[English] 日本語
Yorodumi
- PDB-8tpj: Top cylinder bound to OCP from high-resolution phycobilisome quen... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8tpj
TitleTop cylinder bound to OCP from high-resolution phycobilisome quenched by OCP (local refinement)
Components
  • (Allophycocyanin ...) x 2
  • (Phycobilisome ...) x 2
  • Orange carotenoid-binding protein
  • Phycobiliprotein ApcE
KeywordsPHOTOSYNTHESIS / Complex / light harvesting / pigment
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
beta,beta-carotene-4,4'-dione / PHYCOCYANOBILIN / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.1 Å
AuthorsSauer, P.V. / Sutter, M. / Cupellini, L.
Funding support United States, European Union, Czech Republic, 4items
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, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phycobiliprotein ApcE
B: Orange carotenoid-binding protein
b: Orange carotenoid-binding protein
C: Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core
D: Allophycocyanin alpha chain
E: Allophycocyanin beta chain
F: Allophycocyanin alpha chain
G: Allophycocyanin beta chain
H: Allophycocyanin alpha chain
I: Allophycocyanin beta chain
J: Allophycocyanin alpha chain
K: Allophycocyanin beta chain
L: Allophycocyanin alpha chain
M: Allophycocyanin beta chain
N: Allophycocyanin alpha chain
O: Allophycocyanin beta chain
P: Phycobilisome rod-core linker polypeptide CpcG
Q: Phycobilisome rod-core linker polypeptide CpcG
R: Phycobilisome rod-core linker polypeptide CpcG
S: Phycobilisome rod-core linker polypeptide CpcG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)509,03633
Polymers501,40720
Non-polymers7,62913
Water42,8042376
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 2 types, 3 molecules ABb

#1: Protein Phycobiliprotein ApcE


Mass: 100412.703 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q55544
#2: Protein Orange carotenoid-binding protein


Mass: 34684.605 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Gene: slr1963 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P74102

-
Phycobilisome ... , 2 types, 5 molecules CPQRS

#3: Protein Phycobilisome 7.8 kDa linker polypeptide, allophycocyanin-associated, core


Mass: 7817.174 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q02925
#6: Protein
Phycobilisome rod-core linker polypeptide CpcG


Mass: 28938.758 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: P73093

-
Allophycocyanin ... , 2 types, 12 molecules DFHJLNEGIKMO

#4: Protein
Allophycocyanin alpha chain


Mass: 17429.807 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q01951
#5: Protein
Allophycocyanin beta chain


Mass: 17245.629 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Synechocystis sp. PCC 6803 (bacteria) / References: UniProt: Q01952

-
Non-polymers , 3 types, 2389 molecules

#7: Chemical ChemComp-45D / beta,beta-carotene-4,4'-dione / Isomer of Canthaxanthin


Mass: 564.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H52O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2376 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Phycobilisome bound to OCP / Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Buffer solutionpH: 7.4
SpecimenConc.: 3.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1200 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

-
Processing

EM softwareName: cryoSPARC / Version: 4.2 / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 153576 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 31.56 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.004121687
ELECTRON MICROSCOPYf_angle_d0.576129397
ELECTRON MICROSCOPYf_chiral_restr0.03963321
ELECTRON MICROSCOPYf_plane_restr0.00484130
ELECTRON MICROSCOPYf_dihedral_angle_d5.47413470

+
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