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- EMDB-0418: T.elongatus NDH Peripheral Arm Focus Map without NdhS(data-set 1) -

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Basic information

Entry
Database: EMDB / ID: EMD-0418
TitleT.elongatus NDH Peripheral Arm Focus Map without NdhS(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: 3.8 Å
AuthorsLaughlin TG / Davies KM
Funding support United States, 3 items
OrganizationGrant numberCountry
Department of Energy (United States)DE-AC02-O5CH11231 United States
Department of Energy (United States)DE-SC00016240 United States
National Institutes of Health/National Institute of General Medical Sciences5T32GM007232-38 United States
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-
UpdateDec 2, 2020-
Current statusDec 2, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.027
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.027
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_0418.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationunsharpened
Voxel sizeX=Y=Z: 1.068 Å
Density
Contour LevelBy AUTHOR: 0.027 / Movie #1: 0.027
Minimum - Maximum-0.057742726 - 0.22954209
Average (Standard dev.)-0.00013712772 (±0.0027296988)
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-0.0580.230-0.000

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Supplemental data

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Mask #1

Fileemd_0418_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_0418_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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Half map: em-half-volume P2.

Fileemd_0418_half_map_2.map
Annotationem-half-volume_P2.
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
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-TrisBis-tris methane
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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
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.
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

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
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1.1) / Number images used: 44097
DetailsSuper-resolution movies were aligned, exposure-weighted, and Fourier cropped to the physical pixel size.
FSC plot (resolution estimation)

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