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- EMDB-9221: Cryo-EM structures and dynamics of substrate-engaged human 26S pr... -

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Basic information

Entry
Database: EMDB / ID: EMD-9221
TitleCryo-EM structures and dynamics of substrate-engaged human 26S proteasome
Map data
SampleProteasome
  • (26S proteasome non-ATPase regulatory subunit ...) x 11
  • 26S proteasome complex subunit SEM1Proteasome
  • (26S proteasome regulatory subunit ...) x 5
  • Rpt2, NP_002793.2 (26SHA chain B)
  • substrate
  • (Proteasome subunit alpha type- ...) x 8
  • (Proteasome subunit beta type- ...) x 7
  • (ligand) x 4
Function / homology
Function and homology information


purine ribonucleoside triphosphate binding / modulation by host of viral transcription / thyrotropin-releasing hormone receptor binding / positive regulation of inclusion body assembly / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / meiosis I / nuclear proteasome complex / proteasome regulatory particle / regulation of endopeptidase activity ...purine ribonucleoside triphosphate binding / modulation by host of viral transcription / thyrotropin-releasing hormone receptor binding / positive regulation of inclusion body assembly / Hydrolases; Acting on peptide bonds (peptidases); Omega peptidases / proteasome accessory complex / meiosis I / nuclear proteasome complex / proteasome regulatory particle / regulation of endopeptidase activity / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / Lys63-specific deubiquitinase activity / cytosolic proteasome complex / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / negative regulation of programmed cell death / myofibril / proteasome binding / regulation of protein catabolic process / SCF-dependent proteasomal ubiquitin-dependent protein catabolic process / polyubiquitin modification-dependent protein binding / negative regulation of G2/M transition of mitotic cell cycle / proteasome storage granule / NIK/NF-kappaB signaling / Wnt signaling pathway, planar cell polarity pathway / proteasomal ubiquitin-independent protein catabolic process / proteasome complex / endopeptidase activator activity / proteasome core complex / regulation of hematopoietic stem cell differentiation / isopeptidase activity / proteasome core complex, beta-subunit complex / proteasome endopeptidase complex / NF-kappaB binding / regulation of mitotic cell cycle phase transition / stem cell differentiation / proteasome assembly / proteasome core complex, alpha-subunit complex / regulation of cellular amino acid metabolic process / threonine-type endopeptidase activity / ciliary basal body / polysome / ubiquitin-dependent ERAD pathway / sarcomere / inclusion body / mRNA export from nucleus / response to organonitrogen compound / proteolysis involved in cellular protein catabolic process / regulation of proteasomal protein catabolic process / enzyme regulator activity / TBP-class protein binding / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Regulation of activated PAK-2p34 by proteasome mediated degradation / osteoblast differentiation / CDT1 association with the CDC6:ORC:origin complex / Degradation of DVL / pre-replicative complex assembly / 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 / positive regulation of RNA polymerase II transcription preinitiation complex assembly / Hh mutants are degraded by ERAD / Ubiquitin-dependent degradation of Cyclin D / Vif-mediated degradation of APOBEC3G / Defective CFTR causes cystic fibrosis / Hedgehog ligand biogenesis / AUF1 (hnRNP D0) binds and destabilizes mRNA / Vpu mediated degradation of CD4 / Degradation of GLI1 by the proteasome / TNFR2 non-canonical NF-kB pathway / P-body / Negative regulation of NOTCH4 signaling / Dectin-1 mediated noncanonical NF-kB signaling / Hedgehog 'on' state / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / ABC-family proteins mediated transport / modulation of chemical synaptic transmission / cytoplasmic ribonucleoprotein granule / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Activation of NF-kappaB in B cells / GLI3 is processed to GLI3R by the proteasome / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Degradation of GLI2 by the proteasome / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Degradation of AXIN / negative regulation of neuron death / G2/M Checkpoints / tumor necrosis factor-mediated signaling pathway / Autodegradation of the E3 ubiquitin ligase COP1 / Metalloprotease DUBs / Degradation of beta-catenin by the destruction complex / response to virus / Regulation of RUNX3 expression and activity / double-strand break repair via homologous recombination / lipopolysaccharide binding / Regulation of expression of SLITs and ROBOs
Similarity search - Function
26S Proteasome non-ATPase regulatory subunit 11 / 26S Proteasome regulatory subunit 4 / 26S proteasome regulatory subunit 10B / Proteasome subunit beta 6 / Proteasome subunit alpha 7 / Ubiquitin interaction motif / Proteasome regulatory subunit C-terminal / 26S proteasome non-ATPase regulatory subunit Rpn12 / 26S proteasome regulatory subunit, C-terminal / 26S Proteasome non-ATPase regulatory subunit 6 ...26S Proteasome non-ATPase regulatory subunit 11 / 26S Proteasome regulatory subunit 4 / 26S proteasome regulatory subunit 10B / Proteasome subunit beta 6 / Proteasome subunit alpha 7 / Ubiquitin interaction motif / Proteasome regulatory subunit C-terminal / 26S proteasome non-ATPase regulatory subunit Rpn12 / 26S proteasome regulatory subunit, C-terminal / 26S Proteasome non-ATPase regulatory subunit 6 / 26S proteasome non-ATPase regulatory subunit 3 / DSS1/SEM1 / 26S proteasome regulatory subunit RPN5, C-terminal domain / DSS1_SEM1 / 26S proteasome regulatory subunit RPN5 C-terminal domain / 26S Proteasome non-ATPase regulatory subunit 12 / DSS1/SEM1 family / 26S proteasome regulatory subunit RPN6 N-terminal domain / 26S proteasome regulatory subunit Rpn6, N-terminal / 26S proteasome subunit RPN6 C-terminal helix domain / 6S proteasome subunit Rpn6, C-terminal helix domain / 26S Proteasome non-ATPase regulatory subunit 1 / 26S proteasome regulatory subunit RPN2, C-terminal / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S Proteasome non-ATPase regulatory subunit 13 / 26S proteasome regulatory subunit RPN2 C-terminal domain / 26S Proteasome non-ATPase regulatory subunit 14 / 26S Proteasome non-ATPase regulatory subunit 7/8 / RPN1 N-terminal domain / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / RPN1, N-terminal / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S Proteasome regulatory subunit 6A / 26S proteasome subunit RPN7 / 26S Proteasome regulatory subunit 7 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / Proteasome/cyclosome repeat / 26S Proteasome regulatory subunit 6B / von Willebrand factor type A domain / Proteasome/cyclosome repeat / Ubiquitin-interacting motif. / CSN8/PSMD8/EIF3K family / CSN8/PSMD8/EIF3K / 26S proteasome regulatory subunit P45-like / Rpn11/EIF3F, C-terminal / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / Maintenance of mitochondrial structure and function / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / PCI domain profile. / Proteasome component (PCI) domain / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / von Willebrand factor (vWF) type A domain / Proteasome subunit beta 5 / Proteasome beta subunits C terminal / Proteasome beta subunit, C-terminal / Proteasome subunit beta 7 / Proteasome subunit beta 4 / Proteasome subunit beta 1 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / VWFA domain profile. / Proteasome subunit alpha4 / Proteasome subunit alpha 1 / Proteasome subunit alpha2 / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome subunit alpha 3 / von Willebrand factor, type A / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / AAA+ lid domain / AAA ATPase, AAA+ lid domain / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / 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 / MPN domain / MPN domain profile. / Proteasome alpha-type subunit profile. / Proteasome alpha-type subunit / Proteasome B-type subunit / Proteasome beta-type subunit profile. / Proteasome subunit / AAA-protein family signature. / ATPase, AAA-type, conserved site / Proteasome, subunit alpha/beta / von Willebrand factor A-like domain superfamily / Nucleophile aminohydrolases, N-terminal / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Armadillo-like helical
Similarity search - Domain/homology
26S proteasome non-ATPase regulatory subunit 8 / Proteasome subunit beta type-3 / Proteasome subunit beta type-2 / 26S proteasome non-ATPase regulatory subunit 7 / 26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome complex subunit SEM1 / 26S proteasome regulatory subunit 4 / Proteasome subunit alpha type-6 / 26S proteasome regulatory subunit 8 / 26S proteasome regulatory subunit 10B ...26S proteasome non-ATPase regulatory subunit 8 / Proteasome subunit beta type-3 / Proteasome subunit beta type-2 / 26S proteasome non-ATPase regulatory subunit 7 / 26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome complex subunit SEM1 / 26S proteasome regulatory subunit 4 / Proteasome subunit alpha type-6 / 26S proteasome regulatory subunit 8 / 26S proteasome regulatory subunit 10B / 26S proteasome non-ATPase regulatory subunit 2 / 26S proteasome non-ATPase regulatory subunit 6 / Proteasome subunit beta type-7 / 26S proteasome non-ATPase regulatory subunit 1 / 26S proteasome regulatory subunit 6B / Proteasome subunit beta type-5 / 26S proteasome regulatory subunit 7 / 26S proteasome regulatory subunit 6A / 26S proteasome regulatory subunit 10B / 26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome non-ATPase regulatory subunit 12 / 26S proteasome non-ATPase regulatory subunit 14 / Proteasome subunit alpha type-7 / 26S proteasome non-ATPase regulatory subunit 3 / Proteasome subunit beta type-1 / Proteasome subunit beta type-6 / 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 / 26S proteasome non-ATPase regulatory subunit 13
Similarity search - Component
Biological speciesHomo sapiens (human) / Saccharomyces cerevisiae RM11-1a (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsMao YD
Funding support China, United States, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)11774012 China
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)GM43601 United States
National Natural Science Foundation of China (NSFC)91530321 China
CitationJournal: Nature / Year: 2019
Title: Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome.
Authors: Yuanchen Dong / Shuwen Zhang / Zhaolong Wu / Xuemei Li / Wei Li Wang / Yanan Zhu / Svetla Stoilova-McPhie / Ying Lu / Daniel Finley / Youdong Mao /
Abstract: The proteasome is an ATP-dependent, 2.5-megadalton molecular machine that is responsible for selective protein degradation in eukaryotic cells. Here we present cryo-electron microscopy structures of ...The proteasome is an ATP-dependent, 2.5-megadalton molecular machine that is responsible for selective protein degradation in eukaryotic cells. Here we present cryo-electron microscopy structures of the substrate-engaged human proteasome in seven conformational states at 2.8-3.6 Å resolution, captured during breakdown of a polyubiquitylated protein. These structures illuminate a spatiotemporal continuum of dynamic substrate-proteasome interactions from ubiquitin recognition to substrate translocation, during which ATP hydrolysis sequentially navigates through all six ATPases. There are three principal modes of coordinated hydrolysis, featuring hydrolytic events in two oppositely positioned ATPases, in two adjacent ATPases and in one ATPase at a time. These hydrolytic modes regulate deubiquitylation, initiation of translocation and processive unfolding of substrates, respectively. Hydrolysis of ATP powers a hinge-like motion in each ATPase that regulates its substrate interaction. Synchronization of ATP binding, ADP release and ATP hydrolysis in three adjacent ATPases drives rigid-body rotations of substrate-bound ATPases that are propagated unidirectionally in the ATPase ring and unfold the substrate.
History
DepositionOct 16, 2018-
Header (metadata) releaseNov 21, 2018-
Map releaseNov 21, 2018-
UpdateDec 18, 2019-
Current statusDec 18, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.006
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6msj
  • Surface level: 0.006
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9221.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.)
0.69 Å/pix.
x 600 pix.
= 411. Å
0.69 Å/pix.
x 600 pix.
= 411. Å
0.69 Å/pix.
x 600 pix.
= 411. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.685 Å
Density
Contour LevelBy AUTHOR: 0.006 / Movie #1: 0.006
Minimum - Maximum-0.005119373 - 0.017518379
Average (Standard dev.)0.0000302961 (±0.0010034199)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 411.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6850.6850.685
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z411.000411.000411.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.0050.0180.000

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Supplemental data

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Additional map: The complete map of state ED1 of substrate-engaged...

Fileemd_9221_additional_1.map
AnnotationThe complete map of state ED1 of substrate-engaged human proteasome, low pass-filtered to 3 Angstrom with amplitude correction with a B-factor of -35
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Additional map: Unfiltered, uncorrected raw ED1 map of complete holoenzyme

Fileemd_9221_additional_2.map
AnnotationUnfiltered, uncorrected raw ED1 map of complete holoenzyme
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Sample components

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Entire Proteasome

EntireName: Proteasome / Number of components: 39

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Component #1: protein, Proteasome

ProteinName: Proteasome / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, 26S proteasome non-ATPase regulatory subunit 1

ProteinName: 26S proteasome non-ATPase regulatory subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 105.958234 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, 26S proteasome non-ATPase regulatory subunit 3

ProteinName: 26S proteasome non-ATPase regulatory subunit 3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 60.935297 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, 26S proteasome non-ATPase regulatory subunit 12

ProteinName: 26S proteasome non-ATPase regulatory subunit 12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.979359 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, 26S proteasome non-ATPase regulatory subunit 11

ProteinName: 26S proteasome non-ATPase regulatory subunit 11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 47.526688 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: protein, 26S proteasome non-ATPase regulatory subunit 6

ProteinName: 26S proteasome non-ATPase regulatory subunit 6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.592285 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #7: protein, 26S proteasome non-ATPase regulatory subunit 7

ProteinName: 26S proteasome non-ATPase regulatory subunit 7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.086441 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #8: protein, 26S proteasome non-ATPase regulatory subunit 13

ProteinName: 26S proteasome non-ATPase regulatory subunit 13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 42.995359 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #9: protein, 26S proteasome non-ATPase regulatory subunit 4

ProteinName: 26S proteasome non-ATPase regulatory subunit 4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.78159 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #10: protein, 26S proteasome non-ATPase regulatory subunit 14

ProteinName: 26S proteasome non-ATPase regulatory subunit 14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.488824 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #11: protein, 26S proteasome non-ATPase regulatory subunit 8

ProteinName: 26S proteasome non-ATPase regulatory subunit 8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.536676 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #12: protein, 26S proteasome complex subunit SEM1

ProteinName: 26S proteasome complex subunit SEM1Proteasome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.284611 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #13: protein, 26S proteasome non-ATPase regulatory subunit 2

ProteinName: 26S proteasome non-ATPase regulatory subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 98.425414 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #14: protein, 26S proteasome regulatory subunit 7

ProteinName: 26S proteasome regulatory subunit 7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.700805 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #15: protein, Rpt2, NP_002793.2 (26SHA chain B)

ProteinName: Rpt2, NP_002793.2 (26SHA chain B) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.260504 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #16: protein, 26S proteasome regulatory subunit 8

ProteinName: 26S proteasome regulatory subunit 8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 44.852121 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #17: protein, 26S proteasome regulatory subunit 6B

ProteinName: 26S proteasome regulatory subunit 6B / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 47.426141 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #18: protein, 26S proteasome regulatory subunit 10B

ProteinName: 26S proteasome regulatory subunit 10B / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.867027 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #19: protein, 26S proteasome regulatory subunit 6A

ProteinName: 26S proteasome regulatory subunit 6A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.266457 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #20: protein, substrate

ProteinName: substrate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.08179 kDa
SourceSpecies: Saccharomyces cerevisiae RM11-1a (yeast)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #21: protein, Proteasome subunit alpha type-6

ProteinName: Proteasome subunit alpha type-6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.301262 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #22: protein, Proteasome subunit alpha type-2

ProteinName: Proteasome subunit alpha type-2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 25.796338 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #23: protein, Proteasome subunit alpha type-4

ProteinName: Proteasome subunit alpha type-4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 29.394648 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #24: protein, Proteasome subunit alpha type-7

ProteinName: Proteasome subunit alpha type-7 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 27.798695 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #25: protein, Proteasome subunit alpha type-5

ProteinName: Proteasome subunit alpha type-5 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 26.304779 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #26: protein, Proteasome subunit alpha type-1

ProteinName: Proteasome subunit alpha type-1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 30.150277 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #27: protein, Proteasome subunit alpha type-3

ProteinName: Proteasome subunit alpha type-3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 28.338057 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #28: protein, Proteasome subunit beta type-6

ProteinName: Proteasome subunit beta type-6 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 25.246455 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #29: protein, Proteasome subunit beta type-7

ProteinName: Proteasome subunit beta type-7 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 29.869223 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #30: protein, Proteasome subunit beta type-3

ProteinName: Proteasome subunit beta type-3PSMB3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 22.841701 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #31: protein, Proteasome subunit beta type-2

ProteinName: Proteasome subunit beta type-2PSMB2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 22.864277 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #32: protein, Proteasome subunit beta type-5

ProteinName: Proteasome subunit beta type-5PSMB5 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 28.379053 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #33: protein, Proteasome subunit beta type-1

ProteinName: Proteasome subunit beta type-1PSMB1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 26.391201 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #34: protein, Proteasome subunit beta type-4

ProteinName: Proteasome subunit beta type-4PSMB4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 29.099986 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #35: protein, Proteasome subunit alpha type-6

ProteinName: Proteasome subunit alpha type-6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.727658 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #36: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #37: ligand, ADENOSINE-5'-TRIPHOSPHATE

LigandName: ADENOSINE-5'-TRIPHOSPHATE / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.507181 kDa

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Component #38: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #39: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
Support filmunspecified
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 44 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 288915
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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