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- EMDB-0416: T.elongatus NDH Peripheral Arm Focus Map(data-set 1) -

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Basic information

Database: EMDB / ID: 0416
TitleT.elongatus NDH Peripheral Arm Focus Map(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 / 3.6 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 23, 2019 / Map release: Feb 27, 2019 / Last update: Mar 6, 2019

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_0416.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

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



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.068 Å
Contour Level:0.04 (by author), 0.04 (movie #1):
Minimum - Maximum-0.08094301 - 0.26424924
Average (Standard dev.)-0.00013323223 (0.002660771)


Space Group Number1
Map Geometry
Axis orderXYZ
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
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-0.0810.264-0.000

Supplemental data

Mask #1

Projections & Slices
Slices (1/2)
Density Histograms

Sample components

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

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)

Experimental details

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.

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
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 2519 / Details: One image per hole, focusing at each image.

Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 91000
Details: Super-resolution movies were aligned, exposure-weighted, and Fourier cropped to the physical pixel size.
3D reconstructionAlgorithm: BACK PROJECTION / Software: RELION / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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