-ATPase regulatory subunit 1 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 103.755023 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MITSAAGIIS LLDEDEPQLK EFALHKLNAV VNDFWAEISE SVDKIEVLYE DEGFRSRQFA ALVASKVFYH LGAFEESLNY ALGAGDLFN VNDNSEYVET IIAKCIDHYT KQCVENADLP EGEKKPIDQR LEGIVNKMFQ RCLDDHKYKQ AIGIALETRR L DVFEKTIL ...String:
MITSAAGIIS LLDEDEPQLK EFALHKLNAV VNDFWAEISE SVDKIEVLYE DEGFRSRQFA ALVASKVFYH LGAFEESLNY ALGAGDLFN VNDNSEYVET IIAKCIDHYT KQCVENADLP EGEKKPIDQR LEGIVNKMFQ RCLDDHKYKQ AIGIALETRR L DVFEKTIL ESNDVPGMLA YSLKLCMSLM QNKQFRNKVL RVLVKIYMNL EKPDFINVCQ CLIFLDDPQA VSDILEKLVK ED NLLMAYQ ICFDLYESAS QQFLSSVIQN LRTVGTPIAS VPGSTNTGTV PGSEKDSDSM ETEEKTSSAF VGKTPEASPE PKD QTLKMI KILSGEMAIE LHLQFLIRNN NTDLMILKNT KDAVRNSVCH TATVIANSFM HCGTTSDQFL RDNLEWLARA TNWA KFTAT ASLGVIHKGH EKEALQLMAT YLPKDTSPGS AYQEGGGLYA LGLIHANHGG DIIDYLLNQL KNASNDIVRH GGSLG LGLA AMGTARQDVY DLLKTNLYQD DAVTGEAAGL ALGLVMLGSK NAQAIEDMVG YAQETQHEKI LRGLAVGIAL VMYGRM EEA DALIESLCRD KDPILRRSGM YTVAMAYCGS GNNKAIRRLL HVAVSDVNDD VRRAAVESLG FILFRTPEQC PSVVSLL SE SYNPHVRYGA AMALGICCAG TGNKEAINLL EPMTNDPVNY VRQGALIASA LIMIQQTEIT CPKVNQFRQL YSKVINDK H DDVMAKFGAI LAQGILDAGG HNVTISLQSR TGHTHMPSVV GVLVFTQFWF WFPLSHFLSL AYTPTCVIGL NKDLKMPKV QYKSNCKPST FAYPAPLEVP KEKEKEKVST AVLSITAKAK KKEKEKEKKE EEKMEVDEAE KKEEKEKKKE PEPNFQLLDN PARVMPAQL KVLTMPETCR YQPFKPLSIG GIIILKDTSE DIEELVEPVA AHGPKI

UniProtKB: 26S proteasome non-ATPase regulatory subunit 1

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Macromolecule #8: 26S proteasome non-ATPase regulatory subunit 3

MacromoleculeName: 26S proteasome non-ATPase regulatory subunit 3 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.703727 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PPGGGEQEPP PPPAPQDVEM KEEAATGGGS TGEADGKTAA AAAEHSQREL DTVTLEDIKE HVKQLEKAVS GKEPRFVLRA LRMLPSTSR RLNHYVLYKA VQGFFTSNNA TRDFLLPFLE EPMDTEADLQ FRPRTGKAAS TPLLPEVEAY LQLLVVIFMM N SKRYKEAQ ...String:
PPGGGEQEPP PPPAPQDVEM KEEAATGGGS TGEADGKTAA AAAEHSQREL DTVTLEDIKE HVKQLEKAVS GKEPRFVLRA LRMLPSTSR RLNHYVLYKA VQGFFTSNNA TRDFLLPFLE EPMDTEADLQ FRPRTGKAAS TPLLPEVEAY LQLLVVIFMM N SKRYKEAQ KISDDLMQKI STQNRRALDL VAAKCYYYHA RVYEFLDKLD VVRSFLHARL RTATLRHDAD GQATLLNLLL RN YLHYSLY DQAEKLVSKS VFPEQANNNE WARYLYYTGR IKAIQLEYSE ARRTMTNALR KAPQHTAVGF KQTVHKLLIV VEL LLGEIP DRLQFRQPSL KRSLMPYFLL TQAVRTGNLA KFNQVLDQFG EKFQADGTYT LIIRLRHNVI KTGVRMISLS YSRI SLADI AQKLQLDSPE DAEFIVAKAI RDGVIEASIN HEKGYVQSKE MIDIYSTREP QLAFHQRISF CLDIHNMSVK AMRFP PKSY NKDL

UniProtKB: 26S proteasome non-ATPase regulatory subunit 3

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Macromolecule #9: 26S proteasome non-ATPase regulatory subunit 12

MacromoleculeName: 26S proteasome non-ATPase regulatory subunit 12 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 52.979359 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MADGGSERAD GRIVKMEVDY SATVDQRLPE CAKLAKEGRL QEVIETLLSL EKQTRTASDM VSTSRILVAV VKMCYEAKEW DLLNENIML LSKRRSQLKQ AVAKMVQQCC TYVEEITDLP IKLRLIDTLR MVTEGKIYVE IERARLTKTL ATIKEQNGDV K EAASILQE ...String:
MADGGSERAD GRIVKMEVDY SATVDQRLPE CAKLAKEGRL QEVIETLLSL EKQTRTASDM VSTSRILVAV VKMCYEAKEW DLLNENIML LSKRRSQLKQ AVAKMVQQCC TYVEEITDLP IKLRLIDTLR MVTEGKIYVE IERARLTKTL ATIKEQNGDV K EAASILQE LQVETYGSME KKERVEFILE QMRLCLAVKD YIRTQIISKK INTKFFQEEN TEKLKLKYYN LMIQLDQHEG SY LSICKHY RAIYDTPCIQ AESEKWQQAL KSVVLYVILA PFDNEQSDLV HRISGDKKLE EIPKYKDLLK LFTTMELMRW STL VEDYGM ELRKGSLESP ATDVFGSTEE GEKRWKDLKN RVVEHNIRIM AKYYTRITMK RMAQLLDLSV DESEAFLSNL VVNK TIFAK VDRLAGIINF QRPKDPNNLL NDWSQKLNSL MSLVNKTTHL IAKEEMIHNL Q

UniProtKB: 26S proteasome non-ATPase regulatory subunit 12

+
Macromolecule #10: 26S proteasome non-ATPase regulatory subunit 11

MacromoleculeName: 26S proteasome non-ATPase regulatory subunit 11 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.427055 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: NDEEAVQVKE QSILELGSLL AKTGQAAELG GLLKYVRPFL NSISKAKAAR LVRSLLDLFL DMEAATGQEV ELCLECIEWA KSEKRTFLR QALEARLVSL YFDTKRYQEA LHLGSQLLRE LKKMDDKALL VEVQLLESKT YHALSNLPKA RAALTSARTT A NAIYCPPK ...String:
NDEEAVQVKE QSILELGSLL AKTGQAAELG GLLKYVRPFL NSISKAKAAR LVRSLLDLFL DMEAATGQEV ELCLECIEWA KSEKRTFLR QALEARLVSL YFDTKRYQEA LHLGSQLLRE LKKMDDKALL VEVQLLESKT YHALSNLPKA RAALTSARTT A NAIYCPPK LQATLDMQSG IIHAAEEKDW KTAYSYFYEA FEGYDSIDSP KAITSLKYML LCKIMLNTPE DVQALVSGKL AL RYAGRQT EALKCVAQAS KNRSLADFEK ALTDYRAELR DDPIISTHLA KLYDNLLEQN LIRVIEPFSR VQIEHISSLI KLS KADVER KLSQMILDKK FHGILDQGEG VLIIFDEPPV DKTYEAALET IQNMSKVVDS LYNKAKKLT

UniProtKB: 26S proteasome non-ATPase regulatory subunit 11

+
Macromolecule #11: 26S proteasome non-ATPase regulatory subunit 6

MacromoleculeName: 26S proteasome non-ATPase regulatory subunit 6 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.336906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: PKNPDLRIAQ LRFLLSLPEH RGDAAVRDEL MAAVRDNNMA PYYEALCKSL DWQIDVDLLN KMKKANEDEL KRLDEELEDA EKNLGESEI RDAMMAKAEY LCRIGDKEGA LTAFRKTYDK TVALGHRLDI VFYLLRIGLF YMDNDLITRN TEKAKSLIEE G GDWDRRNR ...String:
PKNPDLRIAQ LRFLLSLPEH RGDAAVRDEL MAAVRDNNMA PYYEALCKSL DWQIDVDLLN KMKKANEDEL KRLDEELEDA EKNLGESEI RDAMMAKAEY LCRIGDKEGA LTAFRKTYDK TVALGHRLDI VFYLLRIGLF YMDNDLITRN TEKAKSLIEE G GDWDRRNR LKVYQGLYCV AIRDFKQAAE LFLDTVSTFT SYELMDYKTF VTYTVYVSMI ALERPDLREK VIKGAEILEV LH SLPAVRQ YLFSLYECRY SVFFQSLAVV EQEMKKDWLF APHYRYYVRE MRIHAYSQLL ESYRSLTLGY MAEAFGVGVE FID QELSRF IAAGRLHCKI DKVNEIVETN RPDSKNWQYQ ETIKKGDLLL NRVQKLSRVI NM

UniProtKB: 26S proteasome non-ATPase regulatory subunit 6

+
Macromolecule #12: 26S proteasome non-ATPase regulatory subunit 7

MacromoleculeName: 26S proteasome non-ATPase regulatory subunit 7 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.382094 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AVQKVVVHPL VLLSVVDHFN RIGKVGNQKR VVGVLLGSWQ KKVLDVSNSF AVPFDEDDKD DSVWFLDHDY LENMYGMFKK VNARERIVG WYHTGPKLHK NDIAINELMK RYCPNSVLVI IDVKPKDLGL PTEAYISVEE VHDDGTPTSK TFEHVTSEIG A EEAEEVGV ...String:
AVQKVVVHPL VLLSVVDHFN RIGKVGNQKR VVGVLLGSWQ KKVLDVSNSF AVPFDEDDKD DSVWFLDHDY LENMYGMFKK VNARERIVG WYHTGPKLHK NDIAINELMK RYCPNSVLVI IDVKPKDLGL PTEAYISVEE VHDDGTPTSK TFEHVTSEIG A EEAEEVGV EHLLRDIKDT TVGTLSQRIT NQVHGLKGLN SKLLDIRSYL EKVATGKLPI NHQIIYQLQD VFNLLPDVSL QE FVKAFYL KTNDQMVVVY LASLIRSVVA LHNLINNKIA NRDAEKKEG

UniProtKB: 26S proteasome non-ATPase regulatory subunit 7

+
Macromolecule #13: 26S proteasome non-ATPase regulatory subunit 13

MacromoleculeName: 26S proteasome non-ATPase regulatory subunit 13 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.734988 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DVPGFLQQSQ NSGPGQPAVW HRLEELYTKK LWHQLTLQVL DFVQDPCFAQ GDGLIKLYEN FISEFEHRVN PLSLVEIILH VVRQMTDPN VALTFLEKTR EKVKSSDEAV ILCKTAIGAL KLNIGDLQVT KETIEDVEEM LNNLPGVTSV HSRFYDLSSK Y YQTIGNHA ...String:
DVPGFLQQSQ NSGPGQPAVW HRLEELYTKK LWHQLTLQVL DFVQDPCFAQ GDGLIKLYEN FISEFEHRVN PLSLVEIILH VVRQMTDPN VALTFLEKTR EKVKSSDEAV ILCKTAIGAL KLNIGDLQVT KETIEDVEEM LNNLPGVTSV HSRFYDLSSK Y YQTIGNHA SYYKDALRFL GCVDIKDLPV SEQQERAFTL GLAGLLGEGV FNFGELLMHP VLESLRNTDR QWLIDTLYAF NS GNVERFQ TLKTAWGQQP DLAANEAQLL RKIQLLCLME MTFTRPANHR QLTFEEIAKS AKITVNEVEL LVMKALSVGL VKG SIDEVD KRVHMTWVQP RVLDLQQIKG MKDRLEFWCT DVKSMEMLVE HQAHDILT

UniProtKB: 26S proteasome non-ATPase regulatory subunit 13

+
Macromolecule #14: 26S proteasome non-ATPase regulatory subunit 4

MacromoleculeName: 26S proteasome non-ATPase regulatory subunit 4 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.866023 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MVLESTMVCV DNSEYMRNGD FLPTRLQAQQ DAVNIVCHSK TRSNPENNVG LITLANDCEV LTTLTPDTGR ILSKLHTVQP KGKITFCTG IRVAHLALKH RQGKNHKMRI IAFVGSPVED NEKDLVKLAK RLKKEKVNVD IINFGEEEVN TEKLTAFVNT L NGKDGTGS HLVTVPPGPS LADALISSPI LAG

UniProtKB: 26S proteasome non-ATPase regulatory subunit 4

+
Macromolecule #15: 26S proteasome non-ATPase regulatory subunit 14

MacromoleculeName: 26S proteasome non-ATPase regulatory subunit 14 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 32.329355 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: AVDTAEQVYI SSLALLKMLK HGRAGVPMEV MGLMLGEFVD DYTVRVIDVF AMPQSGTGVS VEAVDPVFQA KMLDMLKQTG RPEMVVGWY HSHPGFGCWL SGVDINTQQS FEALSERAVA VVVDPIQSVK GKVVIDAFRL INANMMVLGH EPRQTTSNLG H LNKPSIQA ...String:
AVDTAEQVYI SSLALLKMLK HGRAGVPMEV MGLMLGEFVD DYTVRVIDVF AMPQSGTGVS VEAVDPVFQA KMLDMLKQTG RPEMVVGWY HSHPGFGCWL SGVDINTQQS FEALSERAVA VVVDPIQSVK GKVVIDAFRL INANMMVLGH EPRQTTSNLG H LNKPSIQA LIHGLNRHYY SITINYRKNE LEQKMLLNLH KKSWMEGLTL QDYSEHCKHN ESVVKEMLEL AKNYNKAVEE ED KMTPEQL AIKNVGKQDP KRHLEEHVDV LMTSNIVQCL AAMLDTVVFK

UniProtKB: 26S proteasome non-ATPase regulatory subunit 14

+
Macromolecule #16: 26S proteasome non-ATPase regulatory subunit 8

MacromoleculeName: 26S proteasome non-ATPase regulatory subunit 8 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 30.039699 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MYEQLKGEWN RKSPNLSKCG EELGRLKLVL LELNFLPTTG TKLTKQQLIL ARDILEIGAQ WSILRKDIPS FERYMAQLKC YYFDYKEQL PESAYMHQLL GLNLLFLLSQ NRVAEFHTEL ERLPAKDIQT NVYIKHPVSL EQYLMEGSYN KVFLAKGNIP A ESYTFFID ...String:
MYEQLKGEWN RKSPNLSKCG EELGRLKLVL LELNFLPTTG TKLTKQQLIL ARDILEIGAQ WSILRKDIPS FERYMAQLKC YYFDYKEQL PESAYMHQLL GLNLLFLLSQ NRVAEFHTEL ERLPAKDIQT NVYIKHPVSL EQYLMEGSYN KVFLAKGNIP A ESYTFFID ILLDTIRDEI AGCIEKAYEK ILFTEATRIL FFNTPKKMTD YAKKRGWVLG PNNYYSFASQ QQKPEDTTIP ST ELAKQVI EYARQLEMIV

UniProtKB: 26S proteasome non-ATPase regulatory subunit 8

+
Macromolecule #17: 26S proteasome complex subunit SEM1

MacromoleculeName: 26S proteasome complex subunit SEM1 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 4.020178 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VWEDNWDDDN VEDDFSNQLR AELEKHGYKM ETS

UniProtKB: 26S proteasome complex subunit SEM1

+
Macromolecule #18: 26S proteasome non-ATPase regulatory subunit 2

MacromoleculeName: 26S proteasome non-ATPase regulatory subunit 2 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 86.704523 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: LYRPALEELR RQIRSSTTSM TSVPKPLKFL RPHYGKLKEI YENMAPGENK RFAADIISVL AMTMSGEREC LKYRLVGSQE ELASWGHEY VRHLAGEVAK EWQELDDAEK VQREPLLTLV KEIVPYNMAH NAEHEACDLL MEIEQVDMLE KDIDENAYAK V CLYLTSCV ...String:
LYRPALEELR RQIRSSTTSM TSVPKPLKFL RPHYGKLKEI YENMAPGENK RFAADIISVL AMTMSGEREC LKYRLVGSQE ELASWGHEY VRHLAGEVAK EWQELDDAEK VQREPLLTLV KEIVPYNMAH NAEHEACDLL MEIEQVDMLE KDIDENAYAK V CLYLTSCV NYVPEPENSA LLRCALGVFR KFSRFPEALR LALMLNDMEL VEDIFTSCKD VVVQKQMAFM LGRHGVFLEL SE DVEEYED LTEIMSNVQL NSNFLALARE LDIMEPKVPD DIYKTHLENN RFGGSGSQVD SARMNLASSF VNGFVNAAFG QDK LLTDDG NKWLYKNKDH GMLSAAASLG MILLWDVDGG LTQIDKYLYS SEDYIKSGAL LACGIVNSGV RNECDPALAL LSDY VLHNS NTMRLGSIFG LGLAYAGSNR EDVLTLLLPV MGDSKSSMEV AGVTALACGM IAVGSCNGDV TSTILQTIME KSETE LKDT YARWLPLGLG LNHLGKGEAI EAILAALEVV SEPFRSFANT LVDVCAYAGS GNVLKVQQLL HICSEHFDSK EKEEDK DKK EKKDKDKKEA PADMGAHQGV AVLGIALIAM GEEIGAEMAL RTFGHLLRYG EPTLRRAVPL ALALISVSNP RLNILDT LS KFSHDADPEV SYNSIFAMGM VGSGTNNARL AAMLRQLAQY HAKDPNNLFM VRLAQGLTHL GKGTLTLCPY HSDRQLMS Q VAVAGLLTVL VSFLDVRNII LGKSHYVLYG LVAAMQPRML VTFDEELRPL PVSVRVGQAV DVV

UniProtKB: 26S proteasome non-ATPase regulatory subunit 2

+
Macromolecule #19: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 19 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: PROJECTION MATCHING
Final reconstructionResolution.type: BY AUTHOR / Resolution: 8.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21885

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