8WEY

PSI-LHCI of the red alga Cyanidium caldarium RK-1 (NIES-2137)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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This is version 1.3 of the entry. See complete history


Literature

The structure of PSI-LHCI from Cyanidium caldarium provides evolutionary insights into conservation and diversity of red-lineage LHCs.

Kato, K.Hamaguchi, T.Kumazawa, M.Nakajima, Y.Ifuku, K.Hirooka, S.Hirose, Y.Miyagishima, S.Y.Suzuki, T.Kawakami, K.Dohmae, N.Yonekura, K.Shen, J.R.Nagao, R.

(2024) Proc Natl Acad Sci U S A 121: e2319658121-e2319658121

  • DOI: https://doi.org/10.1073/pnas.2319658121
  • Primary Citation of Related Structures:  
    8WEY

  • PubMed Abstract: 

    Light-harvesting complexes (LHCs) are diversified among photosynthetic organisms, and the structure of the photosystem I-LHC (PSI-LHCI) supercomplex has been shown to be variable depending on the species of organisms. However, the structural and evolutionary correlations of red-lineage LHCs are unknown. Here, we determined a 1.92-Å resolution cryoelectron microscopic structure of a PSI-LHCI supercomplex isolated from the red alga Cyanidium caldarium RK-1 (NIES-2137), which is an important taxon in the Cyanidiophyceae. We subsequently investigated the correlations of PSI-LHCIs from different organisms through structural comparisons and phylogenetic analysis. The PSI-LHCI structure obtained shows five LHCI subunits surrounding a PSI-monomer core. The five LHCIs are composed of two Lhcr1s, two Lhcr2s, and one Lhcr3. Phylogenetic analysis of LHCs bound to PSI in the red-lineage algae showed clear orthology of LHCs between C. caldarium and Cyanidioschyzon merolae , whereas no orthologous relationships were found between C. caldarium Lhcr1-3 and LHCs in other red-lineage PSI-LHCI structures. These findings provide evolutionary insights into conservation and diversity of red-lineage LHCs associated with PSI.


  • Organizational Affiliation

    Division of Photosynthesis and Structural Biology, Research Institute for Interdisciplinary Science, and Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1748Cyanidium caldariumMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2732Cyanidium caldariumMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center81Cyanidium caldariumMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II139Cyanidium caldariumMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV61Cyanidium caldariumMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III178Cyanidium caldariumMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIG [auth I]32Cyanidium caldariumMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXH [auth J]38Cyanidium caldariumMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XI [auth K]68Cyanidium caldariumMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIJ [auth L]141Cyanidium caldariumMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIK [auth M]28Cyanidium caldariumMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I subunit OL [auth O]155Cyanidium caldariumMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Lhcr1M [auth 1],
P [auth 4]
214Cyanidium caldariumMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Lhcr2N [auth 2],
Q [auth 5]
222Cyanidium caldariumMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Lhcr3O [auth 3]219Cyanidium caldariumMutation(s): 0 
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Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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UD [auth B]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
Query on CLA

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AA [auth A]
AB [auth A]
AD [auth B]
AH [auth 3]
BA [auth A]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0
Query on CL0

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R [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LHG
Query on LHG

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FB [auth A],
GB [auth A],
OE [auth J]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
5X6
Query on 5X6

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AI [auth 4]
BI [auth 4]
CI [auth 5]
KE [auth F]
LH [auth 3]
Zeaxanthin
C40 H56 O2
JKQXZKUSFCKOGQ-AYORJBSZSA-N
BCR
Query on BCR

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AC [auth B]
AF [auth L]
BF [auth L]
EF [auth M]
GF [auth O]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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CF [auth L]
GE [auth F]
MB [auth A]
VD [auth B]
WD [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
Query on PQN

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EB [auth A],
ND [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

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EE [auth C],
FE [auth C],
LB [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
UNL
Query on UNL

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AE [auth B]
AG [auth 1]
BE [auth B]
BG [auth 2]
CG [auth 2]
Unknown ligand
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 1.92 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTServalcat0.2.0
MODEL REFINEMENTPHENIX1.18.2-3874

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-02-14
    Type: Initial release
  • Version 1.1: 2024-03-13
    Changes: Database references
  • Version 1.2: 2024-10-16
    Changes: Data collection, Structure summary
  • Version 1.3: 2024-11-27
    Changes: Data collection, Derived calculations, Structure summary