8ZET | pdb_00008zet

Tp-PSI-FCPI-S in Thalassiosira pseudonana


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

Structures of PSI-FCPI from Thalassiosira pseudonana grown under high light provide evidence for convergent evolution and light-adaptive strategies in diatom FCPIs.

Feng, Y.Li, Z.Yang, Y.Shen, L.Li, X.Liu, X.Zhang, X.Zhang, J.Ren, F.Wang, Y.Liu, C.Han, G.Wang, X.Kuang, T.Shen, J.R.Wang, W.

(2024) J Integr Plant Biol 

  • DOI: https://doi.org/10.1111/jipb.13816
  • Primary Citation of Related Structures:  
    8ZEH, 8ZET

  • PubMed Abstract: 

    Diatoms rely on fucoxanthin chlorophyll a/c-binding proteins (FCPs) for light harvesting and energy quenching under marine environments. Here we report two cryo-electron microscopic structures of photosystem I (PSI) with either 13 or five fucoxanthin chlorophyll a/c-binding protein Is (FCPIs) at 2.78 and 3.20 Å resolutions from Thalassiosira pseudonana grown under high light (HL) conditions. Among them, five FCPIs are stably associated with the PSI core, these include Lhcr3, RedCAP, Lhcq8, Lhcf10, and FCP3. The eight additional Lhcr-type FCPIs are loosely associated with the PSI core and detached under the present purification conditions. The pigments of this centric diatom showed a higher proportion of chlorophylls a, diadinoxanthins, and diatoxanthins; some of the chlorophyll as and diadinoxanthins occupy the locations of fucoxanthins found in the huge PSI-FCPI from another centric diatom Chaetoceros gracilis grown under low-light conditions. These additional chlorophyll as may form more energy transfer pathways and additional diadinoxanthins may form more energy dissipation sites relying on the diadinoxanthin-diatoxanthin cycle. These results reveal the assembly mechanism of FCPIs and corresponding light-adaptive strategies of T. pseudonana PSI-FCPI, as well as the convergent evolution of the diatom PSI-FCPI structures.


  • Organizational Affiliation

    Key Laboratory of Photobiology, Photosynthesis Research Center, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A [auth a]743Thalassiosira 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 A2B [auth b]732Thalassiosira 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 centerC [auth c]80Thalassiosira pseudonana CCMP1335Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0T0W4 (Thalassiosira pseudonana)
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UniProt GroupA0T0W4
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IID [auth d]132Thalassiosira 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 IVE [auth e]62Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B8LEQ8 (Thalassiosira pseudonana)
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UniProt GroupB8LEQ8
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIF [auth f]160Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0T0V0 (Thalassiosira pseudonana)
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UniProt GroupA0T0V0
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit Psa29G [auth g]131Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIH [auth i]33Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0T0S9 (Thalassiosira pseudonana)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXI [auth j]40Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0T0V1 (Thalassiosira pseudonana)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIJ [auth l]146Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0T0U5 (Thalassiosira pseudonana)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIK [auth m]29Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Tp-PsaRL [auth r]89Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupB8BRQ8
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcq8M [auth B]165Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B8C770 (Thalassiosira pseudonana)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chl a/c light-harvesting protein, major typeN [auth C]170Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B5YM25 (Thalassiosira pseudonana)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Pt17531-like proteinO [auth D]164Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B8CEQ3 (Thalassiosira pseudonana)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Tp-RedCAPP [auth E]185Thalassiosira pseudonana CCMP1335Mutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chl a/c light-harvesting proteinQ [auth H]168Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B8C2K6 (Thalassiosira pseudonana)
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UniProt GroupB8C2K6
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Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

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BD [auth b]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA (Subject of Investigation/LOI)
Query on CLA

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AA [auth a]
AB [auth a]
AC [auth b]
AF [auth B]
AH [auth E]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD (Subject of Investigation/LOI)
Query on SQD

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NB [auth a]1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG (Subject of Investigation/LOI)
Query on LMG

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AG [auth C]
CG [auth D]
EE [auth j]
IF [auth C]
JH [auth E]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG (Subject of Investigation/LOI)
Query on LHG

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BG [auth D]
CD [auth b]
DE [auth j]
HF [auth B]
IH [auth E]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
A86 (Subject of Investigation/LOI)
Query on A86

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DG [auth D]
EG [auth D]
GG [auth D]
JF [auth C]
KH [auth H]
(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 (Subject of Investigation/LOI)
Query on KC1

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FF [auth B],
PF [auth C],
UF [auth C],
VH [auth H]
Chlorophyll c1
C35 H30 Mg N4 O5
DGNIJJSSARBJSH-QIEHNWLWSA-L
DD6 (Subject of Investigation/LOI)
Query on DD6

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FG [auth D]
KF [auth C]
MH [auth H]
UG [auth E]
VE [auth B]
(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
ET4 (Subject of Investigation/LOI)
Query on ET4

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ME [auth l](1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol
C40 H54 O2
HNYJHQMUSVNWPV-DRCJTWAYSA-N
BCR (Subject of Investigation/LOI)
Query on BCR

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AD [auth b]
AE [auth i]
BE [auth i]
CE [auth j]
DD [auth b]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN (Subject of Investigation/LOI)
Query on PQN

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TA [auth a],
YC [auth b]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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SD [auth c],
TD [auth c],
VB [auth b]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina31970260

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-25
    Type: Initial release