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Yorodumi- PDB-7ext: Cryo-EM structure of cyanobacterial phycobilisome from Synechococ... -
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-Basic information
Entry | Database: PDB / ID: 7ext | ||||||
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Title | Cryo-EM structure of cyanobacterial phycobilisome from Synechococcus sp. PCC 7002 | ||||||
Components |
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Keywords | PHOTOSYNTHESIS / Phycobilisome / Synechococcus sp. PCC 7002 / Cryo-EM | ||||||
Function / homology | Function and homology information Lyases / : / phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis / lyase activity Similarity search - Function | ||||||
Biological species | Synechococcus sp. PCC 7002 (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Zheng, L. / Zheng, Z. / Li, X. / Wang, G. / Zhang, K. / Wei, P. / Zhao, J. / Gao, N. | ||||||
Funding support | 1items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structural insight into the mechanism of energy transfer in cyanobacterial phycobilisomes. Authors: Lvqin Zheng / Zhenggao Zheng / Xiying Li / Guopeng Wang / Kun Zhang / Peijun Wei / Jindong Zhao / Ning Gao / Abstract: Phycobilisomes (PBS) are the major light-harvesting machineries for photosynthesis in cyanobacteria and red algae and they have a hierarchical structure of a core and peripheral rods, with both ...Phycobilisomes (PBS) are the major light-harvesting machineries for photosynthesis in cyanobacteria and red algae and they have a hierarchical structure of a core and peripheral rods, with both consisting of phycobiliproteins and linker proteins. Here we report the cryo-EM structures of PBS from two cyanobacterial species, Anabaena 7120 and Synechococcus 7002. Both PBS are hemidiscoidal in shape and share a common triangular core structure. While the Anabaena PBS has two additional hexamers in the core linked by the 4th linker domain of ApcE (L). The PBS structures predict that, compared with the PBS from red algae, the cyanobacterial PBS could have more direct routes for energy transfer to ApcD. Structure-based systematic mutagenesis analysis of the chromophore environment of ApcD and ApcF subunits reveals that aromatic residues are critical to excitation energy transfer (EET). The structures also suggest that the linker protein could actively participate in the process of EET in both rods and the cores. These results provide insights into the organization of chromophores and the mechanisms of EET within cyanobacterial PBS. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7ext.cif.gz | 6.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7ext.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7ext.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ext_validation.pdf.gz | 19.2 MB | Display | wwPDB validaton report |
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Full document | 7ext_full_validation.pdf.gz | 26 MB | Display | |
Data in XML | 7ext_validation.xml.gz | 1.1 MB | Display | |
Data in CIF | 7ext_validation.cif.gz | 1.4 MB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ex/7ext ftp://data.pdbj.org/pub/pdb/validation_reports/ex/7ext | HTTPS FTP |
-Related structure data
Related structure data | 31373MC 7eydC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Phycobilisome ... , 3 types, 24 molecules A1A2A4A5A6A8N1a1N2a2N4a4N5a5N6a6N8a82333G7N7U7b7
#1: Protein | Mass: 28540.152 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002 / Gene: cpcG / Production host: Synechococcus sp. PCC 7002 (bacteria) / References: UniProt: Q05238 #4: Protein | Mass: 32308.896 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002 / Gene: cpcC / Production host: Synechococcus sp. PCC 7002 (bacteria) / References: UniProt: Q05237 #6: Protein | Mass: 7806.188 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002 / Gene: apcC / Production host: Synechococcus sp. PCC 7002 (bacteria) / References: UniProt: O68971 |
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-C-phycocyanin subunit ... , 2 types, 144 molecules B1D1F1H1J1L1O1Q1S1U1W1Y1B2D2F2H2J2L2O2Q2S2U2W2Y2B4D4F4H4J4L4...
#2: Protein | Mass: 17637.695 Da / Num. of mol.: 72 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002 / Gene: cpcA / Production host: Synechococcus sp. PCC 7002 (bacteria) / References: UniProt: P03943 #3: Protein | Mass: 18353.852 Da / Num. of mol.: 72 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002 / Gene: cpcB / Production host: Synechococcus sp. PCC 7002 (bacteria) / References: UniProt: P03944 |
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-Allophycocyanin ... , 4 types, 70 molecules G3I3K3N3P3R3T3X3Z3b3d3f3i3k3o3q3s3u3w3y3A7C7E7H7J7L7O7Q7S7V7...
#7: Protein | Mass: 17302.660 Da / Num. of mol.: 32 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002 / Gene: apcA / Production host: Synechococcus sp. PCC 7002 (bacteria) / References: UniProt: B1XQM2 #8: Protein | Mass: 17237.590 Da / Num. of mol.: 34 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002 / Gene: apcB / Production host: Synechococcus sp. PCC 7002 (bacteria) / References: UniProt: O68970 #9: Protein | Mass: 18742.137 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002 / Gene: apcF / Production host: Synechococcus sp. PCC 7002 (bacteria) / References: UniProt: O68967 #10: Protein | Mass: 17721.270 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002 / Gene: apcD / Production host: Synechococcus sp. PCC 7002 (bacteria) / References: UniProt: O68966 |
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-Protein / Non-polymers , 2 types, 290 molecules 0313
#11: Chemical | ChemComp-CYC / #5: Protein | Mass: 99391.656 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechococcus sp. PCC 7002 (bacteria) / Strain: PCC 7002 / Gene: apcE / Production host: Synechococcus sp. PCC 7002 (bacteria) / References: UniProt: O68973, Lyases |
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-Details
Has ligand of interest | Y |
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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 |
-Sample preparation
Component | Name: Cryo-EM structure of cyanobacterial phycobilisome from Synechococcus sp. PCC 7002 Type: COMPLEX / Entity ID: #1-#10 / Source: NATURAL |
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Molecular weight | Value: 6 MDa |
Source (natural) | Organism: Synechococcus sp. PCC 7002 (bacteria) |
Buffer solution | pH: 7 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 64 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 64268 / Symmetry type: POINT |