8HG3

Cryo-EM structure of the Lhcp complex from Ostreococcus tauri


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.94 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 S],
B [auth T],
C [auth U]
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
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 U]
BB [auth U]
DA [auth T]
EA [auth T]
FA [auth T]
AB [auth U],
BB [auth U],
DA [auth T],
EA [auth T],
FA [auth T],
G [auth S],
GA [auth T],
H [auth S],
I [auth S],
IB [auth U],
J [auth S],
NA [auth T],
Q [auth S],
TA [auth T],
ZA [auth U]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA
Query on CLA

Download Ideal Coordinates CCD File 
AA [auth T]
BA [auth T]
CA [auth T]
D [auth S]
DB [auth U]
AA [auth T],
BA [auth T],
CA [auth T],
D [auth S],
DB [auth U],
E [auth S],
EB [auth U],
F [auth S],
FB [auth U],
GB [auth U],
HB [auth U],
IA [auth T],
JA [auth T],
KA [auth T],
L [auth S],
LA [auth T],
M [auth S],
MA [auth T],
N [auth S],
O [auth S],
P [auth S],
WA [auth U],
XA [auth U],
YA [auth U]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
KC2
Query on KC2

Download Ideal Coordinates CCD File 
CB [auth U],
HA [auth T],
K [auth S]
Chlorophyll c2
C35 H28 Mg N4 O5
QDRBYWCRXZZVLY-QIEHNWLWSA-L
IWJ (Subject of Investigation/LOI)
Query on IWJ

Download Ideal Coordinates CCD File 
LB [auth U]
RA [auth T]
U [auth S]
UA [auth T]
V [auth S]
LB [auth U],
RA [auth T],
U [auth S],
UA [auth T],
V [auth S],
Y [auth S]
(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 
QA [auth T],
T [auth S]
(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 U]
KB [auth U]
MB [auth U]
OA [auth T]
PA [auth T]
JB [auth U],
KB [auth U],
MB [auth U],
OA [auth T],
PA [auth T],
R [auth S],
S,
SA [auth T],
VA [auth T],
W [auth S],
X [auth S],
Z [auth S]
(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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1

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