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- EMDB-56046: Cryo-EM Structure of the LPOR:Chlide:NADPH Complexes (RD-25) - im... -

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Basic information

Entry
Database: EMDB / ID: EMD-56046
TitleCryo-EM Structure of the LPOR:Chlide:NADPH Complexes (RD-25) - improved resolution of a dimer building block form RF-25
Map dataprimary
Sample
  • Complex: Dimeric building block (RD-25) of the RF-25 oligomeric Chlide:LPOR:NADPH assembly
    • Protein or peptide: Protochlorophyllide reductase B, chloroplastic
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: Chlorophyllide a
  • Ligand: water
Keywordsphotoenzyme / chlorophyllide / oligomer / PHOTOSYNTHESIS
Function / homology
Function and homology information


protochlorophyllide reductase / protochlorophyllide reductase activity / response to ethylene / chlorophyll biosynthetic process / chloroplast outer membrane / chloroplast thylakoid / chloroplast envelope / chloroplast thylakoid membrane / photosynthesis / chloroplast ...protochlorophyllide reductase / protochlorophyllide reductase activity / response to ethylene / chlorophyll biosynthetic process / chloroplast outer membrane / 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: 2.58 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: Gabruk M / Desfosses A / Estrozi LF / Pintscher S / Rawski M / Wazny G / Garbacz A / Zbyradowski M / Kruk J / Fiedor L
History
DepositionDec 10, 2025-
Header (metadata) releaseAug 12, 2026-
Map releaseAug 12, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_56046.png

Downloads & links

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Map

FileDownload / File: emd_56046.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: 0.118
Minimum - Maximum-0.40339476 - 0.8186139
Average (Standard dev.)0.00095873314 (±0.011121814)
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_56046_additional_1.map
Annotationsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half A

Fileemd_56046_half_map_1.map
Annotationhalf A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B

Fileemd_56046_half_map_2.map
Annotationhalf B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dimeric building block (RD-25) of the RF-25 oligomeric Chlide:LPO...

EntireName: Dimeric building block (RD-25) of the RF-25 oligomeric Chlide:LPOR:NADPH assembly
Components
  • Complex: Dimeric building block (RD-25) of the RF-25 oligomeric Chlide:LPOR:NADPH assembly
    • Protein or peptide: Protochlorophyllide reductase B, chloroplastic
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: Chlorophyllide a
  • Ligand: water

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Supramolecule #1: Dimeric building block (RD-25) of the RF-25 oligomeric Chlide:LPO...

SupramoleculeName: Dimeric building block (RD-25) of the RF-25 oligomeric Chlide:LPOR:NADPH assembly
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: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 3 / 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 #4: Chlorophyllide a

MacromoleculeName: Chlorophyllide a / type: ligand / ID: 4 / Number of copies: 2 / Formula: A1JWG
Molecular weightTheoretical: 614.973 Da

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Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 4 / 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 statefilament

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Sample preparation

BufferpH: 7.1
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: 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: 153.125 Å
Applied symmetry - Helical parameters - Δ&Phi: 12.285 °
Applied symmetry - Helical parameters - Axial symmetry: D12 (2x12 fold dihedral)
Resolution.type: BY AUTHOR / Resolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 485376
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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