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- EMDB-25031: Synechocystis PCC 6803 Phycobilisome rod from OCP-PBS complex sample -

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Basic information

Entry
Database: EMDB / ID: EMD-25031
TitleSynechocystis PCC 6803 Phycobilisome rod from OCP-PBS complex sample
Map dataB-factor sharpened map
Sample
  • Complex: Complex of phycobilisome from Synechocystis PCC 6803 with OCP
    • Protein or peptide: C-phycocyanin alpha subunit
    • Protein or peptide: C-phycocyanin beta subunit
    • Protein or peptide: Phycobilisome rod-core linker polypeptide CpcG
    • 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: Phycobilisome 8.9 kDa linker polypeptide, phycocyanin-associated, rod
  • Ligand: PHYCOCYANOBILIN
  • Ligand: water
Function / homology
Function and homology information


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 / Phycocyanin, beta subunit / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. ...Phycobilisome linker protein / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycocyanin, alpha subunit / Phycocyanin, beta subunit / 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 / Globin-like superfamily
Similarity search - Domain/homology
Phycobilisome rod-core linker polypeptide CpcG / Phycobilisome 8.9 kDa linker polypeptide, phycocyanin-associated, rod / Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1 / Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2 / C-phycocyanin beta subunit / C-phycocyanin alpha subunit
Similarity search - Component
Biological speciesSynechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) / Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsSauer PV / Sutter M / Dominguez-Martin MA / Kirst H / Kerfeld CA
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
Marie Sklodowska-Curie Actions, FragNET ITN795070European Union
CitationJournal: Nature / Year: 2022
Title: Structures of a phycobilisome in light-harvesting and photoprotected states.
Authors: María Agustina Domínguez-Martín / Paul V Sauer / Henning Kirst / Markus Sutter / David Bína / Basil J Greber / Eva Nogales / Tomáš Polívka / Cheryl A Kerfeld /
Abstract: Phycobilisome (PBS) structures are elaborate antennae in cyanobacteria and red algae. These large protein complexes capture incident sunlight and transfer the energy through a network of embedded ...Phycobilisome (PBS) structures are elaborate antennae in cyanobacteria and red algae. These large protein complexes capture incident sunlight and transfer the energy through a network of embedded pigment molecules called bilins to the photosynthetic reaction centres. However, light harvesting must also be balanced against the risks of photodamage. A known mode of photoprotection is mediated by orange carotenoid protein (OCP), which binds to PBS when light intensities are high to mediate photoprotective, non-photochemical quenching. Here we use cryogenic electron microscopy to solve four structures of the 6.2 MDa PBS, with and without OCP bound, from the model cyanobacterium Synechocystis sp. PCC 6803. The structures contain a previously undescribed linker protein that binds to the membrane-facing side of PBS. For the unquenched PBS, the structures also reveal three different conformational states of the antenna, two previously unknown. The conformational states result from positional switching of two of the rods and may constitute a new mode of regulation of light harvesting. Only one of the three PBS conformations can bind to OCP, which suggests that not every PBS is equally susceptible to non-photochemical quenching. In the OCP-PBS complex, quenching is achieved through the binding of four 34 kDa OCPs organized as two dimers. The complex reveals the structure of the active form of OCP, in which an approximately 60 Å displacement of its regulatory carboxy terminal domain occurs. Finally, by combining our structure with spectroscopic properties, we elucidate energy transfer pathways within PBS in both the quenched and light-harvesting states. Collectively, our results provide detailed insights into the biophysical underpinnings of the control of cyanobacterial light harvesting. The data also have implications for bioengineering PBS regulation in natural and artificial light-harvesting systems.
History
DepositionSep 27, 2021-
Header (metadata) releaseAug 31, 2022-
Map releaseAug 31, 2022-
UpdateOct 5, 2022-
Current statusOct 5, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_25031.png

Downloads & links

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Map

FileDownload / File: emd_25031.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationB-factor sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 360 pix.
= 378. Å		1.05 Å/pix.
x 360 pix.
= 378. Å		1.05 Å/pix.
x 360 pix.
= 378. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.07
Minimum - Maximum-3.2403314 - 5.898102
Average (Standard dev.)0.001378878 (±0.17421517)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 377.99997 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_25031_msk_1.map
Projections & Slices
AxesZYX

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Additional map: 3D refinement

Fileemd_25031_additional_1.map
Annotation3D refinement
Projections & Slices
AxesZYX

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Additional map: DeepEMhancer sharpened map

Fileemd_25031_additional_2.map
AnnotationDeepEMhancer sharpened map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_25031_half_map_1.map
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Half map: #1

Fileemd_25031_half_map_2.map
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Sample components

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Entire : Complex of phycobilisome from Synechocystis PCC 6803 with OCP

EntireName: Complex of phycobilisome from Synechocystis PCC 6803 with OCP
Components
  • Complex: Complex of phycobilisome from Synechocystis PCC 6803 with OCP
    • Protein or peptide: C-phycocyanin alpha subunit
    • Protein or peptide: C-phycocyanin beta subunit
    • Protein or peptide: Phycobilisome rod-core linker polypeptide CpcG
    • 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: Phycobilisome 8.9 kDa linker polypeptide, phycocyanin-associated, rod
  • Ligand: PHYCOCYANOBILIN
  • Ligand: water

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Supramolecule #1: Complex of phycobilisome from Synechocystis PCC 6803 with OCP

SupramoleculeName: Complex of phycobilisome from Synechocystis PCC 6803 with OCP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (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. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 17.602529 KDa
SequenceString:
MKTPLTEAVS TADSQGRFLS STELQIAFGR LRQANAGLQA AKALTDNAQS LVNGAAQAVY NKFPYTTQTQ GNNFAADQRG KDKCARDIG YYLRIVTYCL VAGGTGPLDE YLIAGIDEIN RTFDLSPSWY VEALKYIKAN HGLSGDARDE ANSYLDYAIN A LS

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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. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 18.142426 KDa
SequenceString:
MFDVFTRVVS QADARGEYLS GSQLDALSAT VAEGNKRIDS VNRITGNASA IVSNAARALF AEQPQLIQPG GNAYTSRRMA ACLRDMEII LRYVTYATFT GDASVLEDRC LNGLRETYVA LGVPGASVAA GVQKMKEAAL DIVNDPNGIT RGDCSAIVAE I AGYFDRAA AAVA

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Macromolecule #3: Phycobilisome rod-core linker polypeptide CpcG

MacromoleculeName: Phycobilisome rod-core linker polypeptide CpcG / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 28.938758 KDa
SequenceString: MALPLLNYAP KSQNVRVEGY EIGSEEKPVV FTTENILSSS DMDNLIEAAY RQIFFHAFKW DREKVLESQL RNGQITVRDF VRGLLLSNT FRNSFYEKNS NYRFVEHCVQ KILGRDVYSE REKIAWSIVV ATKGYQGLID DLLNSDEYLN NFGYDTVPYQ R RRNLPGRE ...String:
MALPLLNYAP KSQNVRVEGY EIGSEEKPVV FTTENILSSS DMDNLIEAAY RQIFFHAFKW DREKVLESQL RNGQITVRDF VRGLLLSNT FRNSFYEKNS NYRFVEHCVQ KILGRDVYSE REKIAWSIVV ATKGYQGLID DLLNSDEYLN NFGYDTVPYQ R RRNLPGRE AGELPFNIKS PRYDAYHRRQ LGFPQIVWQN EVRRFIPQEK KLTAGNPMNF LGMARSINPA ANTIPKVSAQ NI NIEASVP RR

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

MacromoleculeName: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 32.558607 KDa
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

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Macromolecule #5: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated...

MacromoleculeName: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2
type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 30.836346 KDa
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

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Macromolecule #6: Phycobilisome 8.9 kDa linker polypeptide, phycocyanin-associated, rod

MacromoleculeName: Phycobilisome 8.9 kDa linker polypeptide, phycocyanin-associated, rod
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 9.333342 KDa
SequenceString:
MLGQSSLVGY SNTQAANRVF VYEVSGLRQT DANENSAHDI RRSGSVFIKV PYARMNDEMR RISRLGGTIV NIRPYQADSN EQN

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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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Macromolecule #8: water

MacromoleculeName: water / type: ligand / ID: 8 / Number of copies: 1325 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration3.8 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV / Details: Manual blotting.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsStreptavidin lattice was subtracted after movie alignment.
Startup modelType of model: OTHER / Details: Ab initio model
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1) / Number images used: 2133253
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-7sca:
Synechocystis PCC 6803 Phycobilisome rod from OCP-PBS complex sample

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