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Yorodumi- EMDB-41435: Central rod disk in C1 symmetry of high-resolution phycobilisome ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41435 | |||||||||||||||
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Title | Central rod disk in C1 symmetry of high-resolution phycobilisome quenched by OCP (local refinement) | |||||||||||||||
Map data | sharpened map | |||||||||||||||
Sample |
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Keywords | Complex / light harvesting / pigment / PHOTOSYNTHESIS | |||||||||||||||
Function / homology | Function and homology information phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis Similarity search - Function | |||||||||||||||
Biological species | Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) / Synechocystis sp. PCC 6803 (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 1.87 Å | |||||||||||||||
Authors | Sauer PV / Sutter M / Cupellini L / Kirst H / Kerfeld CA | |||||||||||||||
Funding support | European Union, United States, Czech Republic, 4 items
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Citation | Journal: Sci Adv / Year: 2024 Title: Structural and quantum chemical basis for OCP-mediated quenching of phycobilisomes. Authors: Paul V Sauer / Lorenzo Cupellini / Markus Sutter / Mattia Bondanza / María Agustina Domínguez Martin / Henning Kirst / David Bína / Adrian Fujiet Koh / Abhay Kotecha / Basil J Greber / ...Authors: Paul V Sauer / Lorenzo Cupellini / Markus Sutter / Mattia Bondanza / María Agustina Domínguez Martin / Henning Kirst / David Bína / Adrian Fujiet Koh / Abhay Kotecha / Basil J Greber / Eva Nogales / Tomáš Polívka / Benedetta Mennucci / Cheryl A Kerfeld / Abstract: Cyanobacteria use large antenna complexes called phycobilisomes (PBSs) for light harvesting. However, intense light triggers non-photochemical quenching, where the orange carotenoid protein (OCP) ...Cyanobacteria use large antenna complexes called phycobilisomes (PBSs) for light harvesting. However, intense light triggers non-photochemical quenching, where the orange carotenoid protein (OCP) binds to PBS, dissipating excess energy as heat. The mechanism of efficiently transferring energy from phycocyanobilins in PBS to canthaxanthin in OCP remains insufficiently understood. Using cryo-electron microscopy, we unveiled the OCP-PBS complex structure at 1.6- to 2.1-angstrom resolution, showcasing its inherent flexibility. Using multiscale quantum chemistry, we disclosed the quenching mechanism. Identifying key protein residues, we clarified how canthaxanthin's transition dipole moment in its lowest-energy dark state becomes large enough for efficient energy transfer from phycocyanobilins. Our energy transfer model offers a detailed understanding of the atomic determinants of light harvesting regulation and antenna architecture in cyanobacteria. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41435.map.gz | 483.7 MB | EMDB map data format | |
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Header (meta data) | emd-41435-v30.xml emd-41435.xml | 22.2 KB 22.2 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41435_fsc.xml | 16.7 KB | Display | FSC data file |
Images | emd_41435.png | 70.8 KB | ||
Masks | emd_41435_msk_1.map | 512 MB | Mask map | |
Filedesc metadata | emd-41435.cif.gz | 6.4 KB | ||
Others | emd_41435_additional_1.map.gz emd_41435_half_map_1.map.gz emd_41435_half_map_2.map.gz | 258.3 MB 474.5 MB 474.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41435 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41435 | HTTPS FTP |
-Validation report
Summary document | emd_41435_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_41435_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_41435_validation.xml.gz | 26.4 KB | Display | |
Data in CIF | emd_41435_validation.cif.gz | 34.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41435 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41435 | HTTPS FTP |
-Related structure data
Related structure data | 8to5MC 8to2C 8tpjC 8troC C: citing same article (ref.) M: atomic model generated by this map |
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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_41435.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | sharpened map | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.727 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_41435_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: refined map
File | emd_41435_additional_1.map | ||||||||||||
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Annotation | refined map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_41435_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41435_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of phycobilisome from Synechocystis PCC 6803 bound to OCP
Entire | Name: Complex of phycobilisome from Synechocystis PCC 6803 bound to OCP |
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Components |
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-Supramolecule #1: Complex of phycobilisome from Synechocystis PCC 6803 bound to OCP
Supramolecule | Name: Complex of phycobilisome from Synechocystis PCC 6803 bound to OCP type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) |
-Macromolecule #1: C-phycocyanin alpha subunit
Macromolecule | Name: C-phycocyanin alpha subunit / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Synechocystis sp. PCC 6803 (bacteria) |
Molecular weight | Theoretical: 17.602529 KDa |
Sequence | String: MKTPLTEAVS TADSQGRFLS STELQIAFGR LRQANAGLQA AKALTDNAQS LVNGAAQAVY NKFPYTTQTQ GNNFAADQRG KDKCARDIG YYLRIVTYCL VAGGTGPLDE YLIAGIDEIN RTFDLSPSWY VEALKYIKAN HGLSGDARDE ANSYLDYAIN A LS UniProtKB: C-phycocyanin alpha subunit |
-Macromolecule #2: C-phycocyanin beta subunit
Macromolecule | Name: C-phycocyanin beta subunit / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO |
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Source (natural) | Organism: Synechocystis sp. PCC 6803 (bacteria) |
Molecular weight | Theoretical: 18.156451 KDa |
Sequence | String: MFDVFTRVVS QADARGEYLS GSQLDALSAT VAEGNKRIDS VNRITGNASA IVSNAARALF AEQPQLIQPG G(MEN)AYTS RRM AACLRDMEII LRYVTYATFT GDASVLEDRC LNGLRETYVA LGVPGASVAA GVQKMKEAAL DIVNDPNGIT RGDCSAI VA EIAGYFDRAA AAVA UniProtKB: C-phycocyanin beta subunit |
-Macromolecule #3: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated...
Macromolecule | Name: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1 type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Synechocystis sp. PCC 6803 (bacteria) |
Molecular weight | Theoretical: 32.558607 KDa |
Sequence | String: MAITTAASRL GVAPYNESRP VELRPDFSLD DAKMVIRAVY RQVLGNDYIM DSERLKGAES LLTNGSISVR EFVRTVAKSE LYKKKFLYN NFQTRVIELN YKHLLGRAPF SEDEVIFHLD LYENQGFDAD IDSYIDSVEY QENFGENIVP YYRFNNQVGD R TVGFTRMF ...String: MAITTAASRL GVAPYNESRP VELRPDFSLD DAKMVIRAVY RQVLGNDYIM DSERLKGAES LLTNGSISVR EFVRTVAKSE LYKKKFLYN NFQTRVIELN YKHLLGRAPF SEDEVIFHLD LYENQGFDAD IDSYIDSVEY QENFGENIVP YYRFNNQVGD R TVGFTRMF RLYRGYANSD RSQLERSSSR LATELGQNTV SAIVGPSGSN AGWAYRPSRA GNTPAKALGG TVPFGQASKL FR VEITAIS APGYPKVRRS NKAVIVPFEQ LNQTLQQINR LGGKVASITP ASLS UniProtKB: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1 |
-Macromolecule #4: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated...
Macromolecule | Name: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2 type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Synechocystis sp. PCC 6803 (bacteria) |
Molecular weight | Theoretical: 30.836346 KDa |
Sequence | String: MTSLVSAQRL GIVAVDEAIP LELRSRSTEE EVDAVILAVY RQVLGNDHLM SQERLTSAES LLRGREISVR DFVRAVALSE VYRQKFFHS NPQNRFIELN YKHLLGRAPY DQSEIAFHTD LYHQGGYEAE INSYIDSVEY TENFGDWVVP YFRGFATQRN Q KTVGFSRS ...String: MTSLVSAQRL GIVAVDEAIP LELRSRSTEE EVDAVILAVY RQVLGNDHLM SQERLTSAES LLRGREISVR DFVRAVALSE VYRQKFFHS NPQNRFIELN YKHLLGRAPY DQSEIAFHTD LYHQGGYEAE INSYIDSVEY TENFGDWVVP YFRGFATQRN Q KTVGFSRS FQVYRGYATS DRSQGNGSRS RLTRELARNT ASPVYAGSTA ESLRGTSAGS RNQMYRLQVI QGAAPGRGTR VR RGKAEYL VSYDNLSAKL QQINRQGDTV TMISLA UniProtKB: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2 |
-Macromolecule #5: PHYCOCYANOBILIN
Macromolecule | Name: PHYCOCYANOBILIN / type: ligand / ID: 5 / Number of copies: 18 / Formula: CYC |
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Molecular weight | Theoretical: 588.694 Da |
Chemical component information | ChemComp-CYC: |
-Macromolecule #6: water
Macromolecule | Name: water / type: ligand / ID: 6 / Number of copies: 1933 / 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 | particle |
-Sample preparation
Concentration | 3.8 mg/mL |
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Buffer | pH: 7.5 |
Vitrification | Cryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV / Details: Manual blotting. |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.4 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |