[English] 日本語
Yorodumi
- EMDB-41434: Bottom cylinder of high-resolution phycobilisome quenched by OCP ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-41434
TitleBottom cylinder of high-resolution phycobilisome quenched by OCP (local refinement)
Map datarefined map
Sample
  • Complex: Complex of phycobilisome from Synechocystis PCC 6803 bound to 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 domain / Nuclear transport factor 2 (NTF2) domain / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / NTF2-like domain superfamily / Globin-like superfamily
Similarity search - Domain/homology
Translation initiation factor IF-2 / Allophycocyanin subunit alpha-B / Phycobilisome rod-core linker polypeptide CpcG / Orange carotenoid-binding protein / Allophycocyanin subunit beta-18 / Allophycocyanin alpha chain / Allophycocyanin beta chain / Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core / Phycobiliprotein ApcE
Similarity search - Component
Biological speciesSynechocystis sp. (strain PCC 6803 / Kazusa) (bacteria) / Synechocystis sp. PCC 6803 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.0 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_41434.png

Downloads & links

-
Map

FileDownload / File: emd_41434.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationrefined 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: 0.3
Minimum - Maximum-0.49030274 - 1.2958689
Average (Standard dev.)0.0018662286 (±0.037007336)
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_41434_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: sharpened map

Fileemd_41434_additional_1.map
Annotationsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_41434_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_41434_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: Phycobiliprotein ApcE
    • Protein or peptide: Orange carotenoid-binding protein
    • Protein or peptide: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
    • Protein or peptide: Allophycocyanin alpha chain
    • Protein or peptide: Allophycocyanin beta chain
    • Protein or peptide: Phycobilisome rod-core linker polypeptide CpcG
    • Protein or peptide: Allophycocyanin subunit alpha-B
    • Protein or peptide: Allophycocyanin subunit beta-18
    • Protein or peptide: Translation initiation factor IF-2
  • Ligand: PHYCOCYANOBILIN
  • Ligand: beta,beta-carotene-4,4'-dione

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

+
Macromolecule #1: Phycobiliprotein ApcE

MacromoleculeName: Phycobiliprotein ApcE / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
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 #2: Orange carotenoid-binding protein

MacromoleculeName: Orange carotenoid-binding protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 34.684605 KDa
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 #3: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associa...

MacromoleculeName: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 7.817174 KDa
SequenceString:
MRMFRITACV PSQTRIRTQR ELQNTYFTKL VPYDNWFREQ QRIMKMGGKI VKVELATGRP GTNAGLA

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

+
Macromolecule #4: Allophycocyanin alpha chain

MacromoleculeName: Allophycocyanin alpha chain / type: protein_or_peptide / ID: 4 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
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 #5: Allophycocyanin beta chain

MacromoleculeName: Allophycocyanin beta chain / type: protein_or_peptide / ID: 5 / Number of copies: 11 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
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 #6: Phycobilisome rod-core linker polypeptide CpcG

MacromoleculeName: Phycobilisome rod-core linker polypeptide CpcG / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
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 #7: Allophycocyanin subunit alpha-B

MacromoleculeName: Allophycocyanin subunit alpha-B / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
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 #8: Allophycocyanin subunit beta-18

MacromoleculeName: Allophycocyanin subunit beta-18 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
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 #9: Translation initiation factor IF-2

MacromoleculeName: Translation initiation factor IF-2 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 12.927983 KDa
SequenceString:
MLKKLFGAKK EFYVQLDESQ APAQVEEADV AIVKSEVAPV EKPAPTTSKK TSIKKKSATK AAAPVETPAS APVAPAPKAK VDPSQVAFA SGDPIPQNVA RRTPGPSLNR FKEMARQVKV KR

UniProtKB: Translation initiation factor IF-2

+
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 / 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 / Canthaxanthin

-
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: 2.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2) / Number images used: 153576
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