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- EMDB-9770: yeast proteasome in substrate-processing state (C3-b) -

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Entry
Database: EMDB / Id: 9770
Titleyeast proteasome in substrate-processing state (C3-b)
Map datasubstrate-processing C3-b
Sampleyeast 26S proteasome
  • (Proteasome subunit beta type- ...) x 7
  • (Proteasome subunit alpha type- ...) x 6
  • Probable proteasome subunit alpha type-7
  • (26S protease regulatory subunit ...) x 5
  • 26S protease subunit RPT4Proteasome endopeptidase complex
  • (26S proteasome regulatory subunit ...) x 11
  • Ubiquitin carboxyl-terminal hydrolase RPN11
  • 26S proteasome complex subunit SEM1
Func homologyNucleophile aminohydrolases, N-terminal / 26S proteasome regulatory subunit, C-terminal / Proteasomal ATPase OB C-terminal domain / 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 ...Nucleophile aminohydrolases, N-terminal / 26S proteasome regulatory subunit, C-terminal / Proteasomal ATPase OB C-terminal domain / 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 regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / Proteasome subunit beta 4 / Proteasome beta-type subunit, conserved site / Armadillo-type fold / Tetratricopeptide repeat-containing domain / Proteasome beta 3 subunit / Ubiquitin interacting motif / JAB1/MPN/MOV34 metalloenzyme domain / Proteasome component (PCI) domain / Proteasome, subunit alpha/beta / Proteasome/cyclosome repeat / von Willebrand factor, type A / AAA+ ATPase domain / ATPase, AAA-type, core / Tetratricopeptide-like helical domain superfamily / ATPase, AAA-type, conserved site / 26S proteasome regulatory subunit P45-like / 26S proteasome non-ATPase regulatory subunit Rpn12 / Proteasomal ubiquitin receptor Rpn13/ADRM1 / DSS1/SEM1 / Armadillo-like helical / CSN8/PSMD8/EIF3K / Proteasome subunit alpha5 / Peptidase T1A, proteasome beta-subunit / Proteasomal ubiquitin receptor Rpn13/ADRM1 superfamily / Winged helix DNA-binding domain superfamily / von Willebrand factor A-like domain superfamily / MPN domain / Proteasome subunit alpha 3 / Proteasome subunit beta Pre3 / in:ipr037560: / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / 26S Proteasome non-ATPase regulatory subunit 13 / 26S proteasome regulatory subunit RPN2, C-terminal / 26S proteasome regulatory subunit Rpn6, N-terminal / 6S proteasome subunit Rpn6, C-terminal helix domain / ATPase family associated with various cellular activities (AAA) / Proteasome subunit / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Winged helix-like DNA-binding domain superfamily / 26S Proteasome non-ATPase regulatory subunit 12 / 26S Proteasome non-ATPase regulatory subunit 7/8 / Proteasome subunit beta 7 / Proteasome subunit alpha6 / Proteasome subunit alpha2 / in:ipr034647: / Proteasome subunit alpha 1 / Proteasome subunit beta 1 / Proteasome subunit beta 2 / 26S Proteasome regulatory subunit 4 / 26S Proteasome non-ATPase regulatory subunit 6 / 26S Proteasome regulatory subunit 7 / 26S Proteasome regulatory subunit 6A / 26S Proteasome regulatory subunit 6B / in:ipr035261: / 26S Proteasome non-ATPase regulatory subunit 1 / 26S proteasome non-ATPase regulatory subunit 3 / Proteasome alpha-subunit, N-terminal domain / PCI domain / Proteasome/cyclosome repeat / 26S proteasome regulatory subunit RPN2 C-terminal domain / L13a-mediated translational silencing of Ceruloplasmin expression / Proteasome beta-type subunit profile. / Proteasome alpha-type subunit profile. / Ubiquitin-interacting motif (UIM) domain profile. / TPR repeat region circular profile. / Proteasomal ATPase OB C-terminal domain / PCI domain profile. / von Willebrand factor type A domain / MPN domain profile. / VWFA domain profile. / 26S proteasome regulatory subunit RPN6 N-terminal domain / TPR repeat profile. / Proteasome beta-type subunits signature. / AAA-protein family signature. / rt:r-sce-187577: / Maintenance of mitochondrial structure and function / 26S proteasome subunit RPN6 C-terminal helix domain / Proteasome beta subunits C terminal / Ribosomal scanning and start codon recognition / Formation of the ternary complex, and subsequently, the 43S complex / Orc1 removal from chromatin / Neutrophil degranulation / Proteasome complex subunit Rpn13 ubiquitin receptor / DSS1/SEM1 family / Proteasome regulatory subunit C-terminal / CSN8/PSMD8/EIF3K family / Proteasome subunit A N-terminal signature
Function and homology information
SourceSaccharomyces cerevisiae S288c (yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsCong Y
CitationJournal: Mol. Cell / Year: 2019
Title: Structural Snapshots of 26S Proteasome Reveal Tetraubiquitin-Induced Conformations.
P-authors: Zhanyu Ding / Cong Xu / Indrajit Sahu / Yifan Wang / Zhenglin Fu / Min Huang / Catherine C L Wong / Michael H Glickman / Yao Cong /
Abstract: The 26S proteasome is the ATP-dependent protease responsible for regulating the proteome of eukaryotic cells through degradation of mainly ubiquitin-tagged substrates. In order to understand how ...The 26S proteasome is the ATP-dependent protease responsible for regulating the proteome of eukaryotic cells through degradation of mainly ubiquitin-tagged substrates. In order to understand how proteasome responds to ubiquitin signal, we resolved an ensemble of cryo-EM structures of proteasome in the presence of K48-Ub, with three of them resolved at near-atomic resolution. We identified a conformation with stabilized ubiquitin receptors and a previously unreported orientation of the lid, assigned as a Ub-accepted state C1-b. We determined another structure C3-b with localized K48-Ub to the toroid region of Rpn1, assigned as a substrate-processing state. Our structures indicate that tetraUb induced conformational changes in proteasome could initiate substrate degradation. We also propose a CP gate-opening mechanism involving the propagation of the motion of the lid to the gate through the Rpn6-α2 interaction. Our results enabled us to put forward a model of a functional cycle for proteasomes induced by tetraUb and nucleotide.
Validation ReportPDB-ID: 6j2n

SummaryFull reportAbout validation report
DateDeposition: Jan 2, 2019 / Header (metadata) release: Mar 20, 2019 / Map release: Mar 20, 2019 / Last update: Apr 10, 2019

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Strvis

Movie
  • Surface view with section colored by density value
  • Surface level: 0.806
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.806
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6j2n
  • Surface level: 0.806
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downlink

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Map

Fileemd_9770.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
1.32 Å/pix.
= 474.48 Å
360 pix
1.32 Å/pix.
= 474.48 Å
360 pix
1.32 Å/pix.
= 474.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.318 Å
Density
Contour Level:0.806 (by author), 0.806 (movie #1):
Minimum - Maximum-1.4813117 - 2.2945497
Average (Standard dev.)0.016793959 (0.13170238)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin0.00.00.0
Limit359.0359.0359.0
Spacing360360360
CellA=B=C: 474.47998 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3181.3181.318
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z474.480474.480474.480
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-1.4812.2950.017

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Supplemental data

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Sample components

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Entire yeast 26S proteasome

EntireName: yeast 26S proteasome / Number of components: 34

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Component #1: protein, yeast 26S proteasome

ProteinName: yeast 26S proteasome / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

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Component #2: 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) / Strain: ATCC 204508 / S288c

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Component #3: 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) / Strain: ATCC 204508 / S288c

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Component #4: 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) / Strain: ATCC 204508 / S288c

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Component #5: 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) / Strain: ATCC 204508 / S288c

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Component #6: 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) / Strain: ATCC 204508 / S288c

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Component #7: 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) / Strain: ATCC 204508 / S288c

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Component #8: 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) / Strain: ATCC 204508 / S288c

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Component #9: 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) / Strain: ATCC 204508 / S288c

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Component #10: 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) / Strain: ATCC 204508 / S288c

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Component #11: 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) / Strain: ATCC 204508 / S288c

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Component #12: 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) / Strain: ATCC 204508 / S288c

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Component #13: 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) / Strain: ATCC 204508 / S288c

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Component #14: 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) / Strain: ATCC 204508 / S288c

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Component #15: 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) / Strain: ATCC 204508 / S288c

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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) / Strain: ATCC 204508 / S288c

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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) / Strain: ATCC 204508 / S288c

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Component #18: 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) / Strain: ATCC 204508 / S288c

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Component #19: 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) / Strain: ATCC 204508 / S288c

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Component #20: 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) / Strain: ATCC 204508 / S288c

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Component #21: 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) / Strain: ATCC 204508 / S288c

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Component #22: protein, 26S proteasome regulatory subunit RPN2

ProteinName: 26S proteasome regulatory subunit RPN2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 104.351883 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #23: protein, 26S proteasome regulatory subunit RPN9

ProteinName: 26S proteasome regulatory subunit RPN9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.839348 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #24: protein, 26S proteasome regulatory subunit RPN5

ProteinName: 26S proteasome regulatory subunit RPN5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 51.840352 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #25: protein, 26S proteasome regulatory subunit RPN6

ProteinName: 26S proteasome regulatory subunit RPN6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.839812 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #26: protein, 26S proteasome regulatory subunit RPN7

ProteinName: 26S proteasome regulatory subunit RPN7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.016367 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #27: protein, 26S proteasome regulatory subunit RPN3

ProteinName: 26S proteasome regulatory subunit RPN3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 60.464605 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #28: protein, 26S proteasome regulatory subunit RPN12

ProteinName: 26S proteasome regulatory subunit RPN12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.952119 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #29: protein, 26S proteasome regulatory subunit RPN8

ProteinName: 26S proteasome regulatory subunit RPN8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.365508 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #30: protein, Ubiquitin carboxyl-terminal hydrolase RPN11

ProteinName: Ubiquitin carboxyl-terminal hydrolase RPN11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.442281 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #31: protein, 26S proteasome regulatory subunit RPN10

ProteinName: 26S proteasome regulatory subunit RPN10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.776098 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #32: protein, 26S proteasome regulatory subunit RPN13

ProteinName: 26S proteasome regulatory subunit RPN13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.919002 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #33: protein, 26S proteasome complex subunit SEM1

ProteinName: 26S proteasome complex subunit SEM1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.397102 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #34: protein, 26S proteasome regulatory subunit RPN1

ProteinName: 26S proteasome regulatory subunit RPN1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 109.601906 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionPh: 7.5
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: 38 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: 6171
3D reconstructionResolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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