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

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Entry
Database: EMDB / ID: 9045
TitleYeast 26S proteasome bound to ubiquitinated substrate (4D motor state)
Map dataYeast 26S proteasome bound to ubiquitinated substrate (4D motor state)
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 RPT4
  • Ubiquitin carboxyl-terminal hydrolase RPN11
  • Model substrate polypeptide
  • Ubiquitin-60S ribosomal protein L40
  • (ligand) x 2
Function / homology26S Proteasome regulatory subunit 7 / Proteasome beta 3 subunit / 26S proteasome regulatory subunit 8 / 26S Proteasome regulatory subunit 6B / 26S Proteasome regulatory subunit 6A / 26S Proteasome regulatory subunit 4 / Proteasome subunit beta 7 / Proteasome subunit beta 2 / Proteasome subunit beta 1 / Proteasome subunit alpha 1 ...26S Proteasome regulatory subunit 7 / Proteasome beta 3 subunit / 26S proteasome regulatory subunit 8 / 26S Proteasome regulatory subunit 6B / 26S Proteasome regulatory subunit 6A / 26S Proteasome regulatory subunit 4 / Proteasome subunit beta 7 / Proteasome subunit beta 2 / Proteasome subunit beta 1 / Proteasome subunit alpha 1 / Proteasome subunit alpha4 / Proteasome subunit alpha2 / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Ubiquitin-like domain superfamily / Proteasome subunit alpha 3 / Nucleophile aminohydrolases, N-terminal / P-loop containing nucleoside triphosphate hydrolase / Rpn11/EIF3F, C-terminal / Proteasome beta subunit, C-terminal / Proteasome B-type subunit / Proteasome alpha-type subunit / Ubiquitin / Ubiquitin conserved site / Proteasome subunit beta 4 / Proteasome beta-type subunit, conserved site / 26S proteasome regulatory subunit P45-like / ATPase, AAA-type, conserved site / ATPase, AAA-type, core / MPN domain / Proteasome subunit beta Pre3 / Translesion synthesis by POLI / MPN domain profile. / AUF1 (hnRNP D0) binds and destabilizes mRNA / ABC-family proteins mediated transport / SCF(Skp2)-mediated degradation of p27/p21 / SRP-dependent cotranslational protein targeting to membrane / SCF-beta-TrCP mediated degradation of Emi1 / L13a-mediated translational silencing of Ceruloplasmin expression / Cross-presentation of soluble exogenous antigens (endosomes) / Translesion Synthesis by POLH / Recognition of DNA damage by PCNA-containing replication complex / Translesion synthesis by REV1 / Proteasome beta-type subunit profile. / Proteasome alpha-type subunit profile. / Ubiquitin domain profile. / Proteasome subunit alpha 7-like / Proteasome beta-type subunits signature. / AAA-protein family signature. / Proteasome alpha-type subunits signature. / Ubiquitin domain signature. / Maintenance of mitochondrial structure and function / Proteasome beta subunits C terminal / Proteasome subunit A N-terminal signature / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Ribosomal L40e family / Ubiquitin family / Proteasome subunit / ATPase family associated with various cellular activities (AAA) / Ribosomal protein L40e superfamily / AAA+ ATPase domain / Ribosomal protein L40e / Proteasome, subunit alpha/beta / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dual Incision in GG-NER / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Neutrophil degranulation / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / rt:r-sce-69229: / Formation of a pool of free 40S subunits / Formation of Incision Complex in GG-NER / GTP hydrolysis and joining of the 60S ribosomal subunit / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / E3 ubiquitin ligases ubiquitinate target proteins / Peroxisomal protein import / Iron uptake and transport / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Antigen processing: Ubiquitination & Proteasome degradation / Ubiquitin domain / Gap-filling DNA repair synthesis and ligation in GG-NER / DNA Damage Recognition in GG-NER / Metalloprotease DUBs / JAB1/MPN/MOV34 metalloenzyme domain / Proteasome alpha-subunit, N-terminal domain / Peptidase T1A, proteasome beta-subunit / Termination of translesion DNA synthesis / TNFR2 non-canonical NF-kB pathway / Negative regulation of MAPK pathway / MAPK6/MAPK4 signaling / UCH proteinases / Ub-specific processing proteases / Translesion synthesis by POLK / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / proteasome storage granule assembly / peroxisome fission
Function and homology information
SourceSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Homo sapiens (human) / Saccharomyces cerevisiae S288c (yeast)
Methodsingle particle reconstruction / cryo EM / 4.17 Å resolution
Authorsde la Pena AH / Goodall EA / Gates SN / Lander GC / Martin A
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 / A Martin
Abstract: The 26 proteasome is the primary eukaryotic degradation machine and thus critically involved in numerous cellular processes. The hetero-hexameric ATPase motor of the proteasome unfolds and ...The 26 proteasome is the primary eukaryotic degradation machine and thus critically involved in numerous cellular processes. The hetero-hexameric 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-EM 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+ motor to induce conformational changes and propel the substrate through the central pore.
Validation ReportPDB-ID: 6ef3

SummaryFull reportAbout validation report
DateDeposition: Aug 15, 2018 / Header (metadata) release: Oct 17, 2018 / Map release: Oct 17, 2018 / Last update: Oct 17, 2018

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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

Fileemd_9045.map.gz (map file in CCP4 format, 157217 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
340 pix
1.03 Å/pix.
= 350.2 Å
340 pix
1.03 Å/pix.
= 350.2 Å
340 pix
1.03 Å/pix.
= 350.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.03 Å
Density
Contour Level:0.045 (by author), 0.045 (movie #1):
Minimum - Maximum0.0 - 0.22217602
Average (Standard dev.)0.001485774 (0.008148518)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions340340340
Origin0.00.00.0
Limit339.0339.0339.0
Spacing340340340
CellA=B=C: 350.19998 Å
α=β=γ: 90.0 deg.

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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Mask #1

Fileemd_9045_msk_1.map
Projections & Slices
AxesZYX
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Slices (1/2)
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Mask #2

Fileemd_9045_msk_2.map
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Mask #3

Fileemd_9045_msk_3.map
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Mask #4

Fileemd_9045_msk_4.map
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Mask #5

Fileemd_9045_msk_5.map
Projections & Slices
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Mask #6

Fileemd_9045_msk_6.map
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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 RPT4 / 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: 5 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 microns

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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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