8WCL

FCP pentamer in Chaetoceros gracilis


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.65 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/c-binding protein Lhcf6A [auth 6]211Chaetoceros neogracilisMutation(s): 0 
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a/b-binding proteinB [auth 8],
D [auth 5]
207Chaetoceros neogracilisMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin-chlorophyll a/c proteinC [auth 9]195Chaetoceros neogracilisMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a/c-binding protein Lhcf7E [auth 7]207Chaetoceros neogracilisMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA (Subject of Investigation/LOI)
Query on CLA

Download Ideal Coordinates CCD File 
AC [auth 7]
BA [auth 8]
CC [auth 7]
EA [auth 8]
FB [auth 5]
AC [auth 7],
BA [auth 8],
CC [auth 7],
EA [auth 8],
FB [auth 5],
FC [auth 7],
GA [auth 8],
GB [auth 5],
HA [auth 8],
HC [auth 7],
IB [auth 5],
J [auth 6],
K [auth 6],
LB [auth 5],
M [auth 6],
NB [auth 5],
OB [auth 5],
P [auth 6],
QA [auth 9],
R [auth 6],
RA [auth 9],
S [auth 6],
TA [auth 9],
UA [auth 9],
VA [auth 9],
WA [auth 9],
YA [auth 9],
Z [auth 8],
ZB [auth 7]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG (Subject of Investigation/LOI)
Query on LMG

Download Ideal Coordinates CCD File 
IC [auth 7],
ZA [auth 9]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
A86 (Subject of Investigation/LOI)
Query on A86

Download Ideal Coordinates CCD File 
AB [auth 5]
BB [auth 5]
CB [auth 5]
DB [auth 5]
EB [auth 5]
AB [auth 5],
BB [auth 5],
CB [auth 5],
DB [auth 5],
EB [auth 5],
F [auth 6],
G [auth 6],
H [auth 6],
I [auth 6],
JA [auth 9],
KA [auth 9],
LA [auth 9],
MA [auth 9],
NA [auth 9],
OA [auth 9],
PA [auth 9],
RB [auth 5],
SB [auth 7],
T [auth 8],
TB [auth 7],
U [auth 8],
UB [auth 7],
V [auth 8],
VB [auth 7],
W [auth 8],
WB [auth 7],
X [auth 8],
XB [auth 7],
Y [auth 8],
YB [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
KC1 (Subject of Investigation/LOI)
Query on KC1

Download Ideal Coordinates CCD File 
DA [auth 8]
EC [auth 7]
FA [auth 8]
GC [auth 7]
KB [auth 5]
DA [auth 8],
EC [auth 7],
FA [auth 8],
GC [auth 7],
KB [auth 5],
MB [auth 5],
O [auth 6],
Q [auth 6],
XA [auth 9]
Chlorophyll c1
C35 H30 Mg N4 O5
DGNIJJSSARBJSH-QIEHNWLWSA-L
KC2 (Subject of Investigation/LOI)
Query on KC2

Download Ideal Coordinates CCD File 
AA [auth 8]
BC [auth 7]
CA [auth 8]
DC [auth 7]
HB [auth 5]
AA [auth 8],
BC [auth 7],
CA [auth 8],
DC [auth 7],
HB [auth 5],
JB [auth 5],
L [auth 6],
N [auth 6],
SA [auth 9]
Chlorophyll c2
C35 H28 Mg N4 O5
QDRBYWCRXZZVLY-QIEHNWLWSA-L
LMT (Subject of Investigation/LOI)
Query on LMT

Download Ideal Coordinates CCD File 
IA [auth 8],
JC [auth 7],
KC [auth 7],
PB [auth 5],
QB [auth 5]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.65 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