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Open data
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Basic information
Entry | Database: PDB / ID: 9buo | ||||||
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Title | CryoEM structure of DPOR in the presence of ADP-AlF3 | ||||||
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![]() | OXIDOREDUCTASE / Plant Protein / Electron Transfer Enzymes / Photosynthesis | ||||||
Function / homology | ![]() 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 | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.68 Å | ||||||
![]() | Kashyap, R. / Antony, E. | ||||||
Funding support | ![]()
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![]() | ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 469.2 KB | Display | ![]() |
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PDB format | ![]() | 376.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.8 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 104.5 KB | Display | |
Data in CIF | ![]() | 157.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 44913MC ![]() 8vqhC ![]() 8vqiC ![]() 8vqjC ![]() 9e7hC ![]() 9efuC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Components
-Protein , 1 types, 4 molecules GHEF
#1: Protein | Mass: 34850.340 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9RFD6, ferredoxin:protochlorophyllide reductase (ATP-dependent) |
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-Light-independent protochlorophyllide reductase subunit ... , 2 types, 4 molecules ACBD
#2: Protein | Mass: 46188.773 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: B9KK24, ferredoxin:protochlorophyllide reductase (ATP-dependent) #3: Protein | Mass: 58302.234 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q9Z5D9, ferredoxin:protochlorophyllide reductase (ATP-dependent) |
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-Non-polymers , 3 types, 8 molecules 




#4: Chemical | ChemComp-SF4 / #5: Chemical | #6: Chemical | |
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-Details
Has ligand of interest | Y |
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Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: CryoEM structure of DPOR in the presence of ADP-AlF3 / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT |
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Molecular weight | Value: 0.3478 MDa / Experimental value: YES |
Source (natural) | Organism: ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: 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 |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: 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 recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
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Processing
CTF correction | Type: NONE | ||||||||||||||||||||||||
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3D reconstruction | Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 20571 / Symmetry type: POINT | ||||||||||||||||||||||||
Refinement | Highest resolution: 3.68 Å Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS) | ||||||||||||||||||||||||
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