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- PDB-9tl8: Cryo-EM Structure of the LPOR:Chlide:NADPH Complexes (RD-A) - imp... -

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Basic information

Entry
Database: PDB / ID: 9tl8
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
ComponentsProtochlorophyllide reductase B, chloroplastic
KeywordsPHOTOSYNTHESIS / photoenzyme / chlorophyllide / oligomer
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
: / 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: 2.55 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: Gabruk, M. / Desfosses, A. / Estrozi, L.F. / Pintscher, S. / Rawski, M. / Wazny, G. / Garbacz, A. / Zbyradowski, M. / Kruk, J. / Fiedor, L.
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
Revision 1.0Aug 12, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Protochlorophyllide reductase B, chloroplastic
D: Protochlorophyllide reductase B, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,7688
Polymers76,4732
Non-polymers4,2956
Water1,02757
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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: PORB, At4g27440, F27G19.40 / Details (production host): 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.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-A1JWG / Chlorophyllide a


Mass: 614.973 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C35H34MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
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 LPOR:Chlide:NADPH Complexes (RD-A) - improved resolution of a dimer building block form RF-21, RF-23 and RF-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: 14.6 ° / Axial rise/subunit: 153.242 Å / Axial symmetry: D10
3D reconstructionResolution: 2.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1340624 / Symmetry type: HELICAL
Atomic model buildingPDB-ID: 7JK9

7jk9


Accession code: 7JK9 / Details: initial model / Source name: PDB / Type: experimental model
RefinementHighest resolution: 2.55 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0025210
ELECTRON MICROSCOPYf_angle_d0.547104
ELECTRON MICROSCOPYf_dihedral_angle_d8.435812
ELECTRON MICROSCOPYf_chiral_restr0.073790
ELECTRON MICROSCOPYf_plane_restr0.004882

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