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Yorodumi- EMDB-6743: Structure of M-LHCII and CP24 complexes in the stacked C2S2M2-typ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6743 | |||||||||||||||
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Title | Structure of M-LHCII and CP24 complexes in the stacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum | |||||||||||||||
Map data | None | |||||||||||||||
Sample |
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Keywords | Photosystem II / M-LHCII and CP24 complexes / PSII-LHCII / C2S2M2 supercomplex / MEMBRANE PROTEIN | |||||||||||||||
Function / homology | Function and homology information photosynthesis, light harvesting in photosystem II / PSII associated light-harvesting complex II / response to high light intensity / regulation of stomatal movement / plastoglobule / response to abscisic acid / photosynthesis, light harvesting in photosystem I / chloroplast envelope / photosystem I / response to herbicide ...photosynthesis, light harvesting in photosystem II / PSII associated light-harvesting complex II / response to high light intensity / regulation of stomatal movement / plastoglobule / response to abscisic acid / photosynthesis, light harvesting in photosystem I / chloroplast envelope / photosystem I / response to herbicide / photosystem II / chloroplast thylakoid membrane / chlorophyll binding / response to light stimulus / protein domain specific binding / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Pisum sativum (garden pea) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||||||||
Authors | Su XD / Ma J / Wei XP / Cao P / Zhu DJ / Chang WR / Liu ZF / Zhang XZ / Li M | |||||||||||||||
Funding support | China, 4 items
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Citation | Journal: Science / Year: 2017 Title: Structure and assembly mechanism of plant CSM-type PSII-LHCII supercomplex. Authors: Xiaodong Su / Jun Ma / Xuepeng Wei / Peng Cao / Dongjie Zhu / Wenrui Chang / Zhenfeng Liu / Xinzheng Zhang / Mei Li / Abstract: In plants, the photosynthetic machinery photosystem II (PSII) consists of a core complex associated with variable numbers of light-harvesting complexes II (LHCIIs). The supercomplex, comprising a ...In plants, the photosynthetic machinery photosystem II (PSII) consists of a core complex associated with variable numbers of light-harvesting complexes II (LHCIIs). The supercomplex, comprising a dimeric core and two strongly bound and two moderately bound LHCIIs (CSM), is the dominant form in plants acclimated to limited light. Here we report cryo-electron microscopy structures of two forms of CSM (termed stacked and unstacked) from at 2.7- and 3.2-angstrom resolution, respectively. In each CSM, the moderately bound LHCII assembles specifically with a peripheral antenna complex CP24-CP29 heterodimer and the strongly bound LHCII, to establish a pigment network that facilitates light harvesting at the periphery and energy transfer into the core. The high mobility of peripheral antennae, including the moderately bound LHCII and CP24, provides insights into functional regulation of plant PSII. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6743.map.gz | 11.1 MB | EMDB map data format | |
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Header (meta data) | emd-6743-v30.xml emd-6743.xml | 15.2 KB 15.2 KB | Display Display | EMDB header |
Images | emd_6743.png | 269.3 KB | ||
Filedesc metadata | emd-6743.cif.gz | 5.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6743 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6743 | HTTPS FTP |
-Validation report
Summary document | emd_6743_validation.pdf.gz | 557.8 KB | Display | EMDB validaton report |
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Full document | emd_6743_full_validation.pdf.gz | 557.4 KB | Display | |
Data in XML | emd_6743_validation.xml.gz | 5.3 KB | Display | |
Data in CIF | emd_6743_validation.cif.gz | 6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6743 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6743 | HTTPS FTP |
-Related structure data
Related structure data | 5xnnMC 6741C 6742C 6744C 5xnlC 5xnmC 5xnoC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_6743.map.gz / Format: CCP4 / Size: 12.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | None | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.04 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : M-LHCII and CP24 complexes in the stacked C2S2M2-type PSII-LHCII ...
+Supramolecule #1: M-LHCII and CP24 complexes in the stacked C2S2M2-type PSII-LHCII ...
+Macromolecule #1: Chlorophyll a-b binding protein 8, chloroplastic
+Macromolecule #2: Chlorophyll a-b binding protein, chloroplastic
+Macromolecule #3: Light harvesting chlorophyll a/b-binding protein Lhcb6, CP24
+Macromolecule #4: CHLOROPHYLL B
+Macromolecule #5: CHLOROPHYLL A
+Macromolecule #6: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
+Macromolecule #7: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...
+Macromolecule #8: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY...
+Macromolecule #9: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #10: BETA-CAROTENE
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.0 mg/mL |
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Buffer | pH: 5.7 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k 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 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 136521 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | PDB-5xnn: |