7WLM

The Cryo-EM structure of siphonaxanthin chlorophyll a/b type light-harvesting complex II


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into blue-green light utilization by marine green algal light harvesting complex II at 2.78 angstrom.

Seki, S.Nakaniwa, T.Castro-Hartmann, P.Sader, K.Kawamoto, A.Tanaka, H.Qian, P.Kurisu, G.Fujii, R.

(2022) BBA Adv 2: 100064-100064

  • DOI: https://doi.org/10.1016/j.bbadva.2022.100064
  • Primary Citation of Related Structures:  
    7WLM

  • PubMed Abstract: 

    Light-harvesting complex II (LHCII) present in plants and green algae absorbs solar energy to promote photochemical reactions. A marine green macroalga, Codium fragile , exhibits the unique characteristic of absorbing blue-green light from the sun during photochemical reactions while being underwater owing to the presence of pigment-altered LHCII called siphonaxanthin-chlorophyll a/b- binding protein (SCP). In this study, we determined the structure of SCP at a resolution of 2.78 Å using cryogenic electron microscopy. SCP has a trimeric structure, wherein each monomer containing two lutein and two chlorophyll a molecules in the plant-type LHCII are replaced by siphonaxanthin and its ester and two chlorophyll b molecules, respectively. Siphonaxanthin occupies the binding site in SCP having a polarity in the trimeric inner core, and exhibits a distorted conjugated chain comprising a carbonyl group hydrogen bonded to a cysteine residue of apoprotein. These features suggest that the siphonaxanthin molecule is responsible for the characteristic green absorption of SCP. The replaced chlorophyll b molecules extend the region of the stromal side chlorophyll b cluster, spanning two adjacent monomers.


  • Organizational Affiliation

    Division of Molecular Materials Science, Graduate School of Science, Osaka City University, 3-3-138, Sugimoto, Sumiyoshi-ku, Osaka 558-8585, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
siphonaxanthin chlorophyll a/b binding light-harvesting complex II
A, B, C
223Codium fragileMutation(s): 0 
UniProt
Find proteins for A0A8S0G488 (Codium fragile)
Explore A0A8S0G488 
Go to UniProtKB:  A0A8S0G488
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A8S0G488
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CHL (Subject of Investigation/LOI)
Query on CHL

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
D [auth A]
DA [auth B]
AA [auth B],
BA [auth B],
CA [auth B],
D [auth A],
DA [auth B],
E [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
LA [auth C],
M [auth A],
MA [auth C],
PA [auth C],
QA [auth C],
RA [auth C],
SA [auth C],
TA [auth C],
U [auth B],
UA [auth C],
V [auth B],
Y [auth B],
Z [auth B]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA
Query on CLA

Download Ideal Coordinates CCD File 
EA [auth B]
F [auth A]
FA [auth B]
G [auth A]
GA [auth B]
EA [auth B],
F [auth A],
FA [auth B],
G [auth A],
GA [auth B],
N [auth A],
NA [auth C],
O [auth A],
OA [auth C],
P [auth A],
VA [auth C],
W [auth B],
WA [auth C],
X [auth B],
XA [auth C]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
0UR (Subject of Investigation/LOI)
Query on 0UR

Download Ideal Coordinates CCD File 
IA [auth B],
R [auth A],
ZA [auth C]
Siphonein
C52 H76 O5
UERRVASYDCUNEJ-DHYZAJTQSA-N
LHG
Query on LHG

Download Ideal Coordinates CCD File 
BB [auth C],
KA [auth B],
T [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
0IE (Subject of Investigation/LOI)
Query on 0IE

Download Ideal Coordinates CCD File 
AB [auth C],
JA [auth B],
S [auth A]
Siphonaxanthin
C40 H56 O4
SUCKEYMKNGZJHK-ZARIWKGHSA-N
NEX
Query on NEX

Download Ideal Coordinates CCD File 
HA [auth B],
Q [auth A],
YA [auth C]
(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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTCoot0.9.4.1
MODEL REFINEMENTPHENIX1.19.2-4158

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateSasakura Enviro-Science Foundation 2020

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-23
    Type: Initial release
  • Version 1.1: 2023-05-03
    Changes: Database references, Refinement description