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Yorodumi- EMDB-27382: Helical rods of far-red light-absorbing allophycocyanin in Synech... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27382 | ||||||||||||||||||
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Title | Helical rods of far-red light-absorbing allophycocyanin in Synechococcus sp. | ||||||||||||||||||
Map data | Sharpened and masked far-red light allophycocyanin | ||||||||||||||||||
Sample |
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Function / homology | Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis / Globin-like superfamily / Allophycocyanin subunit beta / Allophycocyanin subunit alpha Function and homology information | ||||||||||||||||||
Biological species | Synechococcus sp. 63AY4M1 (bacteria) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.89 Å | ||||||||||||||||||
Authors | Gisriel CJ / Shen GS / Soulier NT / Flesher DA / Brudvig GW / Bryant DA | ||||||||||||||||||
Funding support | United States, 5 items
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Citation | Journal: Sci Adv / Year: 2023 Title: Helical allophycocyanin nanotubes absorb far-red light in a thermophilic cyanobacterium. Authors: Christopher J Gisriel / Eduard Elias / Gaozhong Shen / Nathan T Soulier / David A Flesher / M R Gunner / Gary W Brudvig / Roberta Croce / Donald A Bryant / Abstract: To compete in certain low-light environments, some cyanobacteria express a paralog of the light-harvesting phycobiliprotein, allophycocyanin (AP), that strongly absorbs far-red light (FRL). Using ...To compete in certain low-light environments, some cyanobacteria express a paralog of the light-harvesting phycobiliprotein, allophycocyanin (AP), that strongly absorbs far-red light (FRL). Using cryo-electron microscopy and time-resolved absorption spectroscopy, we reveal the structure-function relationship of this FRL-absorbing AP complex (FRL-AP) that is expressed during acclimation to low light and that likely associates with chlorophyll a-containing photosystem I. FRL-AP assembles as helical nanotubes rather than typical toroids due to alterations of the domain geometry within each subunit. Spectroscopic characterization suggests that FRL-AP nanotubes are somewhat inefficient antenna; however, the enhanced ability to harvest FRL when visible light is severely attenuated represents a beneficial trade-off. The results expand the known diversity of light-harvesting proteins in nature and exemplify how biological plasticity is achieved by balancing resource accessibility with efficiency. | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27382.map.gz | 7 MB | EMDB map data format | |
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Header (meta data) | emd-27382-v30.xml emd-27382.xml | 19.2 KB 19.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27382_fsc.xml | 9.4 KB | Display | FSC data file |
Images | emd_27382.png | 23.3 KB | ||
Others | emd_27382_additional_1.map.gz emd_27382_half_map_1.map.gz emd_27382_half_map_2.map.gz | 54.2 MB 54.5 MB 54.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27382 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27382 | HTTPS FTP |
-Validation report
Summary document | emd_27382_validation.pdf.gz | 803.3 KB | Display | EMDB validaton report |
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Full document | emd_27382_full_validation.pdf.gz | 802.9 KB | Display | |
Data in XML | emd_27382_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | emd_27382_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27382 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-27382 | HTTPS FTP |
-Related structure data
Related structure data | 8ddyMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_27382.map.gz / Format: CCP4 / Size: 70.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened and masked far-red light allophycocyanin | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Unsharpened
File | emd_27382_additional_1.map | ||||||||||||
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Annotation | Unsharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half1
File | emd_27382_half_map_1.map | ||||||||||||
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Annotation | Half1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half2
File | emd_27382_half_map_2.map | ||||||||||||
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Annotation | Half2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Far-red light allophycocyanin
Entire | Name: Far-red light allophycocyanin |
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Components |
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-Supramolecule #1: Far-red light allophycocyanin
Supramolecule | Name: Far-red light allophycocyanin / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Synechococcus sp. 63AY4M1 (bacteria) |
-Macromolecule #1: Allophycocyanin subunit alpha
Macromolecule | Name: Allophycocyanin subunit alpha / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Synechococcus sp. 63AY4M1 (bacteria) |
Molecular weight | Theoretical: 20.526518 KDa |
Recombinant expression | Organism: Synechococcus sp. PCC 7002 (bacteria) |
Sequence | String: MGHHHHHHHH HHSSGHIEGR HMQAAASMSI VAQVIAQSDA ADRFLSSAEI AKLEDFFSKG QVRIRAAQKL AENEQKIVQE GSKRFWAKC PNTPSNKGNP QKTALCQRDQ GWYIRLVSYC ILAGNDKPLE DIGLNGMREM YISLGVPLPN LRVAMSCLKE V AAGILSSE EMALAAPYFD RLIRAF |
-Macromolecule #2: Allophycocyanin subunit beta
Macromolecule | Name: Allophycocyanin subunit beta / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Synechococcus sp. 63AY4M1 (bacteria) |
Molecular weight | Theoretical: 17.712303 KDa |
Recombinant expression | Organism: Synechococcus sp. PCC 7002 (bacteria) |
Sequence | String: MKDTITSLIN PADEKGSYLD AAALEQLNRY FQSGNMRVKA AKTISSSASS IISKTVAKSL LYGDITLPGG (MEN)MYPTR RYA ACLRDLTYFL RYATYAMLAA DPSILDERVL QGLKETYITL GVPIDRVIQA LNAMKEVLTE SLDTEASQEM AVYLDHI IA GLS |
-Macromolecule #3: PHYCOCYANOBILIN
Macromolecule | Name: PHYCOCYANOBILIN / type: ligand / ID: 3 / Number of copies: 6 / Formula: CYC |
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Molecular weight | Theoretical: 588.694 Da |
Chemical component information | ChemComp-CYC: |
-Macromolecule #4: CHLORIDE ION
Macromolecule | Name: CHLORIDE ION / type: ligand / ID: 4 / Number of copies: 3 / Formula: CL |
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Molecular weight | Theoretical: 35.453 Da |
-Macromolecule #5: water
Macromolecule | Name: water / type: ligand / ID: 5 / Number of copies: 330 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7 |
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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 (6k x 4k) / Average electron dose: 59.8 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: 0.8 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |