6A2W | pdb_00006a2w

Crystal structure of fucoxanthin chlorophyll a/c complex from Phaeodactylum tricornutum

• PDB DOI: https://doi.org/10.2210/pdb6A2W/pdb

• Classification: PHOTOSYNTHESIS
• Organism(s): Phaeodactylum tricornutum CCAP 1055/1
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMmpstruc


• Deposited: 2018-06-13 Released: 2019-02-06 
• Deposition Author(s): Wang, W., Yu, L.J., Kuang, T.Y., Shen, J.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.197 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.173 (DCC) 

Literature

Structural basis for blue-green light harvesting and energy dissipation in diatoms.

Wang, W., Yu, L.J., Xu, C., Tomizaki, T., Zhao, S., Umena, Y., Chen, X., Qin, X., Xin, Y., Suga, M., Han, G., Kuang, T., Shen, J.R.

(2019) Science 363

• PubMed: 30733387 
• DOI: https://doi.org/10.1126/science.aav0365
• Primary Citation Related Structures: 
  6A2W


• PubMed Abstract: 
  

  Diatoms are abundant photosynthetic organisms in aquatic environments and contribute 40% of its primary productivity. An important factor that contributes to the success of diatoms is their fucoxanthin chlorophyll a/c-binding proteins (FCPs), which have exceptional light-harvesting and photoprotection capabilities. Here, we report the crystal structure of an FCP from the marine diatom Phaeodactylum tricornutum , which reveals the binding of seven chlorophylls (Chls) a, two Chls c, seven fucoxanthins (Fxs), and probably one diadinoxanthin within the protein scaffold. Efficient energy transfer pathways can be found between Chl a and c, and each Fx is surrounded by Chls, enabling the energy transfer and quenching via Fx highly efficient. The structure provides a basis for elucidating the mechanisms of blue-green light harvesting, energy transfer, and dissipation in diatoms.

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Organizational Affiliation: 
• Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China.
Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, 700-8530 Okayama, Japan.
University of Chinese Academy of Science, Yuquan Road, Shijingshan District, Beijing 100049, China.
Photon Science Division, Laboratory for Macromolecules and Bioimaging (LSB), Paul Scherrer Institut, 5232 Villigen-PSI, Switzerland.
Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, 100093 Beijing, China. [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 34.51 kDa 
• Atom Count: 2,518 
• Modeled Residue Count: 166 
• Deposited Residue Count: 167 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein fucoxanthin chlorophyl a/c protein	A	167	Phaeodactylum tricornutum CCAP 1055/1	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B7FRW2 (Phaeodactylum tricornutum (strain CCAP 1055/1)) Explore B7FRW2  Go to UniProtKB:  B7FRW2

Small Molecules

Ligands 11 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DGD	V [auth A]	DIGALACTOSYL DIACYL GLYCEROL (DGDG) C51 H96 O15 LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA	L [auth A], M [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], T [auth A]	CHLOROPHYLL A C55 H72 Mg N4 O5 ATNHDLDRLWWWCB-AENOIHSZSA-M
LHG	W [auth A]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
A86	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	(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	S [auth A]	Chlorophyll c1 C35 H30 Mg N4 O5 DGNIJJSSARBJSH-QIEHNWLWSA-L
KC2	N [auth A]	Chlorophyll c2 C35 H28 Mg N4 O5 QDRBYWCRXZZVLY-QIEHNWLWSA-L
DD6	K [auth A]	(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
LMT	U [auth A]	DODECYL-BETA-D-MALTOSIDE C24 H46 O11 NLEBIOOXCVAHBD-QKMCSOCLSA-N
SOG	AA [auth A], X [auth A], Y [auth A], Z [auth A]	octyl 1-thio-beta-D-glucopyranoside C14 H28 O5 S CGVLVOOFCGWBCS-RGDJUOJXSA-N
CA	B [auth A], C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
UNL	BA [auth A], CA [auth A], DA [auth A], EA [auth A], FA [auth A], GA [auth A], HA [auth A]	Unknown ligand BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.197 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.173 (DCC) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.749	α = 90
b = 115.718	β = 90
c = 141.261	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PDB_EXTRACT	data extraction
CRANK2	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-02-06 
Deposition Author(s): Wang, W., Yu, L.J., Kuang, T.Y., Shen, J.R.

Revision History  

• Version 1.0: 2019-02-06
  Type: Initial release
  
• Version 2.0: 2019-02-20
  Changes: Advisory, Atomic model, Data collection, Derived calculations
• Version 2.1: 2019-02-27
  Changes: Data collection, Database references
• Version 2.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Derived calculations, Structure summary
• Version 3.0: 2024-03-27
  Changes: Data collection, Database references, Non-polymer description, Structure summary