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- PDB-8iml: Rs2I-Rs2II, Rs1I-Rs1II, RbI-RbII cylinder in cyanobacterial phyco... -

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Basic information

Entry
Database: PDB / ID: 8iml
TitleRs2I-Rs2II, Rs1I-Rs1II, RbI-RbII cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster D)
Components
  • CpcA
  • CpcB
  • CpcD
  • CpcG
  • CpcJ
KeywordsPHOTOSYNTHESIS / Complex
Function / homologyPHYCOCYANOBILIN
Function and homology information
Biological speciesAnthocerotibacter panamensis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsWang, C.H. / Yang, C.H. / Wu, H.Y. / Jiang, H.W. / Ho, M.C. / Ho, M.Y.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
National Science Council (NSC, Taiwan) Taiwan
CitationJournal: Nat Commun / Year: 2023
Title: A structure of the relict phycobilisome from a thylakoid-free cyanobacterium.
Authors: Han-Wei Jiang / Hsiang-Yi Wu / Chun-Hsiung Wang / Cheng-Han Yang / Jui-Tse Ko / Han-Chen Ho / Ming-Daw Tsai / Donald A Bryant / Fay-Wei Li / Meng-Chiao Ho / Ming-Yang Ho /
Abstract: Phycobilisomes (PBS) are antenna megacomplexes that transfer energy to photosystems II and I in thylakoids. PBS likely evolved from a basic, inefficient form into the predominant hemidiscoidal shape ...Phycobilisomes (PBS) are antenna megacomplexes that transfer energy to photosystems II and I in thylakoids. PBS likely evolved from a basic, inefficient form into the predominant hemidiscoidal shape with radiating peripheral rods. However, it has been challenging to test this hypothesis because ancestral species are generally inaccessible. Here we use spectroscopy and cryo-electron microscopy to reveal a structure of a "paddle-shaped" PBS from a thylakoid-free cyanobacterium that likely retains ancestral traits. This PBS lacks rods and specialized ApcD and ApcF subunits, indicating relict characteristics. Other features include linkers connecting two chains of five phycocyanin hexamers (CpcN) and two core subdomains (ApcH), resulting in a paddle-shaped configuration. Energy transfer calculations demonstrate that chains are less efficient than rods. These features may nevertheless have increased light absorption by elongating PBS before multilayered thylakoids with hemidiscoidal PBS evolved. Our results provide insights into the evolution and diversification of light-harvesting strategies before the origin of thylakoids.
History
DepositionMar 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
3: CpcJ
A: CpcA
B: CpcA
C: CpcA
D: CpcA
E: CpcA
F: CpcA
G: CpcB
H: CpcB
I: CpcB
J: CpcB
K: CpcB
L: CpcB
M: CpcD
N: CpcA
O: CpcA
P: CpcA
Q: CpcA
R: CpcA
S: CpcA
T: CpcB
U: CpcB
V: CpcB
W: CpcB
X: CpcB
Y: CpcB
Z: CpcD
4: CpcG
a: CpcA
b: CpcA
c: CpcA
d: CpcA
e: CpcA
f: CpcA
g: CpcB
h: CpcB
i: CpcB
j: CpcB
k: CpcB
l: CpcB
m: CpcD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)801,90395
Polymers770,11341
Non-polymers31,78954
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 41 molecules 3ABCDEFNOPQRSabcdefGHIJKLTUVWX...

#1: Protein CpcJ


Mass: 60337.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Anthocerotibacter panamensis (bacteria)
#2: Protein
CpcA


Mass: 17878.260 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Anthocerotibacter panamensis (bacteria)
#3: Protein
CpcB


Mass: 18477.021 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Anthocerotibacter panamensis (bacteria)
#4: Protein CpcD


Mass: 8764.921 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Anthocerotibacter panamensis (bacteria)
#5: Protein CpcG


Mass: 29086.111 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Anthocerotibacter panamensis (bacteria)

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Non-polymers , 1 types, 54 molecules

#6: Chemical...
ChemComp-CYC / PHYCOCYANOBILIN / Phycocyanobilin


Mass: 588.694 Da / Num. of mol.: 54 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Rs2I-Rs2II, Rs1I-Rs1II, RbI-RbII cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster D)
Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL
Source (natural)Organism: Anthocerotibacter panamensis (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 8100 X / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1109579 / Symmetry type: POINT

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