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- EMDB-56055: Cryo-EM Structure of the oligomeric LPOR:Chlide:NADPH Complexes HF-23 -

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Basic information

Entry
Database: EMDB / ID: EMD-56055
TitleCryo-EM Structure of the oligomeric LPOR:Chlide:NADPH Complexes HF-23
Map dataprimary
Sample
  • Complex: Cryo-EM Structure of the oligomeric LPOR:Chlide:NADPH Complexes HF-23
    • Protein or peptide: Protochlorophyllide reductase B, chloroplastic
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: Chlorophyllide a
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: 3.03 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: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
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_56055.png

Downloads & links

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Map

FileDownload / File: emd_56055.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: 0.11
Minimum - Maximum-0.22250567 - 0.51907563
Average (Standard dev.)0.0011059364 (±0.024287432)
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_56055_additional_1.map
Annotationsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half B

Fileemd_56055_half_map_1.map
Annotationhalf B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half A

Fileemd_56055_half_map_2.map
Annotationhalf A
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 oligomeric LPOR:Chlide:NADPH Complexes HF-23

EntireName: Cryo-EM Structure of the oligomeric LPOR:Chlide:NADPH Complexes HF-23
Components
  • Complex: Cryo-EM Structure of the oligomeric LPOR:Chlide:NADPH Complexes HF-23
    • Protein or peptide: Protochlorophyllide reductase B, chloroplastic
  • Ligand: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: Chlorophyllide a

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Supramolecule #1: Cryo-EM Structure of the oligomeric LPOR:Chlide:NADPH Complexes HF-23

SupramoleculeName: Cryo-EM Structure of the oligomeric LPOR:Chlide:NADPH Complexes HF-23
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: 44 / 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: 44 / 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: 44 / 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: 44 / Formula: A1JWG
Molecular weightTheoretical: 614.973 Da

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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

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 40.39 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: 6.857 Å
Applied symmetry - Helical parameters - Δ&Phi: -96.375 °
Applied symmetry - Helical parameters - Axial symmetry: D1 (2x1 fold dihedral)
Resolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.3) / Number images used: 70789
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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