8IWH

Structure and characteristics of a photosystem II supercomplex containing monomeric LHCX and dimeric FCPII antennae from the diatom Thalassiosira pseudonana


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.68 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

Structure of a diatom photosystem II supercomplex containing a member of Lhcx family and dimeric FCPII.

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

(2023) Sci Adv 9: eadi8446-eadi8446

  • DOI: https://doi.org/10.1126/sciadv.adi8446
  • Primary Citation of Related Structures:  
    8IWH, 8J0D

  • PubMed Abstract: 

    Diatoms rely on fucoxanthin chlorophyll a/c -binding proteins (FCPs) for their great success in oceans, which have a great diversity in their pigment, protein compositions, and subunit organizations. We report a unique structure of photosystem II (PSII)-FCPII supercomplex from Thalassiosira pseudonana at 2.68-Å resolution by cryo-electron microscopy. FCPIIs within this PSII-FCPII supercomplex exist in dimers and monomers, and a homodimer and a heterodimer were found to bind to a PSII core. The FCPII homodimer is formed by Lhcf7 and associates with PSII through an Lhcx family antenna Lhcx6_1, whereas the heterodimer is formed by Lhcf6 and Lhcf11 and connects to the core together with an Lhcf5 monomer through Lhca2 monomer. An extended pigment network consisting of diatoxanthins, diadinoxanthins, fucoxanthins, and chlorophylls a/c is revealed, which functions in efficient light harvesting, energy transfer, and dissipation. These results provide a structural basis for revealing the energy transfer and dissipation mechanisms and also for the structural diversity of FCP antennas in diatoms.


  • Organizational Affiliation

    Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1A,
TA [auth a]
333Thalassiosira pseudonanaMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
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Find proteins for A0T0W2 (Thalassiosira pseudonana)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
UA [auth b]
509Thalassiosira pseudonanaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0T0P5 (Thalassiosira pseudonana)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
D [auth c]
470Thalassiosira pseudonanaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinE [auth D],
F [auth d]
351Thalassiosira pseudonanaMutation(s): 0 
EC: 1.10.3.9
Membrane Entity: Yes 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaG [auth E],
H [auth e]
84Thalassiosira pseudonanaMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaI [auth F],
J [auth f]
43Thalassiosira pseudonanaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II Psb31 protein domain-containing proteinK [auth G],
L [auth g]
176Thalassiosira pseudonanaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B8CC14 (Thalassiosira pseudonana)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HM [auth H],
N [auth h]
66Thalassiosira pseudonanaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IO [auth I],
P [auth i]
34Thalassiosira pseudonanaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein JQ [auth J],
R [auth j]
39Thalassiosira pseudonanaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KS [auth K],
T [auth k]
44Thalassiosira pseudonanaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LU [auth L],
V [auth l]
38Thalassiosira pseudonanaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center M protein, plastidW [auth M],
X [auth m]
113Thalassiosira pseudonanaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II subunit, PsbN.Y [auth n],
Z [auth N]
30Thalassiosira pseudonanaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Oxygen-evolving enhancer protein 1AA [auth O],
BA [auth o]
305Thalassiosira pseudonanaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for B8C4I5 (Thalassiosira pseudonana)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TCA [auth T],
DA [auth t]
28Thalassiosira pseudonanaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for A0T0P6 (Thalassiosira pseudonana)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
PS II complex 12 kDa extrinsic proteinEA [auth U],
FA [auth u]
148Thalassiosira pseudonanaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for B8BVI4 (Thalassiosira pseudonana)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-550GA [auth V],
HA [auth v]
162Thalassiosira pseudonanaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for A0T0N2 (Thalassiosira pseudonana)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II subunit, PsbWIA [auth W],
JA [auth w]
54Thalassiosira pseudonanaMutation(s): 0 
Membrane Entity: Yes 
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Find proteins for B8C8Y3 (Thalassiosira pseudonana)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinKA [auth X],
LA [auth x]
38Thalassiosira pseudonanaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein ZMA [auth Z],
NA [auth z]
61Thalassiosira pseudonanaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chl a/c protein, lhca cladeOA [auth 3]220Thalassiosira pseudonanaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin-chlorophyll a-c binding protein, plastidPA [auth 4]196Thalassiosira pseudonanaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c protein 6QA [auth 5]192Thalassiosira pseudonanaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c protein 5RA [auth 6]199Thalassiosira pseudonanaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c protein-LI818 cladeSA [auth 7],
ZA [auth 0]
199Thalassiosira pseudonanaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein Ycf12VA [auth Y],
WA [auth y]
34Thalassiosira pseudonanaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II subunit, PsbQ.XA [auth Q],
YA [auth q]
211Thalassiosira pseudonanaMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c light-harvesting protein, major typeAB [auth 9],
BB [auth 2],
CB [auth 8],
DB [auth 1]
193Thalassiosira pseudonanaMutation(s): 0 
Membrane Entity: Yes 
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Small Molecules
Ligands 19 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
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AE [auth c]
BE [auth c]
BH [auth 3]
CE [auth c]
DF [auth H]
AE [auth c],
BE [auth c],
BH [auth 3],
CE [auth c],
DF [auth H],
ED [auth C],
FD [auth C],
GD [auth C],
HF [auth h],
SB [auth A],
VJ [auth a]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA
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AC [auth B]
AD [auth C]
AH [auth 3]
AJ [auth 6]
AN [auth 2]
AC [auth B],
AD [auth C],
AH [auth 3],
AJ [auth 6],
AN [auth 2],
BC [auth B],
BD [auth C],
BG [auth W],
BI [auth 5],
BK [auth a],
BN [auth 2],
BO [auth 1],
CC [auth B],
CI [auth 5],
CJ [auth 6],
CK [auth a],
CN [auth 2],
CO [auth 1],
DC [auth B],
DJ [auth 6],
DM [auth 9],
DN [auth 2],
DO [auth 1],
EC [auth B],
EF [auth H],
EG [auth w],
EI [auth 5],
EM [auth 9],
EN [auth 2],
EO [auth 1],
FC [auth B],
FI [auth 5],
FK [auth a],
FM [auth 9],
FN [auth 2],
FO [auth 1],
GC [auth B],
GE [auth D],
GG [auth Z],
GH [auth 4],
GI [auth 5],
GM [auth 9],
GN [auth 2],
GO [auth 1],
HB [auth A],
HC [auth B],
HG [auth z],
HH [auth 4],
HI [auth 5],
HJ [auth 7],
HM [auth 9],
HO [auth 1],
IB [auth A],
IC [auth B],
IJ [auth 7],
IM [auth 9],
IO [auth 1],
JE [auth D],
JG [auth 3],
JH [auth 4],
JI [auth 5],
JM [auth 9],
JO [auth 1],
KE [auth D],
KG [auth 3],
KH [auth 4],
KI [auth 5],
KJ [auth 7],
KK [auth b],
KM [auth 9],
KO [auth 1],
LB [auth A],
LD [auth c],
LG [auth 3],
LH [auth 4],
LJ [auth 7],
LK [auth b],
LM [auth 9],
LN [auth 8],
LO [auth 1],
MD [auth c],
MG [auth 3],
MH [auth 4],
MJ [auth 7],
MK [auth b],
ML [auth 0],
MM [auth 9],
MN [auth 8],
MO [auth 1],
ND [auth c],
NG [auth 3],
NH [auth 4],
NJ [auth 7],
NK [auth b],
NL [auth 0],
NM [auth 9],
NN [auth 8],
OD [auth c],
OG [auth 3],
OH [auth 4],
OJ [auth 7],
OK [auth b],
OM [auth 9],
ON [auth 8],
PC [auth C],
PD [auth c],
PG [auth 3],
PH [auth 4],
PJ [auth 7],
PK [auth b],
PL [auth 0],
PM [auth 9],
PN [auth 8],
QC [auth C],
QD [auth c],
QE [auth d],
QG [auth 3],
QH [auth 4],
QJ [auth 7],
QK [auth b],
QL [auth 0],
QN [auth 8],
RC [auth C],
RD [auth c],
RE [auth d],
RH [auth 4],
RJ [auth 7],
RK [auth b],
RL [auth 0],
RN [auth 8],
SC [auth C],
SD [auth c],
SG [auth 3],
SK [auth b],
SL [auth 0],
SN [auth 8],
TB [auth B],
TC [auth C],
TD [auth c],
TG [auth 3],
TK [auth b],
TL [auth 0],
TN [auth 8],
UB [auth B],
UC [auth C],
UD [auth c],
UG [auth 3],
UI [auth 6],
UK [auth b],
UL [auth 0],
UM [auth 2],
UN [auth 8],
VB [auth B],
VC [auth C],
VD [auth c],
VI [auth 6],
VK [auth b],
VL [auth 0],
VM [auth 2],
VN [auth 8],
WB [auth B],
WC [auth C],
WD [auth c],
WK [auth b],
WM [auth 2],
WN [auth 8],
XB [auth B],
XC [auth C],
XD [auth c],
XI [auth 6],
XK [auth b],
XM [auth 2],
YB [auth B],
YC [auth C],
YE [auth d],
YI [auth 6],
YK [auth b],
YM [auth 2],
ZB [auth B],
ZC [auth C],
ZI [auth 6],
ZK [auth b],
ZM [auth 2]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
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DK [auth a],
EK [auth a],
JB [auth A],
KB [auth A]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
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HE [auth D]
HK [auth a]
JF [auth i]
OC [auth B]
OF [auth L]
HE [auth D],
HK [auth a],
JF [auth i],
OC [auth B],
OF [auth L],
PF [auth l],
QB [auth A],
SF [auth T],
UF [auth T],
UJ [auth 7],
WF [auth t],
YL [auth 0]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG
Query on LMG

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DE [auth c]
DL [auth b]
EE [auth c]
EL [auth b]
FG [auth w]
DE [auth c],
DL [auth b],
EE [auth c],
EL [auth b],
FG [auth w],
FL [auth b],
GL [auth Q],
HD [auth C],
HL [auth q],
ID [auth C],
IE [auth D],
IL [auth q],
JD [auth C],
KD [auth C],
MC [auth B],
MI [auth 5],
NC [auth B],
OE [auth D],
QF [auth M],
RF [auth m],
SJ [auth 7],
VE [auth d],
WL [auth 0],
XG [auth 3],
ZE [auth d],
ZF [auth W]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9

Download Ideal Coordinates CCD File 
ME [auth D],
TE [auth d]
2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
LHG
Query on LHG

Download Ideal Coordinates CCD File 
AG [auth W]
CG [auth w]
FF [auth H]
IF [auth h]
JK [auth b]
AG [auth W],
CG [auth w],
FF [auth H],
IF [auth h],
JK [auth b],
LI [auth 5],
NE [auth D],
OB [auth A],
PB [auth A],
PE [auth D],
RB [auth A],
TH [auth 4],
TJ [auth 7],
UE [auth d],
WE [auth d],
XJ [auth a],
XL [auth 0],
YG [auth 3],
YJ [auth a],
ZG [auth 3]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
A86
Query on A86

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AI [auth 5]
AM [auth 9]
CH [auth 4]
DH [auth 4]
EJ [auth 7]
AI [auth 5],
AM [auth 9],
CH [auth 4],
DH [auth 4],
EJ [auth 7],
FH [auth 4],
GJ [auth 7],
HN [auth 8],
IN [auth 8],
JL [auth 0],
LL [auth 0],
OI [auth 6],
PI [auth 6],
QI [auth 6],
QM [auth 2],
RI [auth 6],
RM [auth 2],
SI [auth 6],
TI [auth 6],
UH [auth 5],
VG [auth 3],
VH [auth 5],
WH [auth 5],
XH [auth 5],
XN [auth 1],
YH [auth 5],
YN [auth 1],
ZH [auth 5],
ZL [auth 9]
(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
HEM
Query on HEM

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AF [auth e],
BF [auth F],
XF [auth V],
YF [auth v]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
KC1
Query on KC1

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BJ [auth 6],
II [auth 5],
RG [auth 3]
Chlorophyll c1
C35 H30 Mg N4 O5
DGNIJJSSARBJSH-QIEHNWLWSA-L
KC2
Query on KC2

Download Ideal Coordinates CCD File 
DI [auth 5],
IH [auth 4],
JJ [auth 7],
OL [auth 0],
WI [auth 6]
Chlorophyll c2
C35 H28 Mg N4 O5
QDRBYWCRXZZVLY-QIEHNWLWSA-L
DD6
Query on DD6

Download Ideal Coordinates CCD File 
AO [auth 1]
BM [auth 9]
CM [auth 9]
EH [auth 4]
JN [auth 8]
AO [auth 1],
BM [auth 9],
CM [auth 9],
EH [auth 4],
JN [auth 8],
KN [auth 8],
SM [auth 2],
TM [auth 2],
WG [auth 3],
ZN [auth 1]
(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
ET4
Query on ET4

Download Ideal Coordinates CCD File 
FJ [auth 7],
KL [auth 0]
(1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol
C40 H54 O2
HNYJHQMUSVNWPV-DRCJTWAYSA-N
BCR
Query on BCR

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AL [auth b]
BL [auth b]
CD [auth C]
CF [auth H]
CL [auth b]
AL [auth b],
BL [auth b],
CD [auth C],
CF [auth H],
CL [auth b],
DD [auth C],
EB [auth A],
GF [auth h],
GK [auth a],
IK [auth a],
JC [auth B],
KC [auth B],
KF [auth K],
LC [auth B],
LE [auth D],
LF [auth K],
MB [auth A],
MF [auth k],
NF [auth k],
SE [auth d],
YD [auth c],
ZD [auth c]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU (Subject of Investigation/LOI)
Query on LMU

Download Ideal Coordinates CCD File 
DG [auth w]
IG [auth 3]
NI [auth 5]
SH [auth 4]
TF [auth T]
DG [auth w],
IG [auth 3],
NI [auth 5],
SH [auth 4],
TF [auth T],
VF [auth t]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
OEX
Query on OEX

Download Ideal Coordinates CCD File 
FB [auth A],
ZJ [auth a]
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT
Query on BCT

Download Ideal Coordinates CCD File 
NB [auth A],
WJ [auth a]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2

Download Ideal Coordinates CCD File 
FE [auth D],
XE [auth d]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
AK [auth a],
GB [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.68 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 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: 2023-10-25
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Database references