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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 / homologyProteasome subunit beta 7 / P-loop containing nucleoside triphosphate hydrolase / 26S Proteasome regulatory subunit 4 / Proteasome subunit beta 2 / Proteasome subunit beta 1 / Proteasome subunit alpha 1 / Proteasome subunit alpha4 / Proteasome subunit alpha2 / Proteasome subunit alpha6 / Proteasome subunit alpha5 ...Proteasome subunit beta 7 / P-loop containing nucleoside triphosphate hydrolase / 26S Proteasome regulatory subunit 4 / Proteasome subunit beta 2 / Proteasome subunit beta 1 / Proteasome subunit alpha 1 / Proteasome subunit alpha4 / Proteasome subunit alpha2 / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome beta 3 subunit / Proteasomal ATPase OB C-terminal domain / Ubiquitin-like domain superfamily / Nucleophile aminohydrolases, N-terminal / Rpn11/EIF3F, C-terminal / 26S Proteasome regulatory subunit 6A / 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 / AAA+ ATPase domain / Ribosomal protein L40e / Proteasome, subunit alpha/beta / 26S Proteasome regulatory subunit 7 / 26S Proteasome regulatory subunit 6B / JAB1/MPN/MOV34 metalloenzyme domain / Ubiquitin domain signature. / 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. / MPN domain profile. / Ubiquitin domain profile. / Proteasome beta-type subunits signature. / AAA-protein family signature. / Proteasome alpha-type subunits signature. / Proteasomal ATPase OB C-terminal domain / 26S proteasome regulatory subunit 8 / 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 / Proteasome subunit alpha 7-like / Proteasome subunit beta Pre3 / Proteasome subunit alpha 3 / MPN domain / Ubiquitin domain / Proteasome alpha-subunit, N-terminal domain / SCF(Skp2)-mediated degradation of p27/p21 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Formation of Incision Complex in GG-NER / Peptidase T1A, proteasome beta-subunit / Gap-filling DNA repair synthesis and ligation in GG-NER / 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 / Formation of a pool of free 40S subunits / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / 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 / Neddylation / 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 / DNA Damage Recognition in GG-NER / rt:r-sce-1799339: / Metalloprotease DUBs / Translesion synthesis by POLK / Termination of translesion DNA synthesis / AUF1 (hnRNP D0) binds and destabilizes mRNA / ABC-family proteins mediated transport / TNFR2 non-canonical NF-kB pathway / Negative regulation of MAPK pathway / MAPK6/MAPK4 signaling / Translesion synthesis by POLI / UCH proteinases / Ub-specific processing proteases
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 / 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
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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