8W4O | pdb_00008w4o

Structure of PSII-FCPII-G/H complex in the PSII-FCPII supercomplex from Cyclotella meneghiniana


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.23 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8W4O

This is version 1.1 of the entry. See complete history

Literature

Structural insights into photosystem II supercomplex and trimeric FCP antennae of a centric diatom Cyclotella meneghiniana.

Zhao, S.Shen, L.Li, X.Tao, Q.Li, Z.Xu, C.Zhou, C.Yang, Y.Sang, M.Han, G.Yu, L.J.Kuang, T.Shen, J.R.Wang, W.

(2023) Nat Commun 14: 8164-8164

  • DOI: https://doi.org/10.1038/s41467-023-44055-8
  • Primary Citation Related Structures: 
    8J5K, 8J7Z, 8W4O, 8W4P

  • PubMed Abstract: 

    Diatoms are dominant marine algae and contribute around a quarter of global primary productivity, the success of which is largely attributed to their photosynthetic capacity aided by specific fucoxanthin chlorophyll-binding proteins (FCPs) to enhance the blue-green light absorption under water. We purified a photosystem II (PSII)-FCPII supercomplex and a trimeric FCP from Cyclotella meneghiniana (Cm) and solved their structures by cryo-electron microscopy (cryo-EM). The structures reveal detailed organizations of monomeric, dimeric and trimeric FCP antennae, as well as distinct assemblies of Lhcx6_1 and dimeric FCPII-H in PSII core. Each Cm-PSII-FCPII monomer contains an Lhcx6_1, an FCP heterodimer and other three FCP monomers, which form an efficient pigment network for harvesting energy. More diadinoxanthins and diatoxanthins are found in FCPs, which may function to quench excess energy. The trimeric FCP contains more chlorophylls c and fucoxanthins. These diversified FCPs and PSII-FCPII provide a structural basis for efficient light energy harvesting, transfer, and dissipation in C. meneghiniana.


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

Macromolecule Content 

  • Total Structure Weight: 97.62 kDa 
  • Atom Count: 6,046 
  • Modeled Residue Count: 497 
  • Deposited Residue Count: 497 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
FCPII-G, Fucoxanthin chlorophyll a/c binding proteinA [auth 5]169Stephanocyclus meneghinianusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B5YLU3 (Thalassiosira pseudonana)
Explore B5YLU3 
Go to UniProtKB:  B5YLU3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB5YLU3
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
FCPII-H2, Fucoxanthin chlorophyll a/c binding proteinB [auth 7]164Stephanocyclus meneghinianusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
FCPII-H1, Fucoxanthin chlorophyll a/c binding proteinC [auth 6]164Stephanocyclus meneghinianusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B8BX93 (Thalassiosira pseudonana)
Explore B8BX93 
Go to UniProtKB:  B8BX93
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB8BX93
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA
(Subject of Investigation/LOI)

Query on CLA



Download:Ideal Coordinates CCD File
AB [auth 6]
BA [auth 7]
BB [auth 6]
CA [auth 7]
CB [auth 6]
AB [auth 6],
BA [auth 7],
BB [auth 6],
CA [auth 7],
CB [auth 6],
DA [auth 7],
EA [auth 7],
FA [auth 7],
G [auth 5],
GA [auth 7],
H [auth 5],
HA [auth 7],
I [auth 5],
IA [auth 7],
J [auth 5],
JA [auth 7],
K [auth 5],
KA [auth 7],
L [auth 5],
LA [auth 7],
M [auth 5],
MA [auth 7],
N [auth 5],
NA [auth 6],
O [auth 5],
P [auth 5],
Q [auth 5],
RA [auth 6],
SA [auth 6],
TA [auth 6],
UA [auth 6],
VA [auth 6],
WA [auth 6],
XA [auth 6],
YA [auth 6],
ZA [auth 6]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD
(Subject of Investigation/LOI)

Query on SQD



Download:Ideal Coordinates CCD File
V [auth 5]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



Download:Ideal Coordinates CCD File
S [auth 5]1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
(Subject of Investigation/LOI)

Query on LHG



Download:Ideal Coordinates CCD File
R [auth 5],
T [auth 5],
U [auth 5]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
A86
(Subject of Investigation/LOI)

Query on A86



Download:Ideal Coordinates CCD File
D [auth 5]
F [auth 5]
OA [auth 6]
W [auth 5]
X [auth 7]
D [auth 5],
F [auth 5],
OA [auth 6],
W [auth 5],
X [auth 7],
Y [auth 7]
(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
DD6

Query on DD6



Download:Ideal Coordinates CCD File
AA [auth 7],
PA [auth 6],
QA [auth 6],
Z [auth 7]
(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

Query on ET4



Download:Ideal Coordinates CCD File
E [auth 5](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

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.23 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina--

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-20
    Type: Initial release
  • Version 1.1: 2025-06-18
    Changes: Data collection, Structure summary