7YCA

Cryo-EM structure of the PSI-LHCI-Lhcp supercomplex from Ostreococcus tauri


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.94 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

The photosystem I supercomplex from a primordial green alga Ostreococcus tauri harbors three light-harvesting complex trimers.

Ishii, A.Shan, J.Sheng, X.Kim, E.Watanabe, A.Yokono, M.Noda, C.Song, C.Murata, K.Liu, Z.Minagawa, J.

(2023) Elife 12

  • DOI: https://doi.org/10.7554/eLife.84488
  • Primary Citation of Related Structures:  
    7YCA, 8HG3, 8HG5, 8HG6

  • PubMed Abstract: 

    As a ubiquitous picophytoplankton in the ocean and an early-branching green alga, Ostreococcus tauri is a model prasinophyte species for studying the functional evolution of the light-harvesting systems in photosynthesis. Here, we report the structure and function of the O. tauri photosystem I (PSI) supercomplex in low light conditions, where it expands its photon-absorbing capacity by assembling with the light-harvesting complexes I (LHCI) and a prasinophyte-specific light-harvesting complex (Lhcp). The architecture of the supercomplex exhibits hybrid features of the plant-type and the green algal-type PSI supercomplexes, consisting of a PSI core, an Lhca1-Lhca4-Lhca2-Lhca3 belt attached on one side and an Lhca5-Lhca6 heterodimer associated on the other side between PsaG and PsaH. Interestingly, nine Lhcp subunits, including one Lhcp1 monomer with a phosphorylated amino-terminal threonine and eight Lhcp2 monomers, oligomerize into three trimers and associate with PSI on the third side between Lhca6 and PsaK. The Lhcp1 phosphorylation and the light-harvesting capacity of PSI were subjected to reversible photoacclimation, suggesting that the formation of Ot PSI-LHCI-Lhcp supercomplex is likely due to a phosphorylation-dependent mechanism induced by changes in light intensity. Notably, this supercomplex did not exhibit far-red peaks in the 77 K fluorescence spectra, which is possibly due to the weak coupling of the chlorophyll a 603- a 609 pair in Ot Lhca1-4.


  • Organizational Affiliation

    Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lhca1A [auth 1]225Ostreococcus tauriMutation(s): 0 
UniProt
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UniProt GroupA0AA97PZG2
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticB [auth 2]242Ostreococcus tauriMutation(s): 0 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticC [auth 3]272Ostreococcus tauriMutation(s): 0 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticD [auth 4]236Ostreococcus tauriMutation(s): 0 
UniProt
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticE [auth 5]217Ostreococcus tauriMutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Lhca6F [auth 6]249Ostreococcus tauriMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1G [auth A]751Ostreococcus tauriMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2H [auth B]733Ostreococcus tauriMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerI [auth C]81Ostreococcus tauriMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II, chloroplasticJ [auth D]188Ostreococcus tauriMutation(s): 0 
UniProt
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction centre subunit IVK [auth E]101Ostreococcus tauriMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIL [auth F]231Ostreococcus tauriMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
PsaGM [auth G]132Ostreococcus tauriMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I PsaH, reaction centre subunit VIN [auth H]166Ostreococcus tauriMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIO [auth I]35Ostreococcus tauriMutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXP [auth J]42Ostreococcus tauriMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I PsaG/PsaK proteinQ [auth K]131Ostreococcus tauriMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
PSI subunit VR [auth L]204Ostreococcus tauriMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIS [auth M]31Ostreococcus tauriMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I PsaN, reaction centre subunit NT [auth N]139Ostreococcus tauriMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
PsaOU [auth O]136Ostreococcus tauriMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplastic233Ostreococcus tauriMutation(s): 0 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticW [auth Q]226Ostreococcus tauriMutation(s): 1 
UniProt
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Small Molecules
Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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HG [auth A],
II [auth B]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL
Query on CHL

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BQ [auth W]
CQ [auth W]
DM [auth R]
DO [auth T]
DQ [auth W]
BQ [auth W],
CQ [auth W],
DM [auth R],
DO [auth T],
DQ [auth W],
EA [auth 1],
EM [auth R],
EQ [auth W],
FM [auth R],
GB [auth 2],
GD [auth 5],
GM [auth R],
GN [auth S],
GP [auth V],
GR [auth X],
HA [auth 1],
HP [auth V],
IL [auth Q],
IP [auth V],
JL [auth Q],
JO [auth T],
JP [auth V],
KC [auth 4],
KK [auth P],
KL [auth Q],
LK [auth P],
LQ [auth W],
MK [auth P],
NK [auth P],
NM [auth R],
OC [auth 4],
PC [auth 4],
PD [auth 6],
PO [auth U],
QC [auth 4],
QO [auth U],
QP [auth V],
RB [auth 3],
RL [auth Q],
RO [auth U],
SA [auth 2],
TD [auth 6],
TN [auth T],
UD [auth 6],
UK [auth P],
UN [auth T],
VN [auth T],
WA [auth 2],
WM [auth S],
WN [auth T],
WQ [auth X],
XL [auth R],
XM [auth S],
XQ [auth X],
YA [auth 2],
YM [auth S],
YO [auth U],
YQ [auth X],
ZM [auth S],
ZQ [auth X]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CL0 (Subject of Investigation/LOI)
Query on CL0

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HE [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
CLA
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AB [auth 2]
AE [auth 6]
AF [auth A]
AH [auth B]
AI [auth B]
AB [auth 2],
AE [auth 6],
AF [auth A],
AH [auth B],
AI [auth B],
AK [auth O],
AM [auth R],
AO [auth T],
AQ [auth W],
BB [auth 2],
BE [auth 6],
BF [auth A],
BH [auth B],
BI [auth B],
BK [auth O],
BM [auth R],
BN [auth S],
BO [auth T],
BR [auth X],
CB [auth 2],
CD [auth 5],
CF [auth A],
CH [auth B],
CK [auth O],
CL [auth Q],
CM [auth R],
CN [auth S],
CO [auth T],
CR [auth X],
DB [auth 2],
DD [auth 5],
DF [auth A],
DH [auth B],
DJ [auth J],
DK [auth O],
DN [auth S],
DP [auth V],
DR [auth X],
EB [auth 2],
ED [auth 5],
EF [auth A],
EH [auth B],
EN [auth S],
EP [auth V],
ER [auth X],
FA [auth 1],
FB [auth 2],
FD [auth 5],
FF [auth A],
FH [auth B],
FL [auth Q],
FN [auth S],
FP [auth V],
FR [auth X],
GA [auth 1],
GF [auth A],
GH [auth B],
GJ [auth K],
GL [auth Q],
GQ [auth W],
HD [auth 5],
HF [auth A],
HH [auth B],
HK [auth P],
HL [auth Q],
HQ [auth W],
IA [auth 1],
ID [auth 5],
IE [auth A],
IF [auth A],
IH [auth B],
IJ [auth K],
IK [auth P],
IM [auth R],
IQ [auth W],
JA [auth 1],
JD [auth 5],
JE [auth A],
JF [auth A],
JG [auth A],
JH [auth B],
JJ [auth K],
JK [auth P],
JM [auth R],
JQ [auth W],
KA [auth 1],
KD [auth 5],
KE [auth A],
KF [auth A],
KH [auth B],
KM [auth R],
KQ [auth W],
LA [auth 1],
LC [auth 4],
LD [auth 5],
LE [auth A],
LF [auth A],
LH [auth B],
LJ [auth K],
LM [auth R],
LP [auth V],
MA [auth 1],
MB [auth 3],
MC [auth 4],
ME [auth A],
MF [auth A],
MG [auth B],
MH [auth B],
MI [auth F],
ML [auth Q],
MM [auth R],
MO [auth U],
MP [auth V],
NA [auth 1],
NB [auth 3],
NC [auth 4],
NE [auth A],
NF [auth A],
NG [auth B],
NH [auth B],
NI [auth F],
NJ [auth L],
NL [auth Q],
NO [auth U],
NP [auth V],
OB [auth 3],
OE [auth A],
OF [auth A],
OG [auth B],
OH [auth B],
OJ [auth L],
OL [auth Q],
OO [auth U],
OP [auth V],
PB [auth 3],
PE [auth A],
PF [auth A],
PG [auth B],
PH [auth B],
PJ [auth L],
PK [auth P],
PL [auth Q],
PP [auth V],
QA [auth 1],
QB [auth 3],
QD [auth 6],
QE [auth A],
QF [auth A],
QG [auth B],
QH [auth B],
QJ [auth L],
QK [auth P],
QL [auth Q],
QN [auth T],
RC [auth 4],
RD [auth 6],
RE [auth A],
RF [auth A],
RG [auth B],
RH [auth B],
RI [auth G],
RK [auth P],
RN [auth T],
SB [auth 3],
SC [auth 4],
SD [auth 6],
SE [auth A],
SF [auth A],
SG [auth B],
SH [auth B],
SI [auth G],
SK [auth P],
SN [auth T],
TA [auth 2],
TB [auth 3],
TC [auth 4],
TE [auth A],
TF [auth A],
TG [auth B],
TH [auth B],
TI [auth G],
TK [auth P],
TM [auth S],
TO [auth U],
TQ [auth X],
UA [auth 2],
UB [auth 3],
UC [auth 4],
UE [auth A],
UF [auth A],
UG [auth B],
UH [auth B],
UM [auth S],
UO [auth U],
UQ [auth X],
VA [auth 2],
VB [auth 3],
VC [auth 4],
VD [auth 6],
VE [auth A],
VF [auth A],
VG [auth B],
VH [auth B],
VI [auth H],
VM [auth S],
VO [auth U],
VQ [auth X],
WB [auth 3],
WC [auth 4],
WD [auth 6],
WE [auth A],
WF [auth A],
WG [auth B],
WH [auth B],
WI [auth H],
WO [auth U],
XA [auth 2],
XB [auth 3],
XC [auth 4],
XD [auth 6],
XE [auth A],
XG [auth B],
XH [auth B],
XJ [auth N],
XO [auth U],
YB [auth 3],
YC [auth 4],
YD [auth 6],
YE [auth A],
YF [auth A],
YG [auth B],
YH [auth B],
YI [auth H],
YJ [auth N],
YN [auth T],
YP [auth W],
ZA [auth 2],
ZB [auth 3],
ZD [auth 6],
ZE [auth A],
ZG [auth B],
ZH [auth B],
ZJ [auth O],
ZN [auth T],
ZP [auth W]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD
Query on SQD

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FE [auth 6],
XI [auth H]
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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FJ [auth J]
GE [auth A]
GK [auth O]
IG [auth A]
KG [auth A]
FJ [auth J],
GE [auth A],
GK [auth O],
IG [auth A],
KG [auth A],
LB [auth 2],
LG [auth B],
OD [auth 5],
PI [auth F],
UJ [auth L],
WJ [auth N]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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AG [auth A]
DL [auth Q]
EE [auth 6]
FC [auth 3]
GC [auth 3]
AG [auth A],
DL [auth Q],
EE [auth 6],
FC [auth 3],
GC [auth 3],
HC [auth 3],
IC [auth 3],
KB [auth 2],
RA [auth 1],
ZF [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
KC2 (Subject of Investigation/LOI)
Query on KC2

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AN [auth S]
AR [auth X]
FQ [auth W]
HM [auth R]
KP [auth V]
AN [auth S],
AR [auth X],
FQ [auth W],
HM [auth R],
KP [auth V],
LL [auth Q],
OK [auth P],
SO [auth U],
XN [auth T]
Chlorophyll c2
C35 H28 Mg N4 O5
QDRBYWCRXZZVLY-QIEHNWLWSA-L
NEX
Query on NEX

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AJ [auth H]
GO [auth T]
JN [auth S]
OQ [auth W]
QM [auth R]
AJ [auth H],
GO [auth T],
JN [auth S],
OQ [auth W],
QM [auth R],
XK [auth P]
(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
XAT
Query on XAT

Download Ideal Coordinates CCD File 
AD [auth 4]
BC [auth 3]
DE [auth 6]
IB [auth 2]
ND [auth 5]
AD [auth 4],
BC [auth 3],
DE [auth 6],
IB [auth 2],
ND [auth 5],
PA [auth 1]
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O4
SZCBXWMUOPQSOX-WVJDLNGLSA-N
IWJ (Subject of Investigation/LOI)
Query on IWJ

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AC [auth 3]
AL [auth P]
BP [auth U]
CE [auth 6]
EL [auth Q]
AC [auth 3],
AL [auth P],
BP [auth U],
CE [auth 6],
EL [auth Q],
HO [auth T],
JC [auth 4],
JR [auth X],
KN [auth S],
KO [auth T],
LN [auth S],
MD [auth 5],
OA [auth 1],
ON [auth S],
PQ [auth W],
RM [auth R],
TP [auth V],
UP [auth V],
VL [auth Q],
WP [auth V],
YK [auth P],
YL [auth R],
ZC [auth 4]
(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-1-[(1~{S},4~{S})-2,2-dimethyl-6-methylidene-1,4-bis(oxidanyl)cyclohexyl]-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaen-2-one
C40 H56 O4
WOJYJHBMWRNRJG-ITGJSFTBSA-N
Q6L (Subject of Investigation/LOI)
Query on Q6L

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AP [auth U]
BL [auth P]
CP [auth U]
EK [auth O]
EO [auth T]
AP [auth U],
BL [auth P],
CP [auth U],
EK [auth O],
EO [auth T],
FK [auth O],
FO [auth T],
HB [auth 2],
HN [auth S],
HR [auth X],
IN [auth S],
IO [auth T],
IR [auth X],
KR [auth X],
LO [auth T],
MN [auth S],
MQ [auth W],
NN [auth S],
NQ [auth W],
OM [auth R],
PM [auth R],
PN [auth S],
QQ [auth W],
RP [auth V],
RQ [auth W],
SL [auth Q],
SM [auth R],
SP [auth V],
SQ [auth X],
TL [auth Q],
UL [auth Q],
VK [auth P],
VP [auth V],
WK [auth P],
WL [auth R],
XP [auth V],
ZK [auth P],
ZL [auth R],
ZO [auth U]
(1~{S})-3,5,5-trimethyl-4-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E})-3,7,12,16-tetramethyl-18-[(1~{R},4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohex-2-en-1-yl]octadeca-3,5,7,9,11,13,15,17-octaenyl]cyclohex-3-en-1-ol
C40 H58 O2
ULGXMGDBVFOYRY-NBTBXAKCSA-N
BCR
Query on BCR

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BD [auth 4]
BG [auth A]
BJ [auth I]
CC [auth 3]
CG [auth A]
BD [auth 4],
BG [auth A],
BJ [auth I],
CC [auth 3],
CG [auth A],
CJ [auth J],
DC [auth 3],
DG [auth A],
DI [auth B],
EC [auth 3],
EG [auth A],
EI [auth B],
EJ [auth J],
FG [auth A],
FI [auth B],
GI [auth B],
HI [auth B],
HJ [auth K],
JB [auth 2],
KJ [auth K],
LI [auth F],
MJ [auth K],
OI [auth F],
QI [auth G],
RJ [auth L],
SJ [auth L],
TJ [auth L],
UI [auth G],
VJ [auth M],
ZI [auth H]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN
Query on PQN

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CI [auth B],
XF [auth A]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

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GG [auth A],
JI [auth C],
KI [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
W [auth Q]L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.94 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.19.2

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan21H04778 and 21H05040
Chinese Academy of SciencesChinaXDB37020101 and YSBR-015
National Natural Science Foundation of China (NSFC)China31925024
Ministry of Science and Technology (MoST, China)China2017YFA0503702

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release