8WCK

FCP tetramer in Chaetoceros gracilis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.71 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

Structural and spectroscopic insights into fucoxanthin chlorophyll a/c-binding proteins of diatoms in diverse oligomeric states.

Zhou, C.Feng, Y.Li, Z.Shen, L.Li, X.Wang, Y.Han, G.Kuang, T.Liu, C.Shen, J.R.Wang, W.

(2024) Plant Commun : 101041-101041

  • DOI: https://doi.org/10.1016/j.xplc.2024.101041
  • Primary Citation of Related Structures:  
    8JP3, 8WCK, 8WCL

  • PubMed Abstract: 

    Diatoms, a group of prevalent marine algae, significantly contribute to global primary productivity. Their substantial biomass is linked to enhanced absorption of blue-green light underwater, facilitated by fucoxanthin chlorophyll a/c-binding proteins (FCPs), exhibiting oligomeric diversity across diatom species. Utilizing mild CN-PAGE analysis on solubilized thylakoid membranes, we displayed monomeric, dimeric, trimeric, tetrameric and pentameric FCPs in diatoms. Mass spectrometry analysis revealed each oligomeric FCP has specific protein compositions, constituting a large Lhcf family of FCP antennas. In addition, we resolved the structures of Thalassiosira pseudonana FCP (Tp-FCP) homotrimer and Chaetoceros gracilis FCP (Cg-FCP) pentamer by cryo-electron microscopy at 2.73 Å and 2.65 Å resolutions, respectively. The distinct pigment composition and organization in various oligomeric FCPs change their blue-green light-harvesting, excitation energy transfer pathways. In comparison to dimeric and trimeric FCPs, Cg-FCP tetramer and Cg-FCP pentamer exhibit stronger absorption by Chls c, red-shifted and broader Chl a fluorescence emission, as well as more robust circular dichroism signals originating from Chl a-carotenoid dimers. These spectroscopic characteristics indicate that Chl a molecules in Cg-FCP tetramer and Cg-FCP pentamer are more heterogeneous than in both dimers and Tp-FCP trimer. The structural and spectroscopic insights provided by this study contribute to a better understanding of the mechanisms that empower diatoms to adapt to fluctuating light environments.


  • Organizational Affiliation

    Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, P. R. China; University of Chinese Academy of Sciences, Beijing 100049, P. R. China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a/b-binding proteinA [auth 1],
B [auth 2],
C [auth 3],
D [auth 4]
207Chaetoceros neogracilisMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A679BXP6 (Chaetoceros neogracilis)
Explore A0A679BXP6 
Go to UniProtKB:  A0A679BXP6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A679BXP6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA (Subject of Investigation/LOI)
Query on CLA

Download Ideal Coordinates CCD File 
BB [auth 3]
DA [auth 2]
DB [auth 3]
EA [auth 2]
EB [auth 3]
BB [auth 3],
DA [auth 2],
DB [auth 3],
EA [auth 2],
EB [auth 3],
GA [auth 2],
JA [auth 2],
K [auth 1],
LA [auth 2],
M [auth 1],
MA [auth 2],
NB [auth 4],
P [auth 1],
PB [auth 4],
R [auth 1],
S [auth 1],
SB [auth 4],
UB [auth 4],
V [auth 1],
VA [auth 3],
VB [auth 4],
W [auth 2],
WA [auth 3],
YA [auth 3]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
A86 (Subject of Investigation/LOI)
Query on A86

Download Ideal Coordinates CCD File 
AA [auth 2]
BA [auth 2]
CA [auth 2]
E [auth 1]
F [auth 1]
AA [auth 2],
BA [auth 2],
CA [auth 2],
E [auth 1],
F [auth 1],
G [auth 1],
H [auth 1],
HB [auth 4],
I [auth 1],
IB [auth 4],
J [auth 1],
JB [auth 4],
KB [auth 4],
LB [auth 4],
MB [auth 4],
PA [auth 3],
QA [auth 3],
RA [auth 3],
SA [auth 3],
TA [auth 3],
UA [auth 3],
X [auth 2],
Y [auth 2],
Z [auth 2]
(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

Download Ideal Coordinates CCD File 
AB [auth 3]
CB [auth 3]
IA [auth 2]
KA [auth 2]
O [auth 1]
AB [auth 3],
CB [auth 3],
IA [auth 2],
KA [auth 2],
O [auth 1],
Q [auth 1],
RB [auth 4],
TB [auth 4]
Chlorophyll c1
C35 H30 Mg N4 O5
DGNIJJSSARBJSH-QIEHNWLWSA-L
KC2 (Subject of Investigation/LOI)
Query on KC2

Download Ideal Coordinates CCD File 
FA [auth 2]
HA [auth 2]
L [auth 1]
N [auth 1]
OB [auth 4]
FA [auth 2],
HA [auth 2],
L [auth 1],
N [auth 1],
OB [auth 4],
QB [auth 4],
XA [auth 3],
ZA [auth 3]
Chlorophyll c2
C35 H28 Mg N4 O5
QDRBYWCRXZZVLY-QIEHNWLWSA-L
LMT (Subject of Investigation/LOI)
Query on LMT

Download Ideal Coordinates CCD File 
FB [auth 3]
GB [auth 3]
NA [auth 2]
OA [auth 2]
T [auth 1]
FB [auth 3],
GB [auth 3],
NA [auth 2],
OA [auth 2],
T [auth 1],
U [auth 1],
WB [auth 4],
XB [auth 4]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.71 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina2021YFA1300403

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-31
    Type: Initial release