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- EMDB-34724: Cryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis s... -

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Basic information

Entry
Database: EMDB / ID: EMD-34724
TitleCryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis sp. PCC 6803
Map data
Sample
  • Complex: Cryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis sp. PCC 6803
    • Protein or peptide: C-phycocyanin alpha subunit
    • Protein or peptide: C-phycocyanin beta subunit
    • Protein or peptide: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1
    • Protein or peptide: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2
    • Protein or peptide: Ferredoxin--NADP reductase
    • Protein or peptide: Photosystem I-associated linker protein CpcL
  • Ligand: PHYCOCYANOBILIN
KeywordsCpcL-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
Phycobilisome linker protein / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycocyanin, alpha subunit / Ferredoxin--NADP reductase, plant and Cyanobacteria type / Phycocyanin, beta subunit / Ferredoxin--NADP reductase / CpcD-like domain ...Phycobilisome linker protein / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycocyanin, alpha subunit / Ferredoxin--NADP reductase, plant and Cyanobacteria type / Phycocyanin, beta subunit / Ferredoxin--NADP reductase / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. / CpcD/allophycocyanin linker domain / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Flavoprotein pyridine nucleotide cytochrome reductase / Oxidoreductase FAD/NAD(P)-binding / Oxidoreductase NAD-binding domain / FAD-binding domain, ferredoxin reductase-type / Ferredoxin-NADP reductase (FNR), nucleotide-binding domain / Ferredoxin reductase-type FAD binding domain profile. / Riboflavin synthase-like beta-barrel / Globin-like superfamily
Similarity search - Domain/homology
Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1 / Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2 / Photosystem I-associated linker protein CpcL / C-phycocyanin beta subunit / C-phycocyanin alpha subunit / Ferredoxin--NADP reductase
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria) / Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.64 Å
AuthorsZheng L / Zhang Z / Wang H / Zheng Z / Gao N / Zhao J
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China) China
CitationJournal: 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
DepositionNov 11, 2022-
Header (metadata) releaseNov 8, 2023-
Map releaseNov 8, 2023-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_34724.png

Downloads & links

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Map

FileDownload / File: emd_34724.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 360 pix.
= 385.2 Å		1.07 Å/pix.
x 360 pix.
= 385.2 Å		1.07 Å/pix.
x 360 pix.
= 385.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0164
Minimum - Maximum-0.096987866 - 0.17594402
Average (Standard dev.)0.00033897127 (±0.005091252)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 385.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_34724_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34724_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis s...

EntireName: Cryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis sp. PCC 6803
Components
  • Complex: Cryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis sp. PCC 6803
    • Protein or peptide: C-phycocyanin alpha subunit
    • Protein or peptide: C-phycocyanin beta subunit
    • Protein or peptide: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1
    • Protein or peptide: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2
    • Protein or peptide: Ferredoxin--NADP reductase
    • Protein or peptide: Photosystem I-associated linker protein CpcL
  • Ligand: PHYCOCYANOBILIN

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Supramolecule #1: Cryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis s...

SupramoleculeName: Cryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis sp. PCC 6803
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)

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Macromolecule #1: C-phycocyanin alpha subunit

MacromoleculeName: C-phycocyanin alpha subunit / type: protein_or_peptide / ID: 1 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Molecular weightTheoretical: 17.602529 KDa
Recombinant expressionOrganism: Synechocystis sp. PCC 6803 (bacteria)
SequenceString:
MKTPLTEAVS TADSQGRFLS STELQIAFGR LRQANAGLQA AKALTDNAQS LVNGAAQAVY NKFPYTTQTQ GNNFAADQRG KDKCARDIG YYLRIVTYCL VAGGTGPLDE YLIAGIDEIN RTFDLSPSWY VEALKYIKAN HGLSGDARDE ANSYLDYAIN A LS

UniProtKB: C-phycocyanin alpha subunit

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Macromolecule #2: C-phycocyanin beta subunit

MacromoleculeName: C-phycocyanin beta subunit / type: protein_or_peptide / ID: 2 / Number of copies: 18 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Molecular weightTheoretical: 18.142426 KDa
Recombinant expressionOrganism: Synechocystis sp. PCC 6803 (bacteria)
SequenceString:
MFDVFTRVVS QADARGEYLS GSQLDALSAT VAEGNKRIDS VNRITGNASA IVSNAARALF AEQPQLIQPG GNAYTSRRMA ACLRDMEII LRYVTYATFT GDASVLEDRC LNGLRETYVA LGVPGASVAA GVQKMKEAAL DIVNDPNGIT RGDCSAIVAE I AGYFDRAA AAVA

UniProtKB: C-phycocyanin beta subunit

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Macromolecule #3: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated...

MacromoleculeName: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Molecular weightTheoretical: 32.558607 KDa
Recombinant expressionOrganism: Synechocystis sp. PCC 6803 (bacteria)
SequenceString: 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

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Macromolecule #4: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated...

MacromoleculeName: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Molecular weightTheoretical: 30.836346 KDa
Recombinant expressionOrganism: Synechocystis sp. PCC 6803 (bacteria)
SequenceString: 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

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Macromolecule #5: Ferredoxin--NADP reductase

MacromoleculeName: Ferredoxin--NADP reductase / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: ferredoxin-NADP+ reductase
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Molecular weightTheoretical: 46.417469 KDa
Recombinant expressionOrganism: Synechocystis sp. PCC 6803 (bacteria)
SequenceString: 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

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Macromolecule #6: Photosystem I-associated linker protein CpcL

MacromoleculeName: Photosystem I-associated linker protein CpcL / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Molecular weightTheoretical: 28.551516 KDa
Recombinant expressionOrganism: Synechocystis sp. PCC 6803 (bacteria)
SequenceString: 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

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Macromolecule #7: PHYCOCYANOBILIN

MacromoleculeName: PHYCOCYANOBILIN / type: ligand / ID: 7 / Number of copies: 54 / Formula: CYC
Molecular weightTheoretical: 588.694 Da
Chemical component information

ChemComp-CYC:
PHYCOCYANOBILIN

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %
DetailsCryo-EM structure of CpcL-PBS from cyanobacterium Synechocystis sp. PCC 6803

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4f0t

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 124441
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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