[English] 日本語
Yorodumi- PDB-6kif: Structure of cyanobacterial photosystem I-IsiA-flavodoxin supercomplex -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kif | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of cyanobacterial photosystem I-IsiA-flavodoxin supercomplex | ||||||
Components |
| ||||||
Keywords | PHOTOSYNTHESIS / Photosystem / Antenna / Chlorophyll-binding protein / Membrane protein / iron stress-induced protein A / Flavodoxin | ||||||
Function / homology | Function and homology information 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 / FMN binding / 4 iron, 4 sulfur cluster binding ...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 / FMN binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / magnesium ion binding / metal ion binding Similarity search - Function | ||||||
Biological species | Synechococcus elongatus (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å | ||||||
Authors | Cao, P. / Cao, D.F. / Si, L. / Su, X.D. / Chang, W.R. / Liu, Z.F. / Zhang, X.Z. / Li, M. | ||||||
Citation | Journal: Nat Plants / Year: 2020 Title: Structural basis for energy and electron transfer of the photosystem I-IsiA-flavodoxin supercomplex. Authors: Peng Cao / Duanfang Cao / Long Si / Xiaodong Su / Lijin Tian / Wenrui Chang / Zhenfeng Liu / Xinzheng Zhang / Mei Li / Abstract: Under iron-deficiency stress, which occurs frequently in natural aquatic environments, cyanobacteria reduce the amount of iron-enriched proteins, including photosystem I (PSI) and ferredoxin (Fd), ...Under iron-deficiency stress, which occurs frequently in natural aquatic environments, cyanobacteria reduce the amount of iron-enriched proteins, including photosystem I (PSI) and ferredoxin (Fd), and upregulate the expression of iron-stress-induced proteins A and B (IsiA and flavodoxin (Fld)). Multiple IsiAs function as the peripheral antennae that encircle the PSI core, whereas Fld replaces Fd as the electron receptor of PSI. Here, we report the structures of the PSI-IsiA-Fld and PSI-IsiA supercomplexes from Synechococcus sp. PCC 7942, revealing features that are different from the previously reported PSI structures, and a sophisticated pigment network that involves previously unobserved pigment molecules. Spectroscopic results demonstrated that IsiAs are efficient light harvesters for PSI. Three Flds bind symmetrically to the trimeric PSI core-we reveal the detailed interaction and the electron transport path between PSI and Fld. Our results provide a structural basis for understanding the mechanisms of light harvesting, energy transfer and electron transport of cyanobacterial PSI under stressed conditions. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6kif.cif.gz | 3.1 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6kif.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6kif.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kif_validation.pdf.gz | 41.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6kif_full_validation.pdf.gz | 44.1 MB | Display | |
Data in XML | 6kif_validation.xml.gz | 642.4 KB | Display | |
Data in CIF | 6kif_validation.cif.gz | 809.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/6kif ftp://data.pdbj.org/pub/pdb/validation_reports/ki/6kif | HTTPS FTP |
-Related structure data
Related structure data | 9994MC 9995C 6kigC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-Photosystem I ... , 10 types, 30 molecules AGeBHfCNgDOhEQiFRjISkJTlKUmLVn
#1: Protein | Mass: 83994.336 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Synechococcus elongatus (strain PCC 7942) (bacteria) Strain: PCC 7942 / References: UniProt: Q31LJ0, photosystem I #2: Protein | Mass: 81554.742 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Synechococcus elongatus (strain PCC 7942) (bacteria) Strain: PCC 7942 / References: UniProt: Q31LJ1, photosystem I #3: Protein | Mass: 8807.235 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Synechococcus elongatus (strain PCC 7942) (bacteria) Strain: PCC 7942 / References: UniProt: Q31QV2, photosystem I #4: Protein | Mass: 15536.583 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Synechococcus elongatus (strain PCC 7942) (bacteria) Strain: PCC 7942 / References: UniProt: Q31PI7 #5: Protein | Mass: 8147.134 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Synechococcus elongatus (strain PCC 7942) (bacteria) Strain: PCC 7942 / References: UniProt: Q31NL7 #6: Protein | Mass: 17125.742 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Synechococcus elongatus (strain PCC 7942) (bacteria) Strain: PCC 7942 / References: UniProt: Q31NT9 #7: Protein/peptide | Mass: 4002.733 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Synechococcus elongatus (strain PCC 7942) (bacteria) Strain: PCC 7942 / References: UniProt: P95823 #8: Protein/peptide | Mass: 4713.585 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Synechococcus elongatus (strain PCC 7942) (bacteria) Strain: PCC 7942 / References: UniProt: Q31NU0 #9: Protein | Mass: 8397.120 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Synechococcus elongatus (strain PCC 7942) (bacteria) Strain: PCC 7942 / References: UniProt: Q31PR9 #10: Protein | Mass: 17302.688 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Synechococcus elongatus (strain PCC 7942) (bacteria) Strain: PCC 7942 / References: UniProt: P95822 |
---|
-Protein , 2 types, 21 molecules PXp123456YZabcdqrstuv
#12: Protein | Mass: 18938.568 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus elongatus (strain PCC 7942) (bacteria) Strain: PCC 7942 / Gene: isiB, Synpcc7942_1541 / Production host: Escherichia coli (E. coli) / References: UniProt: P10340 #13: Protein | Mass: 37004.453 Da / Num. of mol.: 18 / Source method: isolated from a natural source Source: (natural) Synechococcus elongatus (strain PCC 7942) (bacteria) Strain: PCC 7942 / References: UniProt: P15347 |
---|
-Protein/peptide / Sugars , 2 types, 15 molecules MWo
#11: Protein/peptide | Mass: 3239.867 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Synechococcus elongatus (strain PCC 7942) (bacteria) Strain: PCC 7942 / References: photosystem I #19: Sugar | ChemComp-LMU / |
---|
-Non-polymers , 9 types, 885 molecules
#14: Chemical | ChemComp-CLA / #15: Chemical | ChemComp-PQN / #16: Chemical | ChemComp-SF4 / #17: Chemical | ChemComp-BCR / #18: Chemical | ChemComp-LHG / #20: Chemical | ChemComp-LMG / #21: Chemical | ChemComp-SQD / #22: Chemical | #23: Water | ChemComp-HOH / | |
---|
-Details
Has ligand of interest | N |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Photosystem I-IsiA-flavodoxin supercomplex / Type: COMPLEX / Entity ID: #1-#13 / Source: MULTIPLE SOURCES |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: Synechococcus elongatus PCC 7942 (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 50 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
---|---|
Symmetry | Point symmetry: C3 (3 fold cyclic) |
3D reconstruction | Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 29295 / Symmetry type: POINT |
Atomic model building | Space: REAL |