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- EMDB-0419: T.elongatus NDH Peripheral Arm Focus Map with X-cofactor(data-set 1) -

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Basic information

Entry
Database: EMDB / ID: EMD-0419
TitleT.elongatus NDH Peripheral Arm Focus Map with X-cofactor(data-set 1)
Map dataunsharpened
Sample
  • Complex: NAD(P)H dehydrogenase-like complex peripheral arm(NDH/NDH-1_1/NDH1L) from T.elongatus
Biological speciesThermosynechococcus elongatus BP-1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
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 /
Abstract: Cyclic electron flow around photosystem I (PSI) is a mechanism by which photosynthetic organisms balance the levels of ATP and NADPH necessary for efficient photosynthesis. NAD(P)H dehydrogenase-like ...Cyclic electron flow around photosystem I (PSI) is a mechanism by which photosynthetic organisms balance the levels of ATP and NADPH necessary for efficient photosynthesis. NAD(P)H dehydrogenase-like complex (NDH) is a key component of this pathway in most oxygenic photosynthetic organisms and is the last large photosynthetic membrane-protein complex for which the structure remains unknown. Related to the respiratory NADH dehydrogenase complex (complex I), NDH transfers electrons originating from PSI to the plastoquinone pool while pumping protons across the thylakoid membrane, thereby increasing the amount of ATP produced per NADP molecule reduced. NDH possesses 11 of the 14 core complex I subunits, as well as several oxygenic-photosynthesis-specific (OPS) subunits that are conserved from cyanobacteria to plants. However, the three core complex I subunits that are involved in accepting electrons from NAD(P)H are notably absent in NDH, and it is therefore not clear how NDH acquires and transfers electrons to plastoquinone. It is proposed that the OPS subunits-specifically NdhS-enable NDH to accept electrons from its electron donor, ferredoxin. Here we report a 3.1 Å structure of the 0.42-MDa NDH complex from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1, obtained by single-particle cryo-electron microscopy. Our maps reveal the structure and arrangement of the principal OPS subunits in the NDH complex, as well as an unexpected cofactor close to the plastoquinone-binding site in the peripheral arm. The location of the OPS subunits supports a role in electron transfer and defines two potential ferredoxin-binding sites at the apex of the peripheral arm. These results suggest that NDH could possess several electron transfer routes, which would serve to maximize plastoquinone reduction and avoid deleterious off-target chemistry of the semi-plastoquinone radical.
History
DepositionDec 9, 2018-
Header (metadata) releaseJan 9, 2019-
Map releaseFeb 27, 2019-
UpdateMar 6, 2019-
Current statusMar 6, 2019Processing site: RCSB / Status: Released

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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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0419.png

Downloads & links

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Map

FileDownload / File: emd_0419.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 360 pix.
= 384.48 Å		1.07 Å/pix.
x 360 pix.
= 384.48 Å		1.07 Å/pix.
x 360 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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0127 / Movie #1: 0.0127
Minimum - Maximum-0.021727258 - 0.08977797
Average (Standard dev.)-0.00007326881 (±0.0011539819)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 384.47998 Å
α=β=γ: 90.0 °

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
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.0220.090-0.000

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Supplemental data

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Mask #1

Fileemd_0419_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: em-half-volume P1

Fileemd_0419_half_map_1.map
Annotationem-half-volume_P1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: em-half-volume P2

Fileemd_0419_half_map_2.map
Annotationem-half-volume_P2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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
Components
  • Complex: NAD(P)H dehydrogenase-like complex peripheral arm(NDH/NDH-1_1/NDH1L) from T.elongatus

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

SupramoleculeName: NAD(P)H dehydrogenase-like complex peripheral arm(NDH/NDH-1_1/NDH1L) from T.elongatus
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#17
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)

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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

Concentration0.01 mg/mL
BufferpH: 6
Component:
ConcentrationName
20.0 mMBis-Tris
100.0 mMsodium chloride
0.03 %B-dodecyl-maltoside
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV
Details: incubate on grid for 30 seconds and blot 2.5 seconds before plunging.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-35 / Number grids imaged: 1 / Number real images: 2519 / Average exposure time: 0.2 sec. / Average electron dose: 50.0 e/Å2 / Details: One image per hole, focusing at each image.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
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

DetailsSuper-resolution movies were aligned, exposure-weighted, and Fourier cropped to the physical pixel size.
Particle selectionNumber selected: 176592
CTF correctionSoftware: (Name: Gctf (ver. 1.06), RELION (ver. 2.1.1))
Startup modelType of model: OTHER / Details: Signal-subtraction of original map
Final reconstructionAlgorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0.b2) / Number images used: 35662
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1.1)
FSC plot (resolution estimation)

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