[English] 日本語
Yorodumi
- EMDB-41475: Top cylinder bound to OCP from high-resolution phycobilisome quen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-41475
TitleTop cylinder bound to OCP from high-resolution phycobilisome quenched by OCP (local refinement)
Map data
Sample
  • Complex: Phycobilisome 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
  • Ligand: beta,beta-carotene-4,4'-dione
  • Ligand: PHYCOCYANOBILIN
  • Ligand: water
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
Phycobilisome rod-core linker polypeptide CpcG / Orange carotenoid-binding protein / Allophycocyanin alpha chain / Allophycocyanin beta chain / Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core / Phycobiliprotein ApcE
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsSauer PV / Sutter M / Cupellini L
Funding support United States, European Union, Czech Republic, 4 items
OrganizationGrant numberCountry
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
European Research Council (ERC)786714European Union
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 4, 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

Downloads & links

-
Map

FileDownload / File: emd_41475.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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
Contour LevelBy AUTHOR: 0.53
Minimum - Maximum-1.5259525 - 3.2155395
Average (Standard dev.)0.0008492695 (±0.08308973)
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_41475_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Additional map: refined map

Fileemd_41475_additional_1.map
Annotationrefined map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Additional map: 3DFlex map

Fileemd_41475_additional_2.map
Annotation3DFlex map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Additional map: 3DFlex map, locally filtered

Fileemd_41475_additional_3.map
Annotation3DFlex map, locally filtered
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: #1

Fileemd_41475_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: #2

Fileemd_41475_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

+
Entire : Phycobilisome bound to OCP

EntireName: Phycobilisome bound to OCP
Components
  • Complex: Phycobilisome 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
  • Ligand: beta,beta-carotene-4,4'-dione
  • Ligand: PHYCOCYANOBILIN
  • Ligand: water

+
Supramolecule #1: Phycobilisome bound to OCP

SupramoleculeName: Phycobilisome bound to OCP / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Synechocystis sp. PCC 6803 (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: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 34.684605 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
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: 1 / 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: 6 / 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: 6 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Molecular weightTheoretical: 17.245629 KDa
SequenceString:
MQDAITAVIN SADVQGKYLD GAAMDKLKSY FASGELRVRA ASVISANAAT IVKEAVAKSL LYSDVTRPGG (MEN)MYTTR RYA ACIRDLDYYL RYATYAMLAG DASILDERVL NGLKETYNSL GVPISSTVQA IQAIKEVTAS LVGADAGKEM GVYLDYI CS GLS

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: 4 / 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: beta,beta-carotene-4,4'-dione

MacromoleculeName: beta,beta-carotene-4,4'-dione / type: ligand / ID: 7 / Number of copies: 1 / Formula: 45D
Molecular weightTheoretical: 564.84 Da
Chemical component information

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

+
Macromolecule #8: PHYCOCYANOBILIN

MacromoleculeName: PHYCOCYANOBILIN / type: ligand / ID: 8 / Number of copies: 12 / Formula: CYC
Molecular weightTheoretical: 588.694 Da
Chemical component information

ChemComp-CYC:
PHYCOCYANOBILIN / Phycocyanobilin

+
Macromolecule #9: water

MacromoleculeName: water / type: ligand / ID: 9 / Number of copies: 2376 / 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: 7.4
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy

MicroscopeTFS KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.4 µm
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:
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2) / Number images used: 153576
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