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- EMDB-56045: Cryo-EM Structure of the LPOR:Chlide:NADPH Complexes (RD-A) - imp... -

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Basic information

Entry
Database: EMDB / ID: EMD-56045
TitleCryo-EM Structure of the LPOR:Chlide:NADPH Complexes (RD-A) - improved resolution of a dimer building block form RF-21, RF-23 and RF-25
Map dataprimary
Sample
  • Complex: Cryo-EM Structure of the LPOR:Chlide:NADPH Complexes (RD-A) - improved resolution of a dimer building block form RF-21, RF-23 and RF-25
    • Protein or peptide: Protochlorophyllide reductase B, chloroplastic
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: Chlorophyllide a
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: water
Keywordsphotoenzyme / chlorophyllide / oligomer / PHOTOSYNTHESIS
Function / homology
Function and homology information


protochlorophyllide reductase / protochlorophyllide reductase activity / response to ethylene / chloroplast outer membrane / chlorophyll biosynthetic process / chloroplast thylakoid / chloroplast envelope / chloroplast thylakoid membrane / photosynthesis / chloroplast ...protochlorophyllide reductase / protochlorophyllide reductase activity / response to ethylene / chloroplast outer membrane / chlorophyll biosynthetic process / chloroplast thylakoid / chloroplast envelope / chloroplast thylakoid membrane / photosynthesis / chloroplast / protein domain specific binding / mRNA binding / cytosol
Similarity search - Function
Light-dependent protochlorophyllide reductase / short chain dehydrogenase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Protochlorophyllide reductase B, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
Methodhelical reconstruction / cryo EM / Resolution: 2.55 Å
AuthorsGabruk M / Desfosses A / Estrozi LF / Pintscher S / Rawski M
Funding support Poland, 1 items
OrganizationGrant numberCountry
Polish National Science Centre2019/35/D/NZ1/00295 Poland
CitationJournal: Nat Commun / Year: 2026
Title: Structures of LPOR-Chlide complexes reveal the structural basis of membrane remodeling and photocatalysis.
Authors: Michał Gabruk / Ambroise Desfosses / Leandro Farias Estrozi / Sebastian Pintscher / Michał Rawski / Grzegorz Ważny / Agnieszka Garbacz / Mateusz Zbyradowski / Jerzy Kruk / Leszek Fiedor /
Abstract: Light-dependent protochlorophyllide oxidoreductase (LPOR) is a light-driven enzyme in flowering plants. It is involved in chlorophyll biosynthesis while also reorganizing membrane lipids into the ...Light-dependent protochlorophyllide oxidoreductase (LPOR) is a light-driven enzyme in flowering plants. It is involved in chlorophyll biosynthesis while also reorganizing membrane lipids into the cubic membrane network that supports chloroplast development. However, the structural basis of these two activities and their relationship have remained unclear. Here, cryo-electron microscopy of chlorophyllide-bound LPOR oligomers reveals nine distinct assembly states, including helical filaments, stacked rings and segmented strings of dimers. We find that strings of LPOR dimers reshape lipid bilayers into a range of membrane architectures through combinations of three inter-string interfaces, providing a structural explanation for the flexibility of these assemblies. The highest-resolution map (2.55 Å), shows the pigment-binding region in sufficient detail to reveal a solvent-accessible channel near the pigment and a conformation of the propionate group may support hydride transfer from NADPH. Together, these findings establish a structural framework linking LPOR oligomerization, membrane remodeling and photocatalysis, and suggest that chlorophyllide-bound LPOR assemblies may have a regulatory function in mature leaves.
History
DepositionDec 10, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateSep 16, 2026-
Current statusSep 16, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56045.png

Downloads & links

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Map

FileDownload / File: emd_56045.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 640 pix.
= 550.4 Å		0.86 Å/pix.
x 640 pix.
= 550.4 Å		0.86 Å/pix.
x 640 pix.
= 550.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.134
Minimum - Maximum-0.5846602 - 0.8506851
Average (Standard dev.)0.00056591857 (±0.005758889)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 550.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpened

Fileemd_56045_additional_1.map
Annotationsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_56045_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_56045_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM Structure of the LPOR:Chlide:NADPH Complexes (RD-A) - imp...

EntireName: Cryo-EM Structure of the LPOR:Chlide:NADPH Complexes (RD-A) - improved resolution of a dimer building block form RF-21, RF-23 and RF-25
Components
  • Complex: Cryo-EM Structure of the LPOR:Chlide:NADPH Complexes (RD-A) - improved resolution of a dimer building block form RF-21, RF-23 and RF-25
    • Protein or peptide: Protochlorophyllide reductase B, chloroplastic
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: Chlorophyllide a
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: water

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Supramolecule #1: Cryo-EM Structure of the LPOR:Chlide:NADPH Complexes (RD-A) - imp...

SupramoleculeName: Cryo-EM Structure of the LPOR:Chlide:NADPH Complexes (RD-A) - improved resolution of a dimer building block form RF-21, RF-23 and RF-25
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Arabidopsis thaliana (thale cress)

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Macromolecule #1: Protochlorophyllide reductase B, chloroplastic

MacromoleculeName: Protochlorophyllide reductase B, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: protochlorophyllide reductase
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Molecular weightTheoretical: 38.236324 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGST AATSSPTVTK SVDGKKTLRK GNVVVTGASS GLGLATAKAL AETGKWNVIM ACRDFLKAER AAKSVGMPK DSYTVMHLDL ASLDSVRQFV DNFRRTETPL DVLVCNAAVY FPTAKEPTYS AEGFELSVAT NHLGHFLLAR L LLDDLKKS ...String:
MGSSHHHHHH SSGLVPRGST AATSSPTVTK SVDGKKTLRK GNVVVTGASS GLGLATAKAL AETGKWNVIM ACRDFLKAER AAKSVGMPK DSYTVMHLDL ASLDSVRQFV DNFRRTETPL DVLVCNAAVY FPTAKEPTYS AEGFELSVAT NHLGHFLLAR L LLDDLKKS DYPSKRLIIV GSITGNTNTL AGNVPPKANL GDLRGLAGGL NGLNSSAMID GGDFDGAKAY KDSKVCNMLT MQ EFHRRFH EETGVTFASL YPGCIASTGL FREHIPLFRA LFPPFQKYIT KGYVSETESG KRLAQVVSDP SLTKSGVYWS WNN ASASFE NQLSEEASDV EKARKVWEIS EKLVGLA

UniProtKB: Protochlorophyllide reductase B, chloroplastic

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Macromolecule #2: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

MacromoleculeName: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
type: ligand / ID: 2 / Number of copies: 2 / Formula: NDP
Molecular weightTheoretical: 745.421 Da
Chemical component information

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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Macromolecule #3: Chlorophyllide a

MacromoleculeName: Chlorophyllide a / type: ligand / ID: 3 / Number of copies: 2 / Formula: A1JWG
Molecular weightTheoretical: 614.973 Da

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Macromolecule #4: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 4 / Number of copies: 2 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

ChemComp-LMG:
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 57 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.1
Component:
ConcentrationFormulaName
37.0 mMNa2HPO4sodium phosphate
225.0 mMNaClsodium chloride
150.0 mMimidazoleimidazole
5.0 mM2-mercaptoethanol2-mercaptoethanol
25.0 %glycerolglycerol
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 294 K / Instrument: FEI VITROBOT MARK III
Details28 uM AtPORB, 40 uM Chlorophyllide, 600 uM NADPH, 230 uM lipids (50mol% MGDG, 35mol% DGDG, 15mol% PG)

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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: 2.1 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 153.242 Å
Applied symmetry - Helical parameters - Δ&Phi: 14.6 °
Applied symmetry - Helical parameters - Axial symmetry: D10 (2x10 fold dihedral)
Resolution.type: BY AUTHOR / Resolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 1340624
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7jk9

Final angle assignmentType: NOT APPLICABLE

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Atomic model buiding 1

Initial modelPDB ID:

7jk9


Chain - Source name: PDB / Chain - Initial model type: experimental model / Details: initial model
Output model

PDB-9tl8:
Cryo-EM Structure of the LPOR:Chlide:NADPH Complexes (RD-A) - improved resolution of a dimer building block form RF-21, RF-23 and RF-25

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