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- EMDB-9045: Yeast 26S proteasome bound to ubiquitinated substrate (4D motor state) -

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Basic information

Entry
Database: EMDB / ID: EMD-9045
TitleYeast 26S proteasome bound to ubiquitinated substrate (4D motor state)
Map data
SampleSubstrate-engaged 26S proteasome in the 4D state
  • Proteasome
  • substrate
  • (Proteasome subunit beta type- ...) x 8
  • (Proteasome subunit alpha type- ...) x 6
  • Probable proteasome subunit alpha type-7
  • (26S proteasome regulatory subunit ...) x 5
  • 26S proteasome subunit RPT4Proteasome
  • Ubiquitin carboxyl-terminal hydrolase RPN11
  • Model substrate polypeptide
  • Ubiquitin-60S ribosomal protein L40
  • (ligand) x 2
Function / homology
Function and homology information


proteasome storage granule assembly / peroxisome fission / proteasome regulatory particle assembly / nonfunctional rRNA decay / cellular protein-containing complex localization / proteasome-activating ATPase activity / nuclear proteasome complex / mitochondrial fission / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex ...proteasome storage granule assembly / peroxisome fission / proteasome regulatory particle assembly / nonfunctional rRNA decay / cellular protein-containing complex localization / proteasome-activating ATPase activity / nuclear proteasome complex / mitochondrial fission / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / Lys63-specific deubiquitinase activity / cytosolic proteasome complex / proteasome binding / ribosomal large subunit export from nucleus / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / peptide catabolic process / endopeptidase activator activity / proteasomal ubiquitin-independent protein catabolic process / proteasome storage granule / proteasome core complex / proteasome core complex, beta-subunit complex / thiol-dependent ubiquitin-specific protease activity / proteasome endopeptidase complex / proteasome core complex, alpha-subunit complex / ubiquitin-dependent ERAD pathway / proteasome assembly / threonine-type endopeptidase activity / ubiquitinyl hydrolase 1 / TBP-class protein binding / proteasomal protein catabolic process / positive regulation of transcription elongation from RNA polymerase II promoter / nucleotide-excision repair / metallopeptidase activity / positive regulation of RNA polymerase II transcriptional preinitiation complex assembly / modification-dependent protein catabolic process / cytoplasmic translation / positive regulation of protein catabolic process / protein tag / ribosome biogenesis / ribosomal large subunit assembly / cytosolic large ribosomal subunit / negative regulation of DNA-binding transcription factor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / positive regulation of DNA-binding transcription factor activity / ubiquitin-dependent protein catabolic process / structural constituent of ribosome / chromatin remodeling / endopeptidase activity / protein ubiquitination / ATPase activity / cell cycle / protein deubiquitination / mRNA binding / cell division / protein domain specific binding / endoplasmic reticulum membrane / ubiquitin protein ligase binding / mitochondrion / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Proteasome alpha-subunit, N-terminal domain / Ubiquitin conserved site / Proteasome beta 3 subunit / Proteasomal ATPase OB C-terminal domain / Ubiquitin-like domain superfamily / Nucleophile aminohydrolases, N-terminal / ATPase, AAA-type, conserved site / Rpn11/EIF3F, C-terminal / Proteasome beta subunit, C-terminal / Proteasome B-type subunit ...Proteasome alpha-subunit, N-terminal domain / Ubiquitin conserved site / Proteasome beta 3 subunit / Proteasomal ATPase OB C-terminal domain / Ubiquitin-like domain superfamily / Nucleophile aminohydrolases, N-terminal / ATPase, AAA-type, conserved site / Rpn11/EIF3F, C-terminal / Proteasome beta subunit, C-terminal / Proteasome B-type subunit / Proteasome alpha-type subunit / Ubiquitin domain / Proteasome subunit beta 4 / Proteasome subunit alpha6 / Proteasome beta-type subunit, conserved site / Cyclin-like / Cyclin, N-terminal / 26S proteasome regulatory subunit P45-like / Cyclin, C-terminal domain / Peptidase T1A, proteasome beta-subunit / JAB1/MPN/MOV34 metalloenzyme domain / Ubiquitin-like domain / Proteasome, subunit alpha/beta / Ribosomal protein L40e / AAA+ ATPase domain / Proteasome subunit alpha5 / P-loop containing nucleoside triphosphate hydrolase / ATPase, AAA-type, core / Proteasome subunit beta 7 / 26S proteasome regulatory subunit 10B / 26S Proteasome non-ATPase regulatory subunit 14 / Cyclin-like superfamily / 26S Proteasome regulatory subunit 4 / MPN domain / Proteasome subunit alpha 3 / Proteasome subunit beta 2 / 26S Proteasome regulatory subunit 7 / Proteasome subunit beta 1 / Proteasome subunit alpha 1 / Proteasome subunit beta Pre3 / Ribosomal protein L40e superfamily / Cyclin / AAA ATPase, AAA+ lid domain / Proteasome subunit alpha2 / 26S Proteasome regulatory subunit 6B
26S proteasome subunit RPT4 / Ubiquitin carboxyl-terminal hydrolase RPN11 / 26S proteasome regulatory subunit 4 homolog / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-6 / Proteasome subunit beta type-1 / 26S proteasome regulatory subunit 7 homolog / 26S proteasome regulatory subunit 6B homolog / 26S proteasome regulatory subunit 6A / Proteasome subunit alpha type-5 ...26S proteasome subunit RPT4 / Ubiquitin carboxyl-terminal hydrolase RPN11 / 26S proteasome regulatory subunit 4 homolog / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-6 / Proteasome subunit beta type-1 / 26S proteasome regulatory subunit 7 homolog / 26S proteasome regulatory subunit 6B homolog / 26S proteasome regulatory subunit 6A / Proteasome subunit alpha type-5 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 / Proteasome subunit beta type-3 / Proteasome subunit beta type-2 / Proteasome subunit beta type-6 / Proteasome subunit alpha type-2 / Proteasome subunit alpha type-3 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-1 / Probable proteasome subunit alpha type-7 / Ubiquitin-60S ribosomal protein L40 / G2/mitotic-specific cyclin-B / 26S proteasome regulatory subunit 8 homolog
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Homo sapiens (human) / Saccharomyces cerevisiae S288c (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.17 Å
Authorsde la Pena AH / Goodall EA / Gates SN / Lander GC / Martin A
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM094497 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)DP2-EB020402 United States
CitationJournal: Science / Year: 2018
Title: Substrate-engaged 26 proteasome structures reveal mechanisms for ATP-hydrolysis-driven translocation.
Authors: Andres H de la Peña / Ellen A Goodall / Stephanie N Gates / Gabriel C Lander / Andreas Martin /
Abstract: The 26 proteasome is the primary eukaryotic degradation machine and thus is critically involved in numerous cellular processes. The heterohexameric adenosine triphosphatase (ATPase) motor of the ...The 26 proteasome is the primary eukaryotic degradation machine and thus is critically involved in numerous cellular processes. The heterohexameric adenosine triphosphatase (ATPase) motor of the proteasome unfolds and translocates targeted protein substrates into the open gate of a proteolytic core while a proteasomal deubiquitinase concomitantly removes substrate-attached ubiquitin chains. However, the mechanisms by which ATP hydrolysis drives the conformational changes responsible for these processes have remained elusive. Here we present the cryo-electron microscopy structures of four distinct conformational states of the actively ATP-hydrolyzing, substrate-engaged 26 proteasome. These structures reveal how mechanical substrate translocation accelerates deubiquitination and how ATP-binding, -hydrolysis, and phosphate-release events are coordinated within the AAA+ (ATPases associated with diverse cellular activities) motor to induce conformational changes and propel the substrate through the central pore.
Validation ReportPDB-ID: 6ef3

SummaryFull reportAbout validation report
History
DepositionAug 15, 2018-
Header (metadata) releaseOct 17, 2018-
Map releaseOct 17, 2018-
UpdateJan 8, 2020-
Current statusJan 8, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6ef3
  • Surface level: 0.045
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6ef3
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9045.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 340 pix.
= 350.2 Å
1.03 Å/pix.
x 340 pix.
= 350.2 Å
1.03 Å/pix.
x 340 pix.
= 350.2 Å

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density
Contour LevelBy AUTHOR: 0.045 / Movie #1: 0.045
Minimum - Maximum0 - 0.22217602
Average (Standard dev.)0.001485774 (±0.008148518)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 350.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.031.031.03
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z350.200350.200350.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean0.0000.2220.001

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Supplemental data

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Additional map: Motor (sharpened)

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AnnotationMotor (sharpened)
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Sample components

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Entire Substrate-engaged 26S proteasome in the 4D state

EntireName: Substrate-engaged 26S proteasome in the 4D state
Details: Yeast 26S proteasome bound to ubiquitinated substrate in the presence of ATP
Number of components: 29

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Component #1: protein, Substrate-engaged 26S proteasome in the 4D state

ProteinName: Substrate-engaged 26S proteasome in the 4D state
Details: Yeast 26S proteasome bound to ubiquitinated substrate in the presence of ATP
Recombinant expression: No

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Component #2: protein, Proteasome

ProteinName: Proteasome / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae W303 (yeast)

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Component #3: protein, substrate

ProteinName: substrate / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21 (bacteria) / Strain: BL21

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Component #4: protein, Proteasome subunit beta type-1

ProteinName: Proteasome subunit beta type-1PSMB1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.573604 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae W303 (yeast)

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Component #5: protein, Proteasome subunit beta type-2

ProteinName: Proteasome subunit beta type-2PSMB2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.299889 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae W303 (yeast)

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Component #6: protein, Proteasome subunit beta type-3

ProteinName: Proteasome subunit beta type-3PSMB3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.627842 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae W303 (yeast)

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Component #7: protein, Proteasome subunit beta type-4

ProteinName: Proteasome subunit beta type-4PSMB4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.545676 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae W303 (yeast)

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Component #8: protein, Proteasome subunit beta type-5

ProteinName: Proteasome subunit beta type-5PSMB5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.670539 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae W303 (yeast)

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Component #9: protein, Proteasome subunit beta type-6

ProteinName: Proteasome subunit beta type-6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.905076 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae W303 (yeast)

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Component #10: protein, Proteasome subunit beta type-7

ProteinName: Proteasome subunit beta type-7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.471289 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae W303 (yeast)

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Component #11: protein, Proteasome subunit alpha type-1

ProteinName: Proteasome subunit alpha type-1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.03383 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae W303 (yeast)

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Component #12: protein, Proteasome subunit alpha type-2

ProteinName: Proteasome subunit alpha type-2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.191828 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae W303 (yeast)

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Component #13: protein, Proteasome subunit alpha type-3

ProteinName: Proteasome subunit alpha type-3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.74823 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae W303 (yeast)

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Component #14: protein, Proteasome subunit alpha type-4

ProteinName: Proteasome subunit alpha type-4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.478111 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae W303 (yeast)

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Component #15: protein, Proteasome subunit alpha type-5

ProteinName: Proteasome subunit alpha type-5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.649086 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae W303 (yeast)

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Component #16: protein, Proteasome subunit alpha type-6

ProteinName: Proteasome subunit alpha type-6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.634 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae W303 (yeast)

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Component #17: protein, Probable proteasome subunit alpha type-7

ProteinName: Probable proteasome subunit alpha type-7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.575068 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae W303 (yeast)

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Component #18: protein, 26S proteasome regulatory subunit 7 homolog

ProteinName: 26S proteasome regulatory subunit 7 homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.054891 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae W303 (yeast)

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Component #19: protein, 26S proteasome regulatory subunit 4 homolog

ProteinName: 26S proteasome regulatory subunit 4 homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.89816 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae W303 (yeast)

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Component #20: protein, 26S proteasome regulatory subunit 8 homolog

ProteinName: 26S proteasome regulatory subunit 8 homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.342742 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae W303 (yeast)

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Component #21: protein, 26S proteasome regulatory subunit 6B homolog

ProteinName: 26S proteasome regulatory subunit 6B homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 47.953676 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae W303 (yeast)

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Component #22: protein, 26S proteasome subunit RPT4

ProteinName: 26S proteasome subunit RPT4Proteasome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.480137 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae W303 (yeast)

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Component #23: protein, 26S proteasome regulatory subunit 6A

ProteinName: 26S proteasome regulatory subunit 6A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.315727 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae W303 (yeast)

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

ProteinName: Proteasome subunit beta type-7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 1.789039 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)
Source (engineered)Expression System: Saccharomyces cerevisiae W303 (yeast)

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Component #25: protein, Ubiquitin carboxyl-terminal hydrolase RPN11

ProteinName: Ubiquitin carboxyl-terminal hydrolase RPN11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.442281 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Saccharomyces cerevisiae W303 (yeast)

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Component #26: protein, Model substrate polypeptide

ProteinName: Model substrate polypeptide / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 4.068414 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli BL21 (bacteria)

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Component #27: protein, Ubiquitin-60S ribosomal protein L40

ProteinName: Ubiquitin-60S ribosomal protein L40 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.583077 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
Source (engineered)Expression System: Escherichia coli B (bacteria)

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Component #28: ligand, ADENOSINE-5'-TRIPHOSPHATE

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

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Component #29: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 2 / 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 solutionSpecimen conc.: 25 mg/mL / pH: 7.6
Support filmunspecified
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 90 %
Details: specimens were manually blotted with Whatman #1 filter paper.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Details: images were acquired in nanoprobe mode
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 29000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: -1000.0 - -2500.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 11656 / Sampling size: 5 µm

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 48335 / Details: Camera was operated in counting mode
3D reconstructionSoftware: RELION
CTF correction: CTF correction was performed by Relion during reconstruction
Resolution: 4.17 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Input PDB model: 5MPC
Output model

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  • 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.
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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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Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.:Changes in new EM Navigator and Yorodumi

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Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.:Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

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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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