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- PDB-9e7h: CryoEM structure of BchN-BchB bound to Pchlide from the DPOR unde... -

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Basic information

Entry
Database: PDB / ID: 9e7h
TitleCryoEM structure of BchN-BchB bound to Pchlide from the DPOR under turnover complex dataset
Components
  • Light-independent protochlorophyllide reductase subunit B
  • Light-independent protochlorophyllide reductase subunit N
KeywordsOXIDOREDUCTASE / Plant Protein / Electron transfer Enzymes / Photosynthesis
Function / homology
Function and homology information


ferredoxin:protochlorophyllide reductase (ATP-dependent) / photosynthesis, dark reaction / light-independent bacteriochlorophyll biosynthetic process / oxidoreductase activity, acting on iron-sulfur proteins as donors / oxidoreductase activity, acting on the CH-CH group of donors, iron-sulfur protein as acceptor / 4 iron, 4 sulfur cluster binding / ATP binding / metal ion binding
Similarity search - Function
Light-independent protochlorophyllide reductase, N subunit / : / Light-independent protochlorophyllide reductase, B subunit / Protochlorophyllide reductase, ChlB, light independent / Light-independent protochlorophyllide reductase subunit B-like, C-terminal / Proto-chlorophyllide reductase, C-terminal / Proto-chlorophyllide reductase 57 kD subunit / : / Nitrogenase/oxidoreductase, component 1 / Nitrogenase component 1 type Oxidoreductase
Similarity search - Domain/homology
COPPER (II) ION / Protochlorophyllide / IRON/SULFUR CLUSTER / Light-independent protochlorophyllide reductase subunit N / Light-independent protochlorophyllide reductase subunit B
Similarity search - Component
Biological speciesCereibacter sphaeroides (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.29 Å
AuthorsKashyap, R. / Antony, E.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-SC0020965 United States
CitationJournal: Nat Commun / Year: 2025
Title: Cryo-EM captures the coordination of asymmetric electron transfer through a di-copper site in DPOR.
Authors: Rajnandani Kashyap / Natalie Walsh / Jaigeeth Deveryshetty / Monika Tokmina-Lukaszewska / Kewei Zhao / Yunqiao J Gan / Brian M Hoffman / Ritimukta Sarangi / Brian Bothner / Brian Bennett / Edwin Antony /
Abstract: Enzymes that catalyze long-range electron transfer (ET) reactions often function as higher order complexes that possess two structurally symmetrical halves. The functional advantages for such an ...Enzymes that catalyze long-range electron transfer (ET) reactions often function as higher order complexes that possess two structurally symmetrical halves. The functional advantages for such an architecture remain a mystery. Using cryoelectron microscopy we capture snapshots of the nitrogenase-like dark-operative protochlorophyllide oxidoreductase (DPOR) during substrate binding and turnover. DPOR catalyzes reduction of the C17 = C18 double bond in protochlorophyllide during the dark chlorophyll biosynthetic pathway. DPOR is composed of electron donor (L-protein) and acceptor (NB-protein) component proteins that transiently form a complex in the presence of ATP to facilitate ET. NB-protein is an αβ heterotetramer with two structurally identical halves. However, our structures reveal that NB-protein becomes functionally asymmetric upon substrate binding. Asymmetry results in allosteric inhibition of L-protein engagement and ET in one half. Residues that form a conduit for ET are aligned in one half while misaligned in the other. An ATP hydrolysis-coupled conformational switch is triggered once ET is accomplished in one half. These structural changes are then relayed to the other half through a di-nuclear copper center at the tetrameric interface of the NB-protein and leads to activation of ET and substrate reduction. These findings provide a mechanistic blueprint for regulation of long-range electron transfer reactions.
History
DepositionNov 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2025Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 7, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1May 28, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 28, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Light-independent protochlorophyllide reductase subunit N
B: Light-independent protochlorophyllide reductase subunit B
C: Light-independent protochlorophyllide reductase subunit N
D: Light-independent protochlorophyllide reductase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,18210
Polymers209,1264
Non-polymers2,0566
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 Light-independent protochlorophyllide reductase subunit N / DPOR subunit N / LI-POR subunit N


Mass: 46188.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cereibacter sphaeroides (bacteria) / Gene: bchN, RSKD131_1611 / Production host: Escherichia coli (E. coli)
References: UniProt: B9KK24, ferredoxin:protochlorophyllide reductase (ATP-dependent)
#2: Protein Light-independent protochlorophyllide reductase subunit B / DPOR subunit B / LI-POR subunit B


Mass: 58374.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cereibacter sphaeroides (bacteria) / Gene: bchB, RSKD131_1612 / Production host: Escherichia coli (E. coli)
References: UniProt: B9KK25, ferredoxin:protochlorophyllide reductase (ATP-dependent)
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PMR / Protochlorophyllide


Mass: 612.957 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C35H32MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / 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: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CryoEM structure of BchN-BchB bound to Pchlide from the DPOR under turnover complex dataset
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.236 MDa / Experimental value: NO
Source (natural)Organism: Cereibacter sphaeroides (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3)Suf++ strain (PK11466)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.29 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 69816 / Symmetry type: POINT
RefinementHighest resolution: 3.29 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01912918
ELECTRON MICROSCOPYf_angle_d2.49117612
ELECTRON MICROSCOPYf_dihedral_angle_d12.481861
ELECTRON MICROSCOPYf_chiral_restr0.4031971
ELECTRON MICROSCOPYf_plane_restr0.0092287

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