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- EMDB-8359: Autoinhibited E. coli ATP synthase state 3 -

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Basic information

Entry
Database: EMDB / ID: 8359
TitleAutoinhibited E. coli ATP synthase state 3
SampleATP synthase
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataAutoinhibited E. coli ATP synthase state 3
Methodsingle particle reconstruction, at 8.53 A resolution
AuthorsSobti M / Smits C / Wong AS / Ishmukhametov R / Stock D / Sandin S / Stewart AG
CitationElife, 2016, 5

Elife, 2016, 5 StrPapers
Cryo-EM structures of the autoinhibited E. coli ATP synthase in three rotational states.
Meghna Sobti / Callum Smits / Andrew Sw Wong / Robert Ishmukhametov / Daniela Stock / Sara Sandin / Alastair G Stewart

DateDeposition: Aug 29, 2016 / Header (metadata) release: Jan 4, 2017 / Map release: Jan 4, 2017 / Last update: Aug 29, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.045
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.045
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5t4q
  • Surface level: 0.045
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_8359.map.gz (map file in CCP4 format, 62501 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
250 pix
1.4 A/pix
= 350. A
250 pix
1.4 A/pix
= 350. A
250 pix
1.4 A/pix
= 350. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.4 A
Density
Contour Level:0.048 (by author), 0.045 (movie #1):
Minimum - Maximum-0.02577311 - 0.1047882
Average (Standard dev.)-0.00014185307 (0.009308554)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions250250250
Origin000
Limit249249249
Spacing250250250
CellA=B=C: 350 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.41.41.4
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z350.000350.000350.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.0260.105-0.000

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Supplemental data

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Sample components

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Entire ATP synthase

EntireName: ATP synthase / Number of components: 11
MassTheoretical: 558 kDa

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Component #1: protein, ATP synthase

ProteinName: ATP synthase / Recombinant expression: No
MassTheoretical: 558 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pFV2

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Component #2: protein, ATP synthase subunit alpha

ProteinName: ATP synthase subunit alpha / Recombinant expression: No
MassTheoretical: 55.138531 kDa
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #3: protein, ATP synthase subunit beta

ProteinName: ATP synthase subunit beta / Recombinant expression: No
MassTheoretical: 51.664574 kDa
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #4: protein, ATP synthase gamma chain

ProteinName: ATP synthase gamma chain / Recombinant expression: No
MassTheoretical: 31.539285 kDa
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #5: protein, ATP synthase epsilon chain

ProteinName: ATP synthase epsilon chain / Recombinant expression: No
MassTheoretical: 15.087244 kDa
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #6: protein, ATP synthase subunit b

ProteinName: ATP synthase subunit b / Recombinant expression: No
MassTheoretical: 17.126691 kDa
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #7: protein, ATP synthase subunit a

ProteinName: ATP synthase subunit a / Recombinant expression: No
MassTheoretical: 30.324096 kDa
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #8: protein, ATP synthase subunit delta

ProteinName: ATP synthase subunit delta / Recombinant expression: No
MassTheoretical: 19.289061 kDa
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #9: protein, ATP synthase subunit c

ProteinName: ATP synthase subunit c / Recombinant expression: No
MassTheoretical: 8.259064 kDa
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #10: ligand, ADENOSINE-5'-TRIPHOSPHATE

LigandName: ADENOSINE-5'-TRIPHOSPHATE / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 0.507181 kDa

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Component #11: 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

Specimen stateparticle
Sample solutionpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 29 e/A2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 95345
3D reconstructionResolution: 8.53 A / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Atomic model buiding

Output model

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