[English] 日本語
Yorodumi
- EMDB-25032: B-cylinder of Synechocystis PCC 6803 Phycobilisome, complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-25032
TitleB-cylinder of Synechocystis PCC 6803 Phycobilisome, complex with OCP - local refinement
Map data
Sample
  • Complex: Complex of phycobilisome from Synechocystis PCC 6803 with OCP
    • Protein or peptide: x 9 types
  • Ligand: x 2 types
KeywordsComplex / light harvesting / pigment / PHOTOSYNTHESIS
Function / homology
Function and homology information


light absorption / Lyases / phycobilisome / chloride ion binding / plasma membrane-derived thylakoid membrane / photoreceptor activity / photosynthesis / lyase activity
Similarity search - Function
Allophycocyanin linker protein / Allophycocyanin linker chain / Phycobilisome linker protein / Orange carotenoid-binding protein, N-terminal / Orange carotenoid-binding protein, N-terminal domain superfamily / Orange carotenoid protein, N-terminal / Orange carotenoid protein (OCP) N-terminal domain profile. / Allophycocyanin, beta subunit / Phycobilisome linker domain / Phycobilisome linker domain superfamily ...Allophycocyanin linker protein / Allophycocyanin linker chain / Phycobilisome linker protein / Orange carotenoid-binding protein, N-terminal / Orange carotenoid-binding protein, N-terminal domain superfamily / Orange carotenoid protein, N-terminal / Orange carotenoid protein (OCP) N-terminal domain profile. / Allophycocyanin, beta subunit / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. / CpcD/allophycocyanin linker domain / Nuclear transport factor 2 (NTF2) domain / Nuclear transport factor 2 domain / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / NTF2-like domain superfamily / Globin-like superfamily
Similarity search - Domain/homology
Allophycocyanin subunit alpha-B / Phycobilisome rod-core linker polypeptide CpcG / Orange carotenoid-binding protein / Sll1873 protein / Allophycocyanin subunit beta-18 / Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core / Allophycocyanin alpha chain / Allophycocyanin beta chain / Phycobiliprotein ApcE
Similarity search - Component
Biological speciesSynechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) / Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.5 Å
AuthorsSauer PV / Sutter M
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-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_25032.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.)
1.05 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
Contour LevelBy AUTHOR: 0.457
Minimum - Maximum-0.6073159 - 1.85999
Average (Standard dev.)0.003313619 (±0.060307663)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Mask #1

Fileemd_25032_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: #2

Fileemd_25032_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: #1

Fileemd_25032_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

+
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: Allophycocyanin alpha chain
    • Protein or peptide: Allophycocyanin beta chain
    • Protein or peptide: Allophycocyanin subunit alpha-B
    • Protein or peptide: Allophycocyanin subunit beta-18
    • Protein or peptide: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
    • Protein or peptide: Phycobiliprotein ApcE
    • Protein or peptide: Phycobilisome rod-core linker polypeptide CpcG
    • Protein or peptide: Orange carotenoid-binding protein
    • Protein or peptide: Sll1873 protein
  • Ligand: PHYCOCYANOBILIN
  • Ligand: beta,beta-carotene-4,4'-dione

+
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-#9
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)

+
Macromolecule #1: Allophycocyanin alpha chain

MacromoleculeName: Allophycocyanin alpha chain / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 17.429807 KDa
SequenceString:
MSIVTKSIVN ADAEARYLSP GELDRIKAFV TGGAARLRIA ETLTGSRETI VKQAGDRLFQ KRPDIVSPGG NAYGEEMTAT CLRDMDYYL RLVTYGVVSG DVTPIEEIGL VGVREMYRSL GTPIEAVAQS VREMKEVASG LMSSDDAAEA SAYFDFVIGK M S

UniProtKB: Allophycocyanin alpha chain

+
Macromolecule #2: Allophycocyanin beta chain

MacromoleculeName: Allophycocyanin beta chain / type: protein_or_peptide / ID: 2 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 17.231604 KDa
SequenceString:
MQDAITAVIN SADVQGKYLD GAAMDKLKSY FASGELRVRA ASVISANAAT IVKEAVAKSL LYSDVTRPGG NMYTTRRYAA CIRDLDYYL RYATYAMLAG DASILDERVL NGLKETYNSL GVPISSTVQA IQAIKEVTAS LVGADAGKEM GVYLDYICSG L S

UniProtKB: Allophycocyanin beta chain

+
Macromolecule #3: Allophycocyanin subunit alpha-B

MacromoleculeName: Allophycocyanin subunit alpha-B / 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: 17.940393 KDa
SequenceString:
MSVVSQVILQ ADDQLRYPTS GELKGIQAFL TTGAQRIRIA ETLAENEKKI VDQAQKQLFK KHPEYRAPGG NAYGQRQYNQ CLRDYGWYL RLVTYGVLAG NKEPIETTGL IGVKEMYNSL NVPVPGMVDA VTVLKDAALG LLSAEDANET APYFDYIIQF M S

UniProtKB: Allophycocyanin subunit alpha-B

+
Macromolecule #4: Allophycocyanin subunit beta-18

MacromoleculeName: Allophycocyanin subunit beta-18 / 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: 18.911424 KDa
SequenceString:
MRDAVTTLIK NYDLTGRYLD RNAMDELKAY FESGSARIAA AAMINANSAT IVKRAAAQLF EEIPELIRPS GNAYTTRRFS ACLRDMDYY LRYASYALIA ADNNVLDERV LQGLRETYNS LGVPIGPTVR GIQIMKEMIE AMAEDSSLNS TDFIASPFDH M TRELSELS V

UniProtKB: Allophycocyanin subunit beta-18

+
Macromolecule #5: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associa...

MacromoleculeName: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 7.817174 KDa
SequenceString:
MRMFRITACV PSQTRIRTQR ELQNTYFTKL VPYDNWFREQ QRIMKMGGKI VKVELATGRP GTNAGLA

UniProtKB: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core

+
Macromolecule #6: Phycobiliprotein ApcE

MacromoleculeName: Phycobiliprotein ApcE / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: Lyases
Source (natural)Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 100.412703 KDa
SequenceString: MSVKASGGSS LARPQLYQTV PVSAISQAEQ QDRFLEGSEL NELTAYFQSG ALRLEIAETL TQNADLIVSR AANRIFTGGS PLSYLEKPV ERQPALVGAS SDSRNGSVTY AESNGSGGLF GGLRSVFSST GPIPPGFRPI NIARYGPSNM QKSLRDMSWF L RYTTYAIV ...String:
MSVKASGGSS LARPQLYQTV PVSAISQAEQ QDRFLEGSEL NELTAYFQSG ALRLEIAETL TQNADLIVSR AANRIFTGGS PLSYLEKPV ERQPALVGAS SDSRNGSVTY AESNGSGGLF GGLRSVFSST GPIPPGFRPI NIARYGPSNM QKSLRDMSWF L RYTTYAIV AGDPNIIVVN TRGLKEVIEN ACSIDATIVA IQEMRAASAD YFRNNAQAKE IVLQYFDILL SEFKAPTPAN KV RQGPSND IQGLELPQSY FNAAAKRQKY AMKPGLSALE KNAVIKAAYR QIFERDITKA YSQSISYLES QVRNGDISMK EFV RRLAKS PLYRKQFFEP FINSRALELA FRHILGRGPS SREEVQKYFS IVSSGGLPAL VDALVDSQEY ADYFGEETVP YLRG LGVEA QECRNWGMQQ DLFSYSAPFR KVPQFITTFA QYDRPLPDQH VYGSGNDPLE IQFGAIFPKE TRNPSKRPAP FNKDT KRIL IHRGPAVNNQ VGNPSAVGEF PGSLGAKVFR LNGGLPGAKV GKNTGTSVKF GESSTQALIR AAYRQVFGRD LYEGQR LSV AEIQLENGDI SVREFIKRLA KSELFLKLYW APHYVCKAIE YMHRRLLGRP TYGRQEMNQY FDIASKQGFY AVVEAMI DS KEYSDAFGED TVPYERYLTP GGLQMRSARV GSLREDIGQR VDKEVTPRFV ELGQVSAIRT EPEIAYRSNQ GVTRQRQQ T KVFKLVSTYD KVAVKNAIRA AYRQVFERDL EPYIINSEFT ALESKLSNNE INVKEFIEGL GTSELYMKEF YAPYPNTKV IEMGTKHFLG RAPLNQKEIQ QYNQILASQG LKAFIGAMVN GMEYLQTFGE DTVPYRRFPT LPAANFPNTE RLYNKLTKQD KELVVPSFT PVVKVGG

UniProtKB: Phycobiliprotein ApcE

+
Macromolecule #7: Phycobilisome rod-core linker polypeptide CpcG

MacromoleculeName: Phycobilisome rod-core linker polypeptide CpcG / type: protein_or_peptide / ID: 7 / 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

UniProtKB: Phycobilisome rod-core linker polypeptide CpcG

+
Macromolecule #8: Orange carotenoid-binding protein

MacromoleculeName: Orange carotenoid-binding protein / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 34.684605 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPFTIDSARG IFPNTLAADV VPATIARFSQ LNAEDQLALI WFAYLEMGKT LTIAAPGAAS MQLAENALKE IQAMGPLQQT QAMCDLANR ADTPLCRTYA SWSPNIKLGF WYRLGELMEQ GFVAPIPAGY QLSANANAVL ATIQGLESGQ QITVLRNAVV D MGFTAGKD ...String:
MPFTIDSARG IFPNTLAADV VPATIARFSQ LNAEDQLALI WFAYLEMGKT LTIAAPGAAS MQLAENALKE IQAMGPLQQT QAMCDLANR ADTPLCRTYA SWSPNIKLGF WYRLGELMEQ GFVAPIPAGY QLSANANAVL ATIQGLESGQ QITVLRNAVV D MGFTAGKD GKRIAEPVVP PQDTASRTKV SIEGVTNATV LNYMDNLNAN DFDTLIELFT SDGALQPPFQ RPIVGKENVL RF FREECQN LKLIPERGVT EPAEDGFTQI KVTGKVQTPW FGGNVGMNIA WRFLLNPEGK IFFVAIDLLA SPKELLNFAR

UniProtKB: Orange carotenoid-binding protein

+
Macromolecule #9: Sll1873 protein

MacromoleculeName: Sll1873 protein / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 substr. Kazusa (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 12.927983 KDa
SequenceString:
MLKKLFGAKK EFYVQLDESQ APAQVEEADV AIVKSEVAPV EKPAPTTSKK TSIKKKSATK AAAPVETPAS APVAPAPKAK VDPSQVAFA SGDPIPQNVA RRTPGPSLNR FKEMARQVKV KR

UniProtKB: Sll1873 protein

+
Macromolecule #10: PHYCOCYANOBILIN

MacromoleculeName: PHYCOCYANOBILIN / type: ligand / ID: 10 / Number of copies: 24 / Formula: CYC
Molecular weightTheoretical: 588.694 Da
Chemical component information

ChemComp-CYC:
PHYCOCYANOBILIN

+
Macromolecule #11: beta,beta-carotene-4,4'-dione

MacromoleculeName: beta,beta-carotene-4,4'-dione / type: ligand / ID: 11 / Number of copies: 1 / Formula: 45D
Molecular weightTheoretical: 564.84 Da
Chemical component information

ChemComp-45D:
beta,beta-carotene-4,4'-dione

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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 / Details: Grids were coated with streptavidin prior to use.
VitrificationCryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV / Details: Manual blotting.

-
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

+
Image processing

DetailsStreptavidin lattice was subtracted after movie alignment
Startup modelType of model: OTHER / Details: Ab initio model
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.1) / Number images used: 340838
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-7scb:
B-cylinder of Synechocystis PCC 6803 Phycobilisome, complex with OCP - local refinement

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more