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- EMDB-0420: T.elongatus NDH Peripheral Arm Focus Map without X-cofactor(data-... -

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Basic information

Entry
Database: EMDB / ID: 0420
TitleT.elongatus NDH Peripheral Arm Focus Map without X-cofactor(data-set 1)
Map dataunsharpened
SampleNAD(P)H dehydrogenase-like complex peripheral arm(NDH/NDH-1_1/NDH1L) from T.elongatus:
SourceThermosynechococcus elongatus BP-1 (Cyanobacteria)
Methodsingle particle reconstruction / cryo EM / 3.4 Å resolution
AuthorsLaughlin TG / Davies KM
CitationJournal: Nature / Year: 2019
Title: Structure of the complex I-like molecule NDH of oxygenic photosynthesis.
Authors: Thomas G Laughlin / Andrew N Bayne / Jean-François Trempe / David F Savage / Karen M Davies
DateDeposition: Dec 9, 2018 / Header (metadata) release: Jan 9, 2019 / Map release: Feb 27, 2019 / Last update: Mar 6, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0127
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0127
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0420.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
1.07 Å/pix.
= 384.48 Å
360 pix
1.07 Å/pix.
= 384.48 Å
360 pix
1.07 Å/pix.
= 384.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Density
Contour Level:0.0127 (by author), 0.0127 (movie #1):
Minimum - Maximum-0.021188328 - 0.08769522
Average (Standard dev.)-0.00007435941 (0.0011153436)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin0.00.00.0
Limit359.0359.0359.0
Spacing360360360
CellA=B=C: 384.47998 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0681.0681.068
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z384.480384.480384.480
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-0.0210.088-0.000

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Supplemental data

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Mask #1

Fileemd_0420_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire NAD(P)H dehydrogenase-like complex peripheral arm(NDH/NDH-1_1/NDH...

EntireName: NAD(P)H dehydrogenase-like complex peripheral arm(NDH/NDH-1_1/NDH1L) from T.elongatus
Number of components: 1

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Component #1: protein, NAD(P)H dehydrogenase-like complex peripheral arm(NDH/ND...

ProteinName: NAD(P)H dehydrogenase-like complex peripheral arm(NDH/NDH-1_1/NDH1L) from T.elongatus
Recombinant expression: No
SourceSpecies: Thermosynechococcus elongatus BP-1 (Cyanobacteria)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.01 mg/ml / pH: 6
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 100 %
Details: incubate on grid for 30 seconds and blot 2.5 seconds before plunging.

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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: 5 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
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: 2519 / Details: One image per hole, focusing at each image.

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 39941
Details: Super-resolution movies were aligned, exposure-weighted, and Fourier cropped to the physical pixel size.
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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