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Yorodumi- EMDB-34724: Cryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis s... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34724 | |||||||||
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Title | Cryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis sp. PCC 6803 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | CpcL-phycobilisome / energy transfer / ferredoxin:NADP+ oxidoreductase / ultrafast spectroscopy / PHOTOSYNTHESIS | |||||||||
Function / homology | Function and homology information ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis Similarity search - Function | |||||||||
Biological species | Synechocystis sp. PCC 6803 (bacteria) / Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.64 Å | |||||||||
Authors | Zheng L / Zhang Z / Wang H / Zheng Z / Gao N / Zhao J | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2023 Title: Cryo-EM and femtosecond spectroscopic studies provide mechanistic insight into the energy transfer in CpcL-phycobilisomes. Authors: Lvqin Zheng / Zhengdong Zhang / Hongrui Wang / Zhenggao Zheng / Jiayu Wang / Heyuan Liu / Hailong Chen / Chunxia Dong / Guopeng Wang / Yuxiang Weng / Ning Gao / Jindong Zhao / Abstract: Phycobilisomes (PBS) are the major light harvesting complexes of photosynthesis in the cyanobacteria and red algae. CpcL-PBS is a type of small PBS in cyanobacteria that transfers energy directly to ...Phycobilisomes (PBS) are the major light harvesting complexes of photosynthesis in the cyanobacteria and red algae. CpcL-PBS is a type of small PBS in cyanobacteria that transfers energy directly to photosystem I without the core structure. Here we report the cryo-EM structure of the CpcL-PBS from the cyanobacterium Synechocystis sp. PCC 6803 at 2.6-Å resolution. The structure shows the CpcD domain of ferredoxin: NADP oxidoreductase is located at the distal end of CpcL-PBS, responsible for its attachment to PBS. With the evidence of ultrafast transient absorption and fluorescence spectroscopy, the roles of individual bilins in energy transfer are revealed. The bilin β located near photosystem I has an enhanced planarity and is the red-bilin responsible for the direct energy transfer to photosystem I. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34724.map.gz | 16.2 MB | EMDB map data format | |
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Header (meta data) | emd-34724-v30.xml emd-34724.xml | 21.2 KB 21.2 KB | Display Display | EMDB header |
Images | emd_34724.png | 37.6 KB | ||
Filedesc metadata | emd-34724.cif.gz | 6.6 KB | ||
Others | emd_34724_half_map_1.map.gz emd_34724_half_map_2.map.gz | 140.9 MB 140.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34724 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34724 | HTTPS FTP |
-Validation report
Summary document | emd_34724_validation.pdf.gz | 842.8 KB | Display | EMDB validaton report |
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Full document | emd_34724_full_validation.pdf.gz | 842.3 KB | Display | |
Data in XML | emd_34724_validation.xml.gz | 14.8 KB | Display | |
Data in CIF | emd_34724_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34724 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34724 | HTTPS FTP |
-Related structure data
Related structure data | 8hfqMC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_34724.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_34724_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34724_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis s...
Entire | Name: Cryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis sp. PCC 6803 |
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Components |
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-Supramolecule #1: Cryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis s...
Supramolecule | Name: Cryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis sp. PCC 6803 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6 |
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Source (natural) | Organism: Synechocystis sp. PCC 6803 (bacteria) |
-Macromolecule #1: C-phycocyanin alpha subunit
Macromolecule | Name: C-phycocyanin alpha subunit / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO |
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Source (natural) | Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) |
Molecular weight | Theoretical: 17.602529 KDa |
Recombinant expression | Organism: Synechocystis sp. PCC 6803 (bacteria) |
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: 18 / Enantiomer: LEVO |
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Source (natural) | Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) |
Molecular weight | Theoretical: 18.142426 KDa |
Recombinant expression | Organism: Synechocystis sp. PCC 6803 (bacteria) |
Sequence | String: MFDVFTRVVS QADARGEYLS GSQLDALSAT VAEGNKRIDS VNRITGNASA IVSNAARALF AEQPQLIQPG GNAYTSRRMA ACLRDMEII LRYVTYATFT GDASVLEDRC LNGLRETYVA LGVPGASVAA GVQKMKEAAL DIVNDPNGIT RGDCSAIVAE I AGYFDRAA 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. (strain PCC 6803 / Kazusa) (bacteria) |
Molecular weight | Theoretical: 32.558607 KDa |
Recombinant expression | Organism: Synechocystis sp. PCC 6803 (bacteria) |
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. (strain PCC 6803 / Kazusa) (bacteria) |
Molecular weight | Theoretical: 30.836346 KDa |
Recombinant expression | Organism: Synechocystis sp. PCC 6803 (bacteria) |
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: Ferredoxin--NADP reductase
Macromolecule | Name: Ferredoxin--NADP reductase / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: ferredoxin-NADP+ reductase |
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Source (natural) | Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) |
Molecular weight | Theoretical: 46.417469 KDa |
Recombinant expression | Organism: Synechocystis sp. PCC 6803 (bacteria) |
Sequence | String: MYSPGYVATS SRQSDAGNRL FVYEVIGLSQ STMTDGLDYP IRRSGSTFIT VPLKRMNQEM RRITRMGGKI VSIKPLEGDS PLPHTEGIA KPSQSEGSGS EAVANPAPES NKTMTTTPKE KKADDIPVNI YRPKTPYIGK VLENYPLVRE GAIGTVQHLT F DLSAGDLR ...String: MYSPGYVATS SRQSDAGNRL FVYEVIGLSQ STMTDGLDYP IRRSGSTFIT VPLKRMNQEM RRITRMGGKI VSIKPLEGDS PLPHTEGIA KPSQSEGSGS EAVANPAPES NKTMTTTPKE KKADDIPVNI YRPKTPYIGK VLENYPLVRE GAIGTVQHLT F DLSAGDLR YLEGQSIGII PPGEDDKGKP HKLRLYSIAS TRHGDFGDDK TVSLCVRQLE YQNEAGETVQ GVCSTYLCNI KE GDDIAIT GPVGKEMLLP PDEDANIVML ATGTGIAPFR AFLWRMFKEQ HEDYKFKGLA WLIFGIPKSE NILYKDDLEK MAA EFPDNF RLTYAISREQ QNAEGGRMYI QHRVAENAEE LWNLMQNPKT HTYMCGLKGM EPGIDEAFTA LAEQNGKEWT TFQR EMKKE HRWHVETY UniProtKB: Ferredoxin--NADP reductase |
-Macromolecule #6: Photosystem I-associated linker protein CpcL
Macromolecule | Name: Photosystem I-associated linker protein CpcL / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) |
Molecular weight | Theoretical: 28.551516 KDa |
Recombinant expression | Organism: Synechocystis sp. PCC 6803 (bacteria) |
Sequence | String: MTLPLIAYAP VSQNQRVTNY EVSGDEHARI FTTEGTLSPS AMDNLIAAAY RQVFNEQQMI QSNRQIALES QFKNQQITVR DFIRGLALS DSFRRRNFEV NNNYRFVQMC IQRLLGRDVY SEEEKIAWSI VIATKGLPGF INELLNSQEY LENFGYDTVP Y QRRRILPQ ...String: MTLPLIAYAP VSQNQRVTNY EVSGDEHARI FTTEGTLSPS AMDNLIAAAY RQVFNEQQMI QSNRQIALES QFKNQQITVR DFIRGLALS DSFRRRNFEV NNNYRFVQMC IQRLLGRDVY SEEEKIAWSI VIATKGLPGF INELLNSQEY LENFGYDTVP Y QRRRILPQ RISGELPFAR MPRYGADHRE KLEAIGYFRN QAPLTYRWEW QKQPYPAGVY LAGKVVLYVG GALVSLGIIA VA LSAWGII GL UniProtKB: Photosystem I-associated linker protein CpcL |
-Macromolecule #7: PHYCOCYANOBILIN
Macromolecule | Name: PHYCOCYANOBILIN / type: ligand / ID: 7 / Number of copies: 54 / Formula: CYC |
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Molecular weight | Theoretical: 588.694 Da |
Chemical component information | ChemComp-CYC: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
Details | Cryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis sp. PCC 6803 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k 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 / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 124441 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: PROJECTION MATCHING |