8XLS

PSI-FCPI of the diatom Thalassiosira pseudonana CCMP1335


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for molecular assembly of fucoxanthin chlorophyll a / c -binding proteins in a diatom photosystem I supercomplex.

Kato, K.Nakajima, Y.Xing, J.Kumazawa, M.Ogawa, H.Shen, J.R.Ifuku, K.Nagao, R.

(2024) Elife 13

  • DOI: https://doi.org/10.7554/eLife.99858
  • Primary Citation of Related Structures:  
    8XLS

  • PubMed Abstract: 

    Photosynthetic organisms exhibit remarkable diversity in their light-harvesting complexes (LHCs). LHCs are associated with photosystem I (PSI), forming a PSI-LHCI supercomplex. The number of LHCI subunits, along with their protein sequences and pigment compositions, has been found to differ greatly among the PSI-LHCI structures. However, the mechanisms by which LHCIs recognize their specific binding sites within the PSI core remain unclear. In this study, we determined the cryo-electron microscopy structure of a PSI supercomplex incorporating fucoxanthin chlorophyll a / c -binding proteins (FCPs), designated as PSI-FCPI, isolated from the diatom Thalassiosira pseudonana CCMP1335. Structural analysis of PSI-FCPI revealed five FCPI subunits associated with a PSI monomer; these subunits were identified as RedCAP, Lhcr3, Lhcq10, Lhcf10, and Lhcq8. Through structural and sequence analyses, we identified specific protein-protein interactions at the interfaces between FCPI and PSI subunits, as well as among FCPI subunits themselves. Comparative structural analyses of PSI-FCPI supercomplexes, combined with phylogenetic analysis of FCPs from T. pseudonana and the diatom Chaetoceros gracilis , underscore the evolutionary conservation of protein motifs crucial for the selective binding of individual FCPI subunits. These findings provide significant insights into the molecular mechanisms underlying the assembly and selective binding of FCPIs in diatoms.


  • Organizational Affiliation

    Research Institute for Interdisciplinary Science and Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1752Thalassiosira pseudonana CCMP1335Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0T0M8 (Thalassiosira pseudonana)
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UniProt GroupA0T0M8
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2733Thalassiosira pseudonana CCMP1335Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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UniProt GroupA0T0M9
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center81Thalassiosira pseudonana CCMP1335Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for B8LEV1 (Thalassiosira pseudonana)
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UniProt GroupB8LEV1
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II139Thalassiosira pseudonana CCMP1335Mutation(s): 0 
UniProt
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UniProt GroupA0T0T5
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV65Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A8F0WFC9 (Thalassiosira pseudonana)
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UniProt GroupA0A8F0WFC9
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III185Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupA0T0V0
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIG [auth I]36Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupA0T0S9
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXH [auth J]41Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XII [auth L]148Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0T0U5 (Thalassiosira pseudonana)
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UniProt GroupA0T0U5
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIJ [auth M]30Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0T0S1 (Thalassiosira pseudonana)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit Psa29K [auth W]188Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B8BUW3 (Thalassiosira pseudonana)
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UniProt GroupB8BUW3
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown proteinL [auth u]84Thalassiosira pseudonana CCMP1335Mutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein RedCAPM [auth 1]221Thalassiosira pseudonana CCMP1335Mutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chl a/c light-harvesting proteinN [auth 2]198Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B8C2K6 (Thalassiosira pseudonana)
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UniProt GroupB8C2K6
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Pt17531-like proteinO [auth 3]196Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B8CEQ3 (Thalassiosira pseudonana)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chl a/c light-harvesting protein, major typeP [auth 4]201Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B5YM25 (Thalassiosira pseudonana)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcq8Q [auth 5]194Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B8C770 (Thalassiosira pseudonana)
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UniProt GroupB8C770
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Small Molecules
Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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OE [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]
AE [auth B]
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
LMG
Query on LMG

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IG [auth 1]1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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CG [auth M]
JE [auth B]
QB [auth A]
RB [auth A]
UI [auth 3]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
A86
Query on A86

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HJ [auth 3]
RI [auth 3]
SK [auth 5]
TH [auth 2]
TI [auth 3]
(3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate
C42 H58 O6
SJWWTRQNNRNTPU-XJUZQKKNSA-N
KC1
Query on KC1

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JJ [auth 4]
KI [auth 3]
LG [auth 1]
NI [auth 3]
OH [auth 2]
Chlorophyll c1
C35 H30 Mg N4 O5
DGNIJJSSARBJSH-QIEHNWLWSA-L
DD6
Query on DD6

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SG [auth 1]
SI [auth 3]
TG [auth 1]
TK [auth 5]
UH [auth 2]
(3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol
C40 H54 O3
OGHZCSINIMWCSB-WMTIXGNLSA-N
5X6
Query on 5X6

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MF [auth J]Zeaxanthin
C40 H56 O2
JKQXZKUSFCKOGQ-AYORJBSZSA-N
BCR
Query on BCR

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BG [auth M]
DF [auth F]
GF [auth I]
HE [auth B]
HF [auth I]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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DH [auth 1],
SB [auth A],
VI [auth 3],
XH [auth 2]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
Query on PQN

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

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KB [auth A],
XE [auth C],
YE [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
UNL
Query on UNL

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AC [auth A]
AF [auth F]
AG [auth M]
AH [auth 1]
AI [auth 2]
Unknown ligand
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4.0
MODEL REFINEMENTServalcat0.4.32
MODEL REFINEMENTREFMAC5.8.0419
MODEL REFINEMENTPHENIX1.20.1

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: 2024-10-30
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Database references
  • Version 1.2: 2024-11-27
    Changes: Data collection, Database references, Derived calculations, Structure summary