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Yorodumi- EMDB-6741: Structure of stacked C2S2M2-type PSII-LHCII supercomplex from Pis... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6741 | |||||||||||||||
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Title | Structure of stacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum | |||||||||||||||
Map data | Structure of stacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum | |||||||||||||||
Sample |
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Keywords | Photosystem II / 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 / photosynthesis, light harvesting / response to abscisic acid / photosystem II oxygen evolving complex / photosynthesis, light harvesting in photosystem I / photosystem II assembly ...photosynthesis, light harvesting in photosystem II / PSII associated light-harvesting complex II / response to high light intensity / regulation of stomatal movement / plastoglobule / photosynthesis, light harvesting / response to abscisic acid / photosystem II oxygen evolving complex / photosynthesis, light harvesting in photosystem I / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II / photosystem II reaction center / chloroplast envelope / photosystem I / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / extrinsic component of membrane / photosystem II / photosynthesis, light reaction / chloroplast thylakoid membrane / phosphate ion binding / chlorophyll binding / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthetic electron transport in photosystem II / response to light stimulus / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / protein domain specific binding / calcium ion binding / heme binding / metal ion binding Similarity search - Function | |||||||||||||||
Biological species | Pisum sativum (garden pea) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | |||||||||||||||
Authors | Su XD / Ma J | |||||||||||||||
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_6741.map.gz | 96.2 MB | EMDB map data format | |
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Header (meta data) | emd-6741-v30.xml emd-6741.xml | 39.8 KB 39.8 KB | Display Display | EMDB header |
Images | emd_6741.png | 478.9 KB | ||
Filedesc metadata | emd-6741.cif.gz | 9.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6741 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6741 | HTTPS FTP |
-Validation report
Summary document | emd_6741_validation.pdf.gz | 692.5 KB | Display | EMDB validaton report |
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Full document | emd_6741_full_validation.pdf.gz | 692.1 KB | Display | |
Data in XML | emd_6741_validation.xml.gz | 6.8 KB | Display | |
Data in CIF | emd_6741_validation.cif.gz | 7.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6741 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6741 | HTTPS FTP |
-Related structure data
Related structure data | 5xnlMC 6742C 6743C 6744C 5xnmC 5xnnC 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_6741.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Structure of stacked C2S2M2-type PSII-LHCII supercomplex from Pisum sativum | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 : C2S2M2-type PSII-LHCII supercomplex from Pisum sativum
+Supramolecule #1: C2S2M2-type PSII-LHCII supercomplex from Pisum sativum
+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: Photosystem II protein D1
+Macromolecule #5: Photosystem II CP47 reaction center protein
+Macromolecule #6: Photosystem II CP43 reaction center protein
+Macromolecule #7: Photosystem II D2 protein
+Macromolecule #8: Cytochrome b559 subunit alpha
+Macromolecule #9: Cytochrome b559 subunit beta, PsbF
+Macromolecule #10: Photosystem II reaction center protein H
+Macromolecule #11: Photosystem II reaction center protein I, PsbI
+Macromolecule #12: Photosystem II reaction center protein J
+Macromolecule #13: Photosystem II reaction center protein K
+Macromolecule #14: Photosystem II reaction center protein L
+Macromolecule #15: Photosystem II reaction center protein M
+Macromolecule #16: Oxygen-evolving enhancer protein 1, chloroplastic
+Macromolecule #17: Oxygen-evolving enhancer protein 2, chloroplastic
+Macromolecule #18: Oxygen-evolving enhancer protein 3
+Macromolecule #19: Light harvesting chlorophyll a/b-binding protein Lhcb4, CP29
+Macromolecule #20: Light harvesting chlorophyll a/b-binding protein Lhcb5, CP26
+Macromolecule #21: Photosystem II reaction center protein T
+Macromolecule #22: Photosystem II reaction center protein W
+Macromolecule #23: Photosystem II reaction center protein X
+Macromolecule #24: Photosystem II reaction center protein Z
+Macromolecule #25: CHLOROPHYLL B
+Macromolecule #26: CHLOROPHYLL A
+Macromolecule #27: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
+Macromolecule #28: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...
+Macromolecule #29: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY...
+Macromolecule #30: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
+Macromolecule #31: BETA-CAROTENE
+Macromolecule #32: CA-MN4-O5 CLUSTER
+Macromolecule #33: FE (II) ION
+Macromolecule #34: CHLORIDE ION
+Macromolecule #35: PHEOPHYTIN A
+Macromolecule #36: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
+Macromolecule #37: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
+Macromolecule #38: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...
+Macromolecule #39: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
+Macromolecule #40: BICARBONATE ION
+Macromolecule #41: PROTOPORPHYRIN IX CONTAINING FE
+Macromolecule #42: water
-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: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 136521 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: PROJECTION MATCHING |
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | PDB-5xnl: |