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- EMDB-3535: 26S proteasome in presence of ATP (s2) -

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Basic information

Entry
Database: EMDB / ID: EMD-3535
Title26S proteasome in presence of ATP (s2)Proteasome
Map data
Sample26S proteasome of Saccharomyces cerevisiae in presence of ATP (s2)
  • (Proteasome subunit alpha type- ...) x 6
  • Probable proteasome subunit alpha type-7
  • (Proteasome subunit beta type- ...) x 7
  • (26S protease regulatory subunit ...) x 5
  • 26S protease subunit RPT4Proteasome endopeptidase complex
  • (ligand) x 3
Function / homology
Function and homology information


SAGA complex localization to transcription regulatory region / proteasome storage granule assembly / peroxisome fission / transcription export complex 2 / maintenance of DNA trinucleotide repeats / proteasome regulatory particle assembly / protein deneddylation / filamentous growth / nonfunctional rRNA decay / histone deubiquitination ...SAGA complex localization to transcription regulatory region / proteasome storage granule assembly / peroxisome fission / transcription export complex 2 / maintenance of DNA trinucleotide repeats / proteasome regulatory particle assembly / protein deneddylation / filamentous growth / nonfunctional rRNA decay / histone deubiquitination / K48-linked polyubiquitin modification-dependent protein binding / proteasome-activating ATPase activity / nuclear proteasome complex / proteasome regulatory particle / COP9 signalosome / mitochondrial fission / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / Lys63-specific deubiquitinase activity / cytosolic proteasome complex / cellular protein-containing complex localization / proteasome binding / proteasome core complex assembly / peptide catabolic process / nuclear outer membrane-endoplasmic reticulum membrane network / polyubiquitin modification-dependent protein binding / regulation of protein catabolic process / proteasome storage granule / endopeptidase activator activity / proteasome complex / proteasomal ubiquitin-independent protein catabolic process / proteasome core complex / isopeptidase activity / proteasome core complex, beta-subunit complex / proteasome endopeptidase complex / proteasome core complex, alpha-subunit complex / proteasome assembly / threonine-type endopeptidase activity / ubiquitin-dependent ERAD pathway / mRNA export from nucleus / TBP-class protein binding / enzyme regulator activity / proteasomal protein catabolic process / nucleotide-excision repair / ubiquitin binding / positive regulation of transcription elongation from RNA polymerase II promoter / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of protein catabolic process / double-strand break repair via homologous recombination / protein-macromolecule adaptor activity / metallopeptidase activity / regulation of cell cycle / ubiquitinyl hydrolase 1 / cysteine-type peptidase activity / negative regulation of DNA-binding transcription factor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / thiol-dependent deubiquitinase / positive regulation of DNA-binding transcription factor activity / ubiquitin-dependent protein catabolic process / chromatin remodeling / endopeptidase activity / protein deubiquitination / ATPase activity / mRNA binding / protein domain specific binding / endoplasmic reticulum membrane / ubiquitin protein ligase binding / structural molecule activity / endoplasmic reticulum / mitochondrion / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Proteasomal ubiquitin receptor Rpn13/ADRM1 / AAA+ ATPase domain / 26S proteasome regulatory subunit, C-terminal / Tetratricopeptide repeat-containing domain / Tetratricopeptide-like helical domain superfamily / Armadillo-like helical / DSS1/SEM1 / 26S proteasome non-ATPase regulatory subunit Rpn12 / 26S proteasome regulatory subunit P45-like / ATPase, AAA-type, conserved site ...Proteasomal ubiquitin receptor Rpn13/ADRM1 / AAA+ ATPase domain / 26S proteasome regulatory subunit, C-terminal / Tetratricopeptide repeat-containing domain / Tetratricopeptide-like helical domain superfamily / Armadillo-like helical / DSS1/SEM1 / 26S proteasome non-ATPase regulatory subunit Rpn12 / 26S proteasome regulatory subunit P45-like / ATPase, AAA-type, conserved site / ATPase, AAA-type, core / Ubiquitin interacting motif / von Willebrand factor, type A / Proteasome beta-type subunit, conserved site / Proteasome/cyclosome repeat / Proteasome, subunit alpha/beta / Proteasome component (PCI) domain / JAB1/MPN/MOV34 metalloenzyme domain / Proteasome alpha-subunit, N-terminal domain / Peptidase T1A, proteasome beta-subunit / 26S proteasome regulatory subunit 10B / 26S Proteasome non-ATPase regulatory subunit 1 / 26S Proteasome regulatory subunit 6B / 26S proteasome non-ATPase regulatory subunit 3 / Armadillo-type fold / Proteasome subunit beta 4 / 26S Proteasome non-ATPase regulatory subunit 12 / CSN8/PSMD8/EIF3K / 26S Proteasome regulatory subunit 4 / Proteasome subunit beta 7 / Proteasome subunit beta 2 / Proteasome subunit beta 1 / Proteasome subunit alpha 1 / Proteasome subunit alpha2 / Proteasome subunit alpha6 / 26S Proteasome non-ATPase regulatory subunit 7/8 / Proteasome subunit alpha5 / Proteasome beta 3 subunit / Proteasomal ATPase OB C-terminal domain / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / Nucleophile aminohydrolases, N-terminal / P-loop containing nucleoside triphosphate hydrolase / Proteasome subunit Rpn10 / Rpn11/EIF3F, C-terminal / Proteasome beta subunit, C-terminal / Proteasome B-type subunit / Proteasome alpha-type subunit / Tetratricopeptide repeat / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / 26S Proteasome non-ATPase regulatory subunit 6 / 26S Proteasome regulatory subunit 7 / Winged helix-like DNA-binding domain superfamily / 26S proteasome regulatory subunit RPN2, C-terminal / Winged helix DNA-binding domain superfamily / von Willebrand factor A-like domain superfamily / MPN domain / Proteasome subunit alpha 3 / Proteasome subunit beta Pre3 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / 26S Proteasome non-ATPase regulatory subunit 13 / Proteasomal ubiquitin receptor Rpn13/ADRM1 superfamily / 26S proteasome regulatory subunit Rpn6, N-terminal / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / AAA ATPase, AAA+ lid domain / 6S proteasome subunit Rpn6, C-terminal helix domain / 26S Proteasome non-ATPase regulatory subunit 14 / 26S proteasome regulatory subunit RPN5, C-terminal domain / RPN1, N-terminal / Rpn9, C-terminal helix
26S proteasome regulatory subunit 4 homolog / 26S proteasome regulatory subunit RPN1 / 26S proteasome regulatory subunit RPN10 / 26S proteasome regulatory subunit RPN3 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4 / 26S proteasome regulatory subunit RPN9 / Ubiquitin carboxyl-terminal hydrolase RPN11 / 26S proteasome subunit RPT4 / 26S proteasome regulatory subunit 8 homolog ...26S proteasome regulatory subunit 4 homolog / 26S proteasome regulatory subunit RPN1 / 26S proteasome regulatory subunit RPN10 / 26S proteasome regulatory subunit RPN3 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4 / 26S proteasome regulatory subunit RPN9 / Ubiquitin carboxyl-terminal hydrolase RPN11 / 26S proteasome subunit RPT4 / 26S proteasome regulatory subunit 8 homolog / 26S proteasome regulatory subunit RPN7 / 26S proteasome regulatory subunit RPN8 / 26S proteasome regulatory subunit RPN5 / 26S proteasome regulatory subunit 7 homolog / Proteasome subunit beta type-1 / Proteasome subunit alpha type-3 / 26S proteasome regulatory subunit 6B homolog / Proteasome subunit beta type-6 / 26S proteasome regulatory subunit RPN13 / 26S proteasome complex subunit SEM1 / Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-2 / 26S proteasome regulatory subunit 6A / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 / Proteasome subunit alpha type-5 / 26S proteasome regulatory subunit RPN12 / 26S proteasome regulatory subunit RPN2 / 26S proteasome regulatory subunit RPN6
Biological speciesSaccharomyces cerevisiae S288c (yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsWehmer M / Rudack T / Beck F / Aufderheide A / Pfeifer G / Plitzko JM / Foerster F / Schulten K / Baumeister W / Sakata E
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Structural insights into the functional cycle of the ATPase module of the 26S proteasome.
Authors: Marc Wehmer / Till Rudack / Florian Beck / Antje Aufderheide / Günter Pfeifer / Jürgen M Plitzko / Friedrich Förster / Klaus Schulten / Wolfgang Baumeister / Eri Sakata /
Abstract: In eukaryotic cells, the ubiquitin-proteasome system (UPS) is responsible for the regulated degradation of intracellular proteins. The 26S holocomplex comprises the core particle (CP), where ...In eukaryotic cells, the ubiquitin-proteasome system (UPS) is responsible for the regulated degradation of intracellular proteins. The 26S holocomplex comprises the core particle (CP), where proteolysis takes place, and one or two regulatory particles (RPs). The base of the RP is formed by a heterohexameric AAA ATPase module, which unfolds and translocates substrates into the CP. Applying single-particle cryo-electron microscopy (cryo-EM) and image classification to samples in the presence of different nucleotides and nucleotide analogs, we were able to observe four distinct conformational states (s1 to s4). The resolution of the four conformers allowed for the construction of atomic models of the AAA ATPase module as it progresses through the functional cycle. In a hitherto unobserved state (s4), the gate controlling access to the CP is open. The structures described in this study allow us to put forward a model for the 26S functional cycle driven by ATP hydrolysis.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionDec 16, 2016-
Header (metadata) releaseJan 25, 2017-
Map releaseMar 8, 2017-
UpdateAug 2, 2017-
Current statusAug 2, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.017
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  • Surface view with fitted model
  • Atomic models: PDB-5mpa, PDB-5mpe
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6fvu
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5mpa
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5mpe
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6fvu
  • 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_3535.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 384 pix.
= 529.92 Å
1.38 Å/pix.
x 384 pix.
= 529.92 Å
1.38 Å/pix.
x 384 pix.
= 529.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.38 Å
Density
Contour LevelBy AUTHOR: 0.017 / Movie #1: 0.017
Minimum - Maximum-0.092161775 - 0.1307914
Average (Standard dev.)-0.0000060000098 (±0.004646115)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 529.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.381.381.38
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z529.920529.920529.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0920.131-0.000

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Supplemental data

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Sample components

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Entire 26S proteasome of Saccharomyces cerevisiae in presence of ATP (s2)

EntireName: 26S proteasome of Saccharomyces cerevisiae in presence of ATP (s2)
Number of components: 24

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Component #1: protein, 26S proteasome of Saccharomyces cerevisiae in presence o...

ProteinName: 26S proteasome of Saccharomyces cerevisiae in presence of ATP (s2)
Recombinant expression: No
MassTheoretical: 1.7 MDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

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Component #2: protein, Proteasome subunit alpha type-1

ProteinName: Proteasome subunit alpha type-1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 28.03383 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #3: protein, Proteasome subunit alpha type-2

ProteinName: Proteasome subunit alpha type-2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 27.191828 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #4: protein, Proteasome subunit alpha type-3

ProteinName: Proteasome subunit alpha type-3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 28.74823 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #5: protein, Proteasome subunit alpha type-4

ProteinName: Proteasome subunit alpha type-4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 28.478111 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #6: protein, Proteasome subunit alpha type-5

ProteinName: Proteasome subunit alpha type-5 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 28.649086 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #7: protein, Proteasome subunit alpha type-6

ProteinName: Proteasome subunit alpha type-6 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 25.634 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #8: protein, Probable proteasome subunit alpha type-7

ProteinName: Probable proteasome subunit alpha type-7 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 31.575068 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #9: protein, Proteasome subunit beta type-1

ProteinName: Proteasome subunit beta type-1PSMB1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 23.573604 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #10: protein, Proteasome subunit beta type-2

ProteinName: Proteasome subunit beta type-2PSMB2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 28.299889 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #11: protein, Proteasome subunit beta type-3

ProteinName: Proteasome subunit beta type-3PSMB3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 22.627842 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #12: protein, Proteasome subunit beta type-4

ProteinName: Proteasome subunit beta type-4PSMB4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 22.545676 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #13: protein, Proteasome subunit beta type-5

ProteinName: Proteasome subunit beta type-5PSMB5 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 31.670539 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #14: protein, Proteasome subunit beta type-6

ProteinName: Proteasome subunit beta type-6 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 26.905076 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #15: protein, Proteasome subunit beta type-7

ProteinName: Proteasome subunit beta type-7 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 29.471289 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #16: protein, 26S protease regulatory subunit 7 homolog

ProteinName: 26S protease regulatory subunit 7 homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.054891 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #17: protein, 26S protease regulatory subunit 4 homolog

ProteinName: 26S protease regulatory subunit 4 homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.89816 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #18: protein, 26S protease regulatory subunit 6B homolog

ProteinName: 26S protease regulatory subunit 6B homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 47.953676 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #19: protein, 26S protease subunit RPT4

ProteinName: 26S protease subunit RPT4Proteasome endopeptidase complex
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.480137 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #20: protein, 26S protease regulatory subunit 6A

ProteinName: 26S protease regulatory subunit 6A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.315727 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #21: protein, 26S protease regulatory subunit 8 homolog

ProteinName: 26S protease regulatory subunit 8 homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.342742 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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Component #22: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #23: ligand, ADENOSINE-5'-TRIPHOSPHATE

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

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Component #24: 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 solutionSpecimen conc.: 1 mg/mL / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: OTHER / Temperature: 277 K / Humidity: 95 %

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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: 45 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD / Defocus: 1500.0 - 3500.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 193337
3D reconstructionSoftware: RELION / Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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