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- EMDB-4273: Fo conformation 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-4273
TitleFo conformation 1
Map dataChloroplast Fo and peripheral stalk conformation 1
Sample
  • Complex: Chloroplast Fo
Biological speciesSpinacia oleracea (spinach)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsHahn A / Vonck J / Mills DJ / Kuehlbrandt W / Meier T
CitationJournal: Science / Year: 2018
Title: Structure, mechanism, and regulation of the chloroplast ATP synthase.
Authors: Alexander Hahn / Janet Vonck / Deryck J Mills / Thomas Meier / Werner Kühlbrandt /
Abstract: The chloroplast adenosine triphosphate (ATP) synthase uses the electrochemical proton gradient generated by photosynthesis to produce ATP, the energy currency of all cells. Protons conducted through ...The chloroplast adenosine triphosphate (ATP) synthase uses the electrochemical proton gradient generated by photosynthesis to produce ATP, the energy currency of all cells. Protons conducted through the membrane-embedded F motor drive ATP synthesis in the F head by rotary catalysis. We determined the high-resolution structure of the complete cFF complex by cryo-electron microscopy, resolving side chains of all 26 protein subunits, the five nucleotides in the F head, and the proton pathway to and from the rotor ring. The flexible peripheral stalk redistributes differences in torsional energy across three unequal steps in the rotation cycle. Plant ATP synthase is autoinhibited by a β-hairpin redox switch in subunit γ that blocks rotation in the dark.
History
DepositionJan 24, 2018-
Header (metadata) releaseFeb 21, 2018-
Map releaseMay 23, 2018-
UpdateMay 23, 2018-
Current statusMay 23, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.061
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.061
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4273.png

Downloads & links

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Map

FileDownload / File: emd_4273.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationChloroplast Fo and peripheral stalk conformation 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 350 pix.
= 368.55 Å		1.05 Å/pix.
x 350 pix.
= 368.55 Å		1.05 Å/pix.
x 350 pix.
= 368.55 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.053 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.061 / Movie #1: 0.061
Minimum - Maximum-0.19256301 - 0.36161965
Average (Standard dev.)-0.0003072826 (±0.010128977)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions350350350
Spacing350350350
CellA=B=C: 368.55 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0531.0531.053
M x/y/z350350350
origin x/y/z0.0000.0000.000
length x/y/z368.550368.550368.550
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS350350350
D min/max/mean-0.1930.362-0.000

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Supplemental data

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Mask #1

Fileemd_4273_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_4273_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_4273_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Chloroplast Fo

EntireName: Chloroplast Fo
Components
  • Complex: Chloroplast Fo

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Supramolecule #1: Chloroplast Fo

SupramoleculeName: Chloroplast Fo / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#13 / Details: masked and realigned Fo from F1Fo complex.
Source (natural)Organism: Spinacia oleracea (spinach)
Molecular weightTheoretical: 600 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
Component:
ConcentrationNameFormula
30.0 mMHEPES
2.0 mMMgCl2
0.5 mMEDTA
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 70 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number real images: 6254 / Average exposure time: 62.0 sec. / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.5 µm / Calibrated defocus min: 1.5 µm / Calibrated magnification: 132953 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 670614
CTF correctionSoftware - Name: CTFFIND (ver. 4)
Startup modelType of model: OTHER
Details: unpublished ab initio reconstruction from data from another microscope
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1)
Details: Fo and peripheral stalk from F1Fo conformation 1 (EMD-4270) was masked and locally realigned.
Number images used: 167171
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 2.1)
Final 3D classificationNumber classes: 3 / Avg.num./class: 70000 / Software - Name: RELION (ver. 2.1)
Details: three classes with 167,000, 15,000 and 14,000 particles. This is the first one.
FSC plot (resolution estimation)

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Atomic model buiding 1

Detailsreal space refinement as described for EMD-4270
RefinementSpace: REAL / Protocol: AB INITIO MODEL

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