+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38419 | |||||||||
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Title | Structure of ACPII-CCPII from cryptophyte algae | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Photosystem II / PHOTOSYNTHESIS / STRUCTURAL PROTEIN | |||||||||
Biological species | Chroomonas placoidea (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.84 Å | |||||||||
Authors | Li XY / Mao ZY / Shen JR / Han GY | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structure and distinct supramolecular organization of a PSII-ACPII dimer from a cryptophyte alga Chroomonas placoidea. Authors: Zhiyuan Mao / Xingyue Li / Zhenhua Li / Liangliang Shen / Xiaoyi Li / Yanyan Yang / Wenda Wang / Tingyun Kuang / Jian-Ren Shen / Guangye Han / Abstract: Cryptophyte algae are an evolutionarily distinct and ecologically important group of photosynthetic unicellular eukaryotes. Photosystem II (PSII) of cryptophyte algae associates with alloxanthin ...Cryptophyte algae are an evolutionarily distinct and ecologically important group of photosynthetic unicellular eukaryotes. Photosystem II (PSII) of cryptophyte algae associates with alloxanthin chlorophyll a/c-binding proteins (ACPs) to act as the peripheral light-harvesting system, whose supramolecular organization is unknown. Here, we purify the PSII-ACPII supercomplex from a cryptophyte alga Chroomonas placoidea (C. placoidea), and analyze its structure at a resolution of 2.47 Å using cryo-electron microscopy. This structure reveals a dimeric organization of PSII-ACPII containing two PSII core monomers flanked by six symmetrically arranged ACPII subunits. The PSII core is conserved whereas the organization of ACPII subunits exhibits a distinct pattern, different from those observed so far in PSII of other algae and higher plants. Furthermore, we find a Chl a-binding antenna subunit, CCPII-S, which mediates interaction of ACPII with the PSII core. These results provide a structural basis for the assembly of antennas within the supercomplex and possible excitation energy transfer pathways in cryptophyte algal PSII, shedding light on the diversity of supramolecular organization of photosynthetic machinery. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38419.map.gz | 256.5 MB | EMDB map data format | |
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Header (meta data) | emd-38419-v30.xml emd-38419.xml | 23.7 KB 23.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_38419_fsc.xml | 16.8 KB | Display | FSC data file |
Images | emd_38419.png | 61.1 KB | ||
Filedesc metadata | emd-38419.cif.gz | 6.9 KB | ||
Others | emd_38419_half_map_1.map.gz emd_38419_half_map_2.map.gz | 474.4 MB 474.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38419 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38419 | HTTPS FTP |
-Validation report
Summary document | emd_38419_validation.pdf.gz | 907.8 KB | Display | EMDB validaton report |
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Full document | emd_38419_full_validation.pdf.gz | 907.4 KB | Display | |
Data in XML | emd_38419_validation.xml.gz | 26.2 KB | Display | |
Data in CIF | emd_38419_validation.cif.gz | 34.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38419 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38419 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_38419.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_38419_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_38419_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Structure of ACPII-CCPII from cryptophyte algae
+Supramolecule #1: Structure of ACPII-CCPII from cryptophyte algae
+Macromolecule #1: ACPII-4
+Macromolecule #2: ACPII-1
+Macromolecule #3: ACPII-2
+Macromolecule #4: ACPII-3
+Macromolecule #5: Photosystem II reaction center protein G
+Macromolecule #6: ACPII-6
+Macromolecule #7: ACPII-5
+Macromolecule #8: CCPII-S
+Macromolecule #9: CHLOROPHYLL A
+Macromolecule #10: Chlorophyll c2
+Macromolecule #11: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E}...
+Macromolecule #12: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E}...
+Macromolecule #13: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #14: (1~{R})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E}...
+Macromolecule #15: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #16: (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta...
+Macromolecule #17: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |