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- PDB-9tlk: Cryo-EM Structure of the oligomeric LPOR:Chlide:NADPH Complexes HF-25 -

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Basic information

Entry
Database: PDB / ID: 9tlk
TitleCryo-EM Structure of the oligomeric LPOR:Chlide:NADPH Complexes HF-25
ComponentsProtochlorophyllide reductase B, chloroplastic
KeywordsPHOTOSYNTHESIS / photoenzyme / chlorophyllide / oligomer
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
: / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-NDP / Protochlorophyllide reductase B, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsGabruk, M. / Desfosses, A. / Estrozi, L.F. / Pintscher, S. / Rawski, M.
Funding support Poland, 1items
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, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 12, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Aug 12, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 12, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2026Group: Data collection / Database references / Category: citation / em_admin
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Revision 1.1Sep 16, 2026Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin
Data content type: EM metadata / EM metadata ...EM metadata / EM metadata / EM metadata / EM metadata
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AA: Protochlorophyllide reductase B, chloroplastic
AB: Protochlorophyllide reductase B, chloroplastic
AC: Protochlorophyllide reductase B, chloroplastic
AD: Protochlorophyllide reductase B, chloroplastic
AE: Protochlorophyllide reductase B, chloroplastic
AF: Protochlorophyllide reductase B, chloroplastic
AG: Protochlorophyllide reductase B, chloroplastic
AH: Protochlorophyllide reductase B, chloroplastic
AI: Protochlorophyllide reductase B, chloroplastic
AJ: Protochlorophyllide reductase B, chloroplastic
AK: Protochlorophyllide reductase B, chloroplastic
AL: Protochlorophyllide reductase B, chloroplastic
BA: Protochlorophyllide reductase B, chloroplastic
BB: Protochlorophyllide reductase B, chloroplastic
BC: Protochlorophyllide reductase B, chloroplastic
BD: Protochlorophyllide reductase B, chloroplastic
BE: Protochlorophyllide reductase B, chloroplastic
BF: Protochlorophyllide reductase B, chloroplastic
BG: Protochlorophyllide reductase B, chloroplastic
BH: Protochlorophyllide reductase B, chloroplastic
BI: Protochlorophyllide reductase B, chloroplastic
BJ: Protochlorophyllide reductase B, chloroplastic
BK: Protochlorophyllide reductase B, chloroplastic
BL: Protochlorophyllide reductase B, chloroplastic
CA: Protochlorophyllide reductase B, chloroplastic
CB: Protochlorophyllide reductase B, chloroplastic
CC: Protochlorophyllide reductase B, chloroplastic
CD: Protochlorophyllide reductase B, chloroplastic
CE: Protochlorophyllide reductase B, chloroplastic
CF: Protochlorophyllide reductase B, chloroplastic
CG: Protochlorophyllide reductase B, chloroplastic
CH: Protochlorophyllide reductase B, chloroplastic
CI: Protochlorophyllide reductase B, chloroplastic
CJ: Protochlorophyllide reductase B, chloroplastic
CK: Protochlorophyllide reductase B, chloroplastic
CL: Protochlorophyllide reductase B, chloroplastic
DA: Protochlorophyllide reductase B, chloroplastic
DB: Protochlorophyllide reductase B, chloroplastic
DC: Protochlorophyllide reductase B, chloroplastic
DD: Protochlorophyllide reductase B, chloroplastic
DE: Protochlorophyllide reductase B, chloroplastic
DF: Protochlorophyllide reductase B, chloroplastic
DG: Protochlorophyllide reductase B, chloroplastic
DH: Protochlorophyllide reductase B, chloroplastic
DI: Protochlorophyllide reductase B, chloroplastic
DJ: Protochlorophyllide reductase B, chloroplastic
DK: Protochlorophyllide reductase B, chloroplastic
DL: Protochlorophyllide reductase B, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,938,426192
Polymers1,835,34448
Non-polymers103,082144
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein ...
Protochlorophyllide reductase B, chloroplastic / PCR B / NADPH-protochlorophyllide oxidoreductase B / POR B


Mass: 38236.324 Da / Num. of mol.: 48
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PORB, At4g27440, F27G19.40 / Plasmid: pET15b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pRIL / References: UniProt: P21218, protochlorophyllide reductase
#2: Chemical...
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical...
ChemComp-A1JWG / Chlorophyllide a


Mass: 614.973 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: C35H34MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Cryo-EM Structure of the oligomeric LPOR:Chlide:NADPH Complexes HF-25
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3)pRIL / Plasmid: pET15b
Buffer solutionpH: 7.1
Buffer component
IDConc.NameFormulaBuffer-ID
137 mMsodium phosphateNa2HPO41
2225 mMsodium chlorideNaCl1
3150 mMimidazoleimidazole1
45 mM2-mercaptoethanol2-mercaptoethanol1
525 %glycerolglycerol1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: 28 uM AtPORB, 40 uM Chlorophyllide, 600 uM NADPH, 230 uM lipids (50mol% MGDG, 35mol% DGDG, 15mol% PG)
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 294 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2100 nm / Nominal defocus min: 900 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.3particle selection
9PHENIX1.21.2_5419model refinement
13cryoSPARC4.33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -114.391 ° / Axial rise/subunit: 25.609 Å / Axial symmetry: D4
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23139 / Symmetry type: HELICAL
Atomic model buildingPDB-ID: 7JK9

7jk9


Accession code: 7JK9 / Details: initial model / Source name: PDB / Type: experimental model

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