7E0I

LHCII-2 in the state transition supercomplex PSI-LHCI-LHCII from the LhcbM1 lacking mutant of Chlamydomonas reinhardti

  • Classification: PHOTOSYNTHESIS
  • Organism(s): Chlamydomonas reinhardtii
  • Mutation(s): No 

  • Deposited: 2021-01-28 Released: 2021-06-30 
  • Deposition Author(s): Pan, X.W., Li, A.J., Liu, Z.F., Li, M.
  • Funding Organization(s): Ministry of Science and Technology (MoST, China), Chinese Academy of Sciences, National Natural Science Foundation of China (NSFC), Japan Society for the Promotion of Science (JSPS)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Structural basis of LhcbM5-mediated state transitions in green algae.

Pan, X.Tokutsu, R.Li, A.Takizawa, K.Song, C.Murata, K.Yamasaki, T.Liu, Z.Minagawa, J.Li, M.

(2021) Nat Plants 7: 1119-1131

  • DOI: https://doi.org/10.1038/s41477-021-00960-8
  • Primary Citation of Related Structures:  
    7DZ7, 7DZ8, 7E0H, 7E0I, 7E0J, 7E0K

  • PubMed Abstract: 

    In green algae and plants, state transitions serve as a short-term light-acclimation process in the regulation of the light-harvesting capacity of photosystems I and II (PSI and PSII, respectively). During the process, a portion of light-harvesting complex II (LHCII) is phosphorylated, dissociated from PSII and binds with PSI to form the supercomplex PSI-LHCI-LHCII. Here, we report high-resolution structures of PSI-LHCI-LHCII from Chlamydomonas reinhardtii, revealing the mechanism of assembly between the PSI-LHCI complex and two phosphorylated LHCII trimers containing all four types of LhcbM protein. Two specific LhcbM isoforms, namely LhcbM1 and LhcbM5, directly interact with the PSI core through their phosphorylated amino terminal regions. Furthermore, biochemical and functional studies on mutant strains lacking either LhcbM1 or LhcbM5 indicate that only LhcbM5 is indispensable in supercomplex formation. The results unravel the specific interactions and potential excitation energy transfer routes between green algal PSI and two phosphorylated LHCIIs.


  • Organizational Affiliation

    National Laboratory of Biomacromolecules, CAS Centre for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticA [auth U]257Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for Q93WL4 (Chlamydomonas reinhardtii)
Explore Q93WL4 
Go to UniProtKB:  Q93WL4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93WL4
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 V]268Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for Q9ZSJ4 (Chlamydomonas reinhardtii)
Explore Q9ZSJ4 
Go to UniProtKB:  Q9ZSJ4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9ZSJ4
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticC [auth W]249Chlamydomonas reinhardtiiMutation(s): 0 
UniProt
Find proteins for Q93WE0 (Chlamydomonas reinhardtii)
Explore Q93WE0 
Go to UniProtKB:  Q93WE0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93WE0
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CHL (Subject of Investigation/LOI)
Query on CHL

Download Ideal Coordinates CCD File 
AA [auth V]
BA [auth V]
CA [auth V]
D [auth U]
DA [auth V]
AA [auth V],
BA [auth V],
CA [auth V],
D [auth U],
DA [auth V],
EA [auth V],
H [auth U],
I [auth U],
J [auth U],
K [auth U],
L [auth U],
QA [auth W],
UA [auth W],
VA [auth W],
W [auth V],
WA [auth W],
XA [auth W],
YA [auth W]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA (Subject of Investigation/LOI)
Query on CLA

Download Ideal Coordinates CCD File 
AB [auth W]
BB [auth W]
CB [auth W]
DB [auth W]
E [auth U]
AB [auth W],
BB [auth W],
CB [auth W],
DB [auth W],
E [auth U],
F [auth U],
FA [auth V],
G [auth U],
GA [auth V],
HA [auth V],
IA [auth V],
JA [auth V],
M [auth U],
N [auth U],
O [auth U],
P [auth U],
Q [auth U],
RA [auth W],
SA [auth W],
TA [auth W],
X [auth V],
Y [auth V],
Z [auth V],
ZA [auth W]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG
Query on LMG

Download Ideal Coordinates CCD File 
PA [auth V]1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

Download Ideal Coordinates CCD File 
IB [auth W],
OA [auth V],
V [auth U]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
NEX
Query on NEX

Download Ideal Coordinates CCD File 
HB [auth W],
NA [auth V],
U
(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
XAT
Query on XAT

Download Ideal Coordinates CCD File 
GB [auth W],
MA [auth V],
T [auth U]
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O4
SZCBXWMUOPQSOX-WVJDLNGLSA-N
LUT
Query on LUT

Download Ideal Coordinates CCD File 
EB [auth W]
FB [auth W]
KA [auth V]
LA [auth V]
R [auth U]
EB [auth W],
FB [auth W],
KA [auth V],
LA [auth V],
R [auth U],
S [auth U]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
B [auth V]L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.53 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2017YFA0503702
Chinese Academy of SciencesChinaXDB27020106
Chinese Academy of SciencesChinaXDB37020101
National Natural Science Foundation of China (NSFC)China31925024
National Natural Science Foundation of China (NSFC)China31930064
Chinese Academy of SciencesChinaZDBS-LY-SM003
Japan Society for the Promotion of Science (JSPS)Japan16H06553
Japan Society for the Promotion of Science (JSPS)JapanJP15H05599

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 2.0: 2021-07-21
    Changes: Data collection, Database references, Non-polymer description
  • Version 2.1: 2021-09-01
    Changes: Database references