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- EMDB-31089: Cryo-EM structure of the octameric state of C-phycocyanin from Th... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-31089 | |||||||||||||||
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Title | Cryo-EM structure of the octameric state of C-phycocyanin from Thermoleptolyngbya sp. O-77 | |||||||||||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | ![]() ![]() | |||||||||||||||
![]() | Minato T / Teramoto T / Adachi N / Hung NK / Yamada K / Kawasaki M / Akutsu M / Moriya T / Senda T / Ogo S ...Minato T / Teramoto T / Adachi N / Hung NK / Yamada K / Kawasaki M / Akutsu M / Moriya T / Senda T / Ogo S / Kakuta Y / Yoon KS | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Non-conventional octameric structure of C-phycocyanin. Authors: Takuo Minato / Takamasa Teramoto / Naruhiko Adachi / Nguyen Khac Hung / Kaho Yamada / Masato Kawasaki / Masato Akutsu / Toshio Moriya / Toshiya Senda / Seiji Ogo / Yoshimitsu Kakuta / Ki-Seok Yoon / ![]() Abstract: C-phycocyanin (CPC), a blue pigment protein, is an indispensable component of giant phycobilisomes, which are light-harvesting antenna complexes in cyanobacteria that transfer energy efficiently to ...C-phycocyanin (CPC), a blue pigment protein, is an indispensable component of giant phycobilisomes, which are light-harvesting antenna complexes in cyanobacteria that transfer energy efficiently to photosystems I and II. X-ray crystallographic and electron microscopy (EM) analyses have revealed the structure of CPC to be a closed toroidal hexamer by assembling two trimers. In this study, the structural characterization of non-conventional octameric CPC is reported for the first time. Analyses of the crystal and cryogenic EM structures of the native CPC from filamentous thermophilic cyanobacterium Thermoleptolyngbya sp. O-77 unexpectedly illustrated the coexistence of conventional hexamer and novel octamer. In addition, an unusual dimeric state, observed via analytical ultracentrifugation, was postulated to be a key intermediate structure in the assemble of the previously unobserved octamer. These observations provide new insights into the assembly processes of CPCs and the mechanism of energy transfer in the light-harvesting complexes. | |||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 219.4 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.5 KB 18.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 14.2 KB | Display | ![]() |
Images | ![]() | 196.7 KB | ||
Masks | ![]() | 244.1 MB | ![]() | |
Others | ![]() ![]() | 189.5 MB 189.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7eh7MC ![]() 7efvC ![]() 7efwC ![]() 7eh8C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | |
EM raw data | ![]() Data size: 1.8 TB Data #1: Non-conventional octameric structure of C-phycocyanin [micrographs - multiframe]) |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 0.88 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_31089_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_31089_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : CPC octamer
Entire | Name: CPC octamer |
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Components |
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-Supramolecule #1: CPC octamer
Supramolecule | Name: CPC octamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: homo octamer |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 320 KDa |
-Macromolecule #1: C-phycocyanin alpha chain
Macromolecule | Name: C-phycocyanin alpha chain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Sequence | String: MKTPITEAIA AADTQGRFLS NTELQAVNGR FERAAASMEA ARALTNNAQQ LIDGAANAVY QKFPYTTQM QGANFASDSR GKSKCARDIG YYLRIITYSL VAGGTGPLDE YLIAGLDEIN R TFDLSPSW YVEALKYIKA NHGLSGQAAN EANTYIDYAI NALS |
-Macromolecule #2: C-phycocyanin beta chain
Macromolecule | Name: C-phycocyanin beta chain / type: protein_or_peptide / ID: 2 / Details: MEN: N-METHYL ASPARAGINE / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Sequence | String: MLDAFAKVVS QADTKGEFLS SAQLDALSNV VKDGSKRLDA VNRMTSNAST IVANAARSLF EEQPQLIQP GG(MEN)AYTNRRM AACLRDMEII LRYVTYATLA GDSSVLDDRC LNGLRETYQA L GVPGGSVA AGVAKMKDAA IAIVNDPNGI TKGDCSALVS EIASYFDRAA AAVA |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 6.7 mg/mL |
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Buffer | pH: 7 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: The grid was washed by acetone prior to use. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV / Details: Blotting time was 5 seconds (blot force 15). |
Details | This sample was mono-disperse. |
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Electron microscopy
Microscope | TFS TALOS |
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Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Sample stage | Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Number real images: 2036 / Average exposure time: 49.2 sec. / Average electron dose: 50.0 e/Å2 |