[English] 日本語
Yorodumi
- EMDB-41435: Central rod disk in C1 symmetry of high-resolution phycobilisome ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-41435
TitleCentral rod disk in C1 symmetry of high-resolution phycobilisome quenched by OCP (local refinement)
Map datasharpened map
Sample
  • Complex: Complex of phycobilisome from Synechocystis PCC 6803 bound to OCP
    • 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
  • Ligand: PHYCOCYANOBILIN
  • Ligand: water
KeywordsComplex / light harvesting / pigment / PHOTOSYNTHESIS
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 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 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.87 Å
AuthorsSauer PV / Sutter M / Cupellini L / Kirst H / Kerfeld CA
Funding supportEuropean Union, United States, Czech Republic, 4 items
OrganizationGrant numberCountry
European Research Council (ERC)Grant ERC-AdG 786714 (LIFETimeS)European Union
Department of Energy (DOE, United States)DE-SC0020606 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM127018 United States
Czech Science Foundation19-28323X Czech Republic
CitationJournal: 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
DepositionAug 2, 2023-
Header (metadata) releaseApr 17, 2024-
Map releaseApr 17, 2024-
UpdateApr 17, 2024-
Current statusApr 17, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_41435.png

Downloads & links

-
Map

FileDownload / File: emd_41435.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 512 pix.
= 372.224 Å		0.73 Å/pix.
x 512 pix.
= 372.224 Å		0.73 Å/pix.
x 512 pix.
= 372.224 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.727 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.9
Minimum - Maximum-1.9368988 - 6.1818624
Average (Standard dev.)-0.0016214112 (±0.11562173)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 372.224 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_41435_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: refined map

Fileemd_41435_additional_1.map
Annotationrefined map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_41435_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_41435_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Complex of phycobilisome from Synechocystis PCC 6803 bound to OCP

EntireName: Complex of phycobilisome from Synechocystis PCC 6803 bound to OCP
Components
  • Complex: Complex of phycobilisome from Synechocystis PCC 6803 bound to OCP
    • 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
  • Ligand: PHYCOCYANOBILIN
  • Ligand: water

-
Supramolecule #1: Complex of phycobilisome from Synechocystis PCC 6803 bound to OCP

SupramoleculeName: Complex of phycobilisome from Synechocystis PCC 6803 bound to OCP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)

-
Macromolecule #1: C-phycocyanin alpha subunit

MacromoleculeName: C-phycocyanin alpha subunit / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 17.602529 KDa
SequenceString:
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

MacromoleculeName: C-phycocyanin beta subunit / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 18.156451 KDa
SequenceString:
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...

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. PCC 6803 (bacteria)
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

UniProtKB: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 1

-
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. PCC 6803 (bacteria)
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

UniProtKB: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod 2

-
Macromolecule #5: PHYCOCYANOBILIN

MacromoleculeName: PHYCOCYANOBILIN / type: ligand / ID: 5 / Number of copies: 18 / Formula: CYC
Molecular weightTheoretical: 588.694 Da
Chemical component information

ChemComp-CYC:
PHYCOCYANOBILIN / Phycocyanobilin

-
Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 1933 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration3.8 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK IV / Details: Manual blotting.

-
Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.4 µm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: EMDB MAP
EMDB ID:

25068

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2) / Number images used: 435854
DetailsStreptavidin lattice was subtracted after movie alignment
FSC plot (resolution estimation)

+
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