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Open data
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Basic information
Entry | Database: PDB / ID: 7y3f | ||||||
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Title | Structure of the Anabaena PSI-monomer-IsiA supercomplex | ||||||
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![]() | PHOTOSYNTHESIS / Photosystem I / ELECTRON TRANSPORT / isiA | ||||||
Function / homology | ![]() photosystem I reaction center / photosystem I / photosystem I / photosynthetic electron transport chain / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthetic electron transport in photosystem I / photosynthesis / 4 iron, 4 sulfur cluster binding / oxidoreductase activity ...photosystem I reaction center / photosystem I / photosystem I / photosynthetic electron transport chain / plasma membrane-derived thylakoid membrane / chlorophyll binding / photosynthetic electron transport in photosystem I / photosynthesis / 4 iron, 4 sulfur cluster binding / oxidoreductase activity / electron transfer activity / magnesium ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.62 Å | ||||||
![]() | Nagao, R. / Kato, K. / Hamaguchi, T. / Kawakami, K. / Yonekura, K. / Shen, J.R. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of a monomeric photosystem I core associated with iron-stress-induced-A proteins from Anabaena sp. PCC 7120. Authors: Ryo Nagao / Koji Kato / Tasuku Hamaguchi / Yoshifumi Ueno / Naoki Tsuboshita / Shota Shimizu / Miyu Furutani / Shigeki Ehira / Yoshiki Nakajima / Keisuke Kawakami / Takehiro Suzuki / Naoshi ...Authors: Ryo Nagao / Koji Kato / Tasuku Hamaguchi / Yoshifumi Ueno / Naoki Tsuboshita / Shota Shimizu / Miyu Furutani / Shigeki Ehira / Yoshiki Nakajima / Keisuke Kawakami / Takehiro Suzuki / Naoshi Dohmae / Seiji Akimoto / Koji Yonekura / Jian-Ren Shen / ![]() Abstract: Iron-stress-induced-A proteins (IsiAs) are expressed in cyanobacteria under iron-deficient conditions. The cyanobacterium Anabaena sp. PCC 7120 has four isiA genes; however, their binding property ...Iron-stress-induced-A proteins (IsiAs) are expressed in cyanobacteria under iron-deficient conditions. The cyanobacterium Anabaena sp. PCC 7120 has four isiA genes; however, their binding property and functional roles in PSI are still missing. We analyzed a cryo-electron microscopy structure of a PSI-IsiA supercomplex isolated from Anabaena grown under an iron-deficient condition. The PSI-IsiA structure contains six IsiA subunits associated with the PsaA side of a PSI core monomer. Three of the six IsiA subunits were identified as IsiA1 and IsiA2. The PSI-IsiA structure lacks a PsaL subunit; instead, a C-terminal domain of IsiA2 occupies the position of PsaL, which inhibits the oligomerization of PSI, leading to the formation of a PSI monomer. Furthermore, excitation-energy transfer from IsiAs to PSI appeared with a time constant of 55 ps. These findings provide insights into both the molecular assembly of the Anabaena IsiA family and the functional roles of IsiAs. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 980.2 KB | Display | ![]() |
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PDB format | ![]() | 848.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 11.4 MB | Display | ![]() |
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Full document | ![]() | 12.1 MB | Display | |
Data in XML | ![]() | 215.1 KB | Display | |
Data in CIF | ![]() | 280.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 33593MC 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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1 |
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Components
-Photosystem I ... , 10 types, 10 molecules ABCDEFIJX1
#1: Protein | Mass: 83289.680 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 83457.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Protein | Mass: 8825.206 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#4: Protein | Mass: 15176.240 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#5: Protein | Mass: 7897.051 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#6: Protein | Mass: 17850.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#7: Protein/peptide | Mass: 5066.925 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#8: Protein/peptide | Mass: 5499.422 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#11: Protein/peptide | Mass: 4872.792 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#12: Protein | Mass: 51717.449 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein , 3 types, 6 molecules K23645
#9: Protein | Mass: 6996.616 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Authors do not know the sequence. / Source: (natural) ![]() | ||
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#13: Protein | Mass: 27676.963 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: Authors do not know the sequence. / Source: (natural) ![]() #14: Protein | Mass: 37701.469 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein/peptide / Sugars , 2 types, 7 molecules M![](data/chem/img/LMT.gif)
![](data/chem/img/LMT.gif)
#10: Protein/peptide | Mass: 4424.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#21: Sugar | ChemComp-LMT / |
-Non-polymers , 8 types, 221 molecules ![](data/chem/img/CL0.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/PQN.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CLA.gif)
![](data/chem/img/PQN.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/BCR.gif)
![](data/chem/img/LHG.gif)
![](data/chem/img/LMG.gif)
![](data/chem/img/HOH.gif)
#15: Chemical | ChemComp-CL0 / | ||||||||||||
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#16: Chemical | ChemComp-CLA / #17: Chemical | #18: Chemical | #19: Chemical | ChemComp-BCR / #20: Chemical | ChemComp-LHG / #22: Chemical | ChemComp-LMG / | #23: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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-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: PSI-monomer-IsiA / Type: COMPLEX / Entity ID: #1-#8, #10-#14 / Source: NATURAL | |||||||||||||||
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Molecular weight | Value: 0.64 MDa / Experimental value: NO | |||||||||||||||
Source (natural) | Organism: ![]() | |||||||||||||||
Buffer solution | pH: 6.5 | |||||||||||||||
Buffer component |
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Specimen | Conc.: 1.68 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R0.6/1 | |||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 11.7 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47602 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: RECIPROCAL |