8HG5

Cryo-EM structure of the prasinophyte-specific light-harvesting complex (Lhcp)from Ostreococcus tauri


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

The photosystem I supercomplex from a primordial green alga Ostreococcus tauri harbors three light-harvesting complex trimers.

Ishii, A.Shan, J.Sheng, X.Kim, E.Watanabe, A.Yokono, M.Noda, C.Song, C.Murata, K.Liu, Z.Minagawa, J.

(2023) Elife 12

  • DOI: https://doi.org/10.7554/eLife.84488
  • Primary Citation of Related Structures:  
    7YCA, 8HG3, 8HG5, 8HG6

  • PubMed Abstract: 

    As a ubiquitous picophytoplankton in the ocean and an early-branching green alga, Ostreococcus tauri is a model prasinophyte species for studying the functional evolution of the light-harvesting systems in photosynthesis. Here, we report the structure and function of the O. tauri photosystem I (PSI) supercomplex in low light conditions, where it expands its photon-absorbing capacity by assembling with the light-harvesting complexes I (LHCI) and a prasinophyte-specific light-harvesting complex (Lhcp). The architecture of the supercomplex exhibits hybrid features of the plant-type and the green algal-type PSI supercomplexes, consisting of a PSI core, an Lhca1-Lhca4-Lhca2-Lhca3 belt attached on one side and an Lhca5-Lhca6 heterodimer associated on the other side between PsaG and PsaH. Interestingly, nine Lhcp subunits, including one Lhcp1 monomer with a phosphorylated amino-terminal threonine and eight Lhcp2 monomers, oligomerize into three trimers and associate with PSI on the third side between Lhca6 and PsaK. The Lhcp1 phosphorylation and the light-harvesting capacity of PSI were subjected to reversible photoacclimation, suggesting that the formation of Ot PSI-LHCI-Lhcp supercomplex is likely due to a phosphorylation-dependent mechanism induced by changes in light intensity. Notably, this supercomplex did not exhibit far-red peaks in the 77 K fluorescence spectra, which is possibly due to the weak coupling of the chlorophyll a 603- a 609 pair in Ot Lhca1-4.


  • Organizational Affiliation

    Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticA [auth P],
C [auth R]
233Ostreococcus tauriMutation(s): 0 
Gene Names: OT_ostta16g00450
UniProt
Find proteins for Q3B9U7 (Ostreococcus tauri)
Explore Q3B9U7 
Go to UniProtKB:  Q3B9U7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3B9U7
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticB [auth Q]226Ostreococcus tauriMutation(s): 1 
Gene Names: OT_ostta01g04940
UniProt
Find proteins for A0A090LYE8 (Ostreococcus tauri)
Explore A0A090LYE8 
Go to UniProtKB:  A0A090LYE8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A090LYE8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CHL
Query on CHL

Download Ideal Coordinates CCD File 
AB [auth R]
BB [auth R]
CA [auth Q]
DA [auth Q]
EA [auth Q]
AB [auth R],
BB [auth R],
CA [auth Q],
DA [auth Q],
EA [auth Q],
G [auth P],
H [auth P],
I [auth P],
IB [auth R],
J [auth P],
LA [auth Q],
Q [auth P],
SA [auth R],
YA [auth R],
ZA [auth R]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA
Query on CLA

Download Ideal Coordinates CCD File 
AA [auth Q]
BA [auth Q]
D [auth P]
DB [auth R]
E [auth P]
AA [auth Q],
BA [auth Q],
D [auth P],
DB [auth R],
E [auth P],
EB [auth R],
F [auth P],
FB [auth R],
GA [auth Q],
GB [auth R],
HA [auth Q],
HB [auth R],
IA [auth Q],
JA [auth Q],
KA [auth Q],
L [auth P],
M [auth P],
N [auth P],
O [auth P],
P,
VA [auth R],
WA [auth R],
XA [auth R],
Z [auth Q]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
KC2
Query on KC2

Download Ideal Coordinates CCD File 
CB [auth R],
FA [auth Q],
K [auth P]
Chlorophyll c2
C35 H28 Mg N4 O5
QDRBYWCRXZZVLY-QIEHNWLWSA-L
IWJ
Query on IWJ

Download Ideal Coordinates CCD File 
MB [auth R]
QA [auth Q]
TA [auth R]
U [auth P]
W [auth P]
MB [auth R],
QA [auth Q],
TA [auth R],
U [auth P],
W [auth P],
Y [auth Q]
(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-1-[(1~{S},4~{S})-2,2-dimethyl-6-methylidene-1,4-bis(oxidanyl)cyclohexyl]-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-2-one
C40 H56 O4
WOJYJHBMWRNRJG-ITGJSFTBSA-N
NEX
Query on NEX

Download Ideal Coordinates CCD File 
LB [auth R],
MA [auth Q],
T [auth P]
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
C40 H56 O4
PGYAYSRVSAJXTE-OQASCVKESA-N
Q6L (Subject of Investigation/LOI)
Query on Q6L

Download Ideal Coordinates CCD File 
JB [auth R]
KB [auth R]
NA [auth Q]
NB [auth R]
OA [auth Q]
JB [auth R],
KB [auth R],
NA [auth Q],
NB [auth R],
OA [auth Q],
PA [auth Q],
R [auth P],
RA [auth R],
S [auth P],
UA [auth R],
V [auth P],
X [auth P]
(1~{S})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaenyl]cyclohex-3-en-1-ol
C40 H58 O2
ULGXMGDBVFOYRY-NBTBXAKCSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
B [auth Q]L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan21H04778 and 21H05040
Chinese Academy of SciencesChinaXDB37020101 and YSBR-015
National Natural Science Foundation of China (NSFC)China31925024
Ministry of Science and Technology (MoST, China)China2017YFA0503702

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release