8HQ8

Bry-LHCII homotrimer of Bryopsis corticulans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 

Starting Model: experimental
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This is version 2.0 of the entry. See complete history


Literature

Structural and functional properties of different types of siphonous LHCII trimers from an intertidal green alga Bryopsis corticulans.

Li, Z.Zhou, C.Zhao, S.Zhang, J.Liu, X.Sang, M.Qin, X.Yang, Y.Han, G.Kuang, T.Shen, J.R.Wang, W.

(2023) Structure 31: 1247-1258.e3

  • DOI: https://doi.org/10.1016/j.str.2023.08.001
  • Primary Citation of Related Structures:  
    8HLV, 8HPD, 8HQ8

  • PubMed Abstract: 

    Light-harvesting complexes of photosystem II (LHCIIs) in green algae and plants are vital antenna apparatus for light harvesting, energy transfer, and photoprotection. Here we determined the structure of a siphonous-type LHCII trimer from the intertidal green alga Bryopsis corticulans by X-ray crystallography and cryo-electron microscopy (cryo-EM), and analyzed its functional properties by spectral analysis. The Bryopsis LHCII (Bry-LHCII) structures in both homotrimeric and heterotrimeric form show that green light-absorbing siphonaxanthin and siphonein occupied the sites of lutein and violaxanthin in plant LHCII, and two extra chlorophylls (Chls) b replaced Chls a. Binding of these pigments expands the blue-green light absorption of B. corticulans in the tidal zone. We observed differences between the Bry-LHCII homotrimer crystal and cryo-EM structures, and also between Bry-LHCII homotrimer and heterotrimer cryo-EM structures. These conformational changes may reflect the flexibility of Bry-LHCII, which may be required to adapt to light fluctuations from tidal rhythms.


  • Organizational Affiliation

    Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Science, Yuquan Road, Shijingshan District, Beijing 100049, China.


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, Bry-Lhcb1
A, B, C, D, E
A, B, C, D, E, F
249Bryopsis corticulansMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CHL (Subject of Investigation/LOI)
Query on CHL

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AC [auth D]
AD [auth E]
BC [auth D]
BD [auth E]
BE [auth F]
AC [auth D],
AD [auth E],
BC [auth D],
BD [auth E],
BE [auth F],
CD [auth E],
EC [auth D],
FB [auth C],
FC [auth D],
GB [auth C],
GC [auth D],
HA [auth B],
HC [auth D],
HD [auth E],
IA [auth B],
IC [auth D],
JB [auth C],
K [auth A],
KB [auth C],
L [auth A],
LA [auth B],
LB [auth C],
MA [auth B],
MB [auth C],
NA [auth B],
NB [auth C],
NC [auth D],
O [auth A],
OA [auth B],
OD [auth F],
P [auth A],
PA [auth B],
PD [auth F],
Q [auth A],
R [auth A],
S [auth A],
SB [auth C],
SD [auth F],
TD [auth F],
UA [auth B],
UC [auth E],
UD [auth F],
VC [auth E],
VD [auth F],
WD [auth F],
X [auth A],
YC [auth E],
ZC [auth E]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA (Subject of Investigation/LOI)
Query on CLA

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AE [auth F]
CC [auth D]
DC [auth D]
DD [auth E]
ED [auth E]
AE [auth F],
CC [auth D],
DC [auth D],
DD [auth E],
ED [auth E],
FD [auth E],
GD [auth E],
HB [auth C],
IB [auth C],
JA [auth B],
JC [auth D],
KA [auth B],
KC [auth D],
LC [auth D],
M [auth A],
MC [auth D],
N [auth A],
OB [auth C],
PB [auth C],
QA [auth B],
QB [auth C],
QD [auth F],
RA [auth B],
RB [auth C],
RD [auth F],
SA [auth B],
T [auth A],
TA [auth B],
U [auth A],
V [auth A],
W [auth A],
WC [auth E],
XC [auth E],
XD [auth F],
YD [auth F],
ZD [auth F]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG (Subject of Investigation/LOI)
Query on LMG

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DE [auth F],
YA [auth B]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
0UR (Subject of Investigation/LOI)
Query on 0UR

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AB [auth B]
BA [auth A]
DA [auth B]
EE [auth F]
KD [auth E]
AB [auth B],
BA [auth A],
DA [auth B],
EE [auth F],
KD [auth E],
QC [auth D],
VB [auth C]
Siphonein
C52 H76 O5
UERRVASYDCUNEJ-DHYZAJTQSA-N
LHG (Subject of Investigation/LOI)
Query on LHG

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CE [auth F]
EB [auth C]
ID [auth E]
OC [auth D]
TB [auth C]
CE [auth F],
EB [auth C],
ID [auth E],
OC [auth D],
TB [auth C],
VA [auth B],
Y [auth A],
ZA [auth B]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
NEX (Subject of Investigation/LOI)
Query on NEX

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DB [auth C]
EA [auth B]
I [auth A]
ND [auth F]
TC [auth E]
DB [auth C],
EA [auth B],
I [auth A],
ND [auth F],
TC [auth E],
YB [auth D]
(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
0IE (Subject of Investigation/LOI)
Query on 0IE

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BB [auth C]
CA [auth B]
CB [auth C]
G [auth A]
H [auth A]
BB [auth C],
CA [auth B],
CB [auth C],
G [auth A],
H [auth A],
LD [auth F],
MD [auth F],
RC [auth E],
SC [auth E],
WB [auth D],
XB [auth D]
Siphonaxanthin
C40 H56 O4
SUCKEYMKNGZJHK-ZARIWKGHSA-N
LMU (Subject of Investigation/LOI)
Query on LMU

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FA [auth B],
GA [auth B],
J [auth A],
JD [auth E],
ZB [auth D]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
BET
Query on BET

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UB [auth C],
WA [auth B],
XA [auth B]
TRIMETHYL GLYCINE
C5 H12 N O2
KWIUHFFTVRNATP-UHFFFAOYSA-O
MG
Query on MG

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AA [auth A],
PC [auth D],
Z [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.72α = 90
b = 91.61β = 103.52
c = 169.22γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina2019YFA0906300
Chinese Academy of SciencesChina2021YFA1300403
Chinese Academy of SciencesChinaXDA26050402
Chinese Academy of SciencesChinaXDB17000000
Chinese Academy of SciencesChina2020081
Chinese Academy of SciencesChinaJCTD-2020-06
Chinese Academy of SciencesChinaYSBR-004
Chinese Academy of SciencesChina31970260
Chinese Academy of SciencesChina32222007

Revision History  (Full details and data files)

  • Version 1.0: 2023-09-06
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Database references
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection