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- EMDB-19247: NDH-PSI-LHCI supercomplex from S. oleracea: local refined border ... -

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Basic information

Entry
Database: EMDB / ID: EMD-19247
TitleNDH-PSI-LHCI supercomplex from S. oleracea: local refined border region between NDH and PSI-LHCI-2
Map datafiltered map
Sample
  • Complex: NDHI-PSI supercomplex
KeywordsNDHI / PSI / Supercomplex / photosynthesis / electron transport chain / lipids / proton translocation / plastoquinone / ELECTRON TRANSPORT
Biological speciesSpinacia oleracea (spinach)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsIntroini B / Hahn A / Kuehlbrandt W
Funding support Germany, 1 items
OrganizationGrant numberCountry
Other private Germany
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Cryo-EM structure of the NDH-PSI-LHCI supercomplex from Spinacia oleracea.
Authors: Bianca Introini / Alexander Hahn / Werner Kühlbrandt /
Abstract: The nicotinamide adenine dinucleotide phosphate (NADPH) dehydrogenase (NDH) complex is crucial for photosynthetic cyclic electron flow and respiration, transferring electrons from ferredoxin to ...The nicotinamide adenine dinucleotide phosphate (NADPH) dehydrogenase (NDH) complex is crucial for photosynthetic cyclic electron flow and respiration, transferring electrons from ferredoxin to plastoquinone while transporting H across the chloroplast membrane. This process boosts adenosine triphosphate production, regardless of NADPH levels. In flowering plants, NDH forms a supercomplex with photosystem I, enhancing its stability under high light. We report the cryo-electron microscopy structure of the NDH supercomplex in Spinacia oleracea at a resolution of 3.0-3.3 Å. The supercomplex consists of 41 protein subunits, 154 chlorophylls and 38 carotenoids. Subunit interactions are reinforced by 46 distinct lipids. The structure of NDH resembles that of mitochondrial complex I closely, including the quinol-binding site and an extensive internal aqueous passage for proton translocation. A well-resolved catalytic plastoquinone (PQ) occupies the PQ channel. The pronounced structural similarity to complex I sheds light on electron transfer and proton translocation within the NDH supercomplex.
History
DepositionDec 21, 2023-
Header (metadata) releaseFeb 5, 2025-
Map releaseFeb 5, 2025-
UpdateFeb 12, 2025-
Current statusFeb 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19247.png

Downloads & links

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Map

FileDownload / File: emd_19247.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfiltered map
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 512 pix.
= 428.544 Å		0.84 Å/pix.
x 512 pix.
= 428.544 Å		0.84 Å/pix.
x 512 pix.
= 428.544 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.1746464 - 1.8641491
Average (Standard dev.)0.0014527868 (±0.061089456)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 428.544 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19247_msk_1.map
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Additional map: unfiltered map

Fileemd_19247_additional_1.map
Annotationunfiltered map
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Half map: half map A

Fileemd_19247_half_map_1.map
Annotationhalf map A
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Half map: half map B

Fileemd_19247_half_map_2.map
Annotationhalf map B
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Sample components

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Entire : NDHI-PSI supercomplex

EntireName: NDHI-PSI supercomplex
Components
  • Complex: NDHI-PSI supercomplex

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Supramolecule #1: NDHI-PSI supercomplex

SupramoleculeName: NDHI-PSI supercomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#42
Source (natural)Organism: Spinacia oleracea (spinach)

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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: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.7 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

19244


Details: This is a local refined map from a NU-refinement map job made in cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 38385
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainPDB ID
source_name: AlphaFold, initial_model_type: in silico model
source_name: PDB, initial_model_type: experimental model

4y28

source_name: PDB, initial_model_type: experimental model

6khj

RefinementSpace: REAL / Protocol: AB INITIO MODEL

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