9S1M | pdb_00009s1m

Cryo-EM structure of Posidonia oceanica L-PSI-LHCI-LHCII supercomplex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.31 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Literature

Structural and spectral adaptation of the seagrass Posidonia oceanica photosystem I to seabed light.

Amelii, A.Capaldi, S.Russo, M.Guardini, Z.Sanita, G.Esposito, E.Olive, I.Maiuri, M.Dall'Osto, L.Cerullo, G.Procaccini, G.Bassi, R.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-75200-8
  • Primary Citation Related Structures: 
    9S1L, 9S1M

  • PubMed Abstract: 

    Seagrasses are marine angiosperms re-adapted to underwater life, forming productive ecosystems and long-term carbon sinks. Posidonia oceanica thrives up to 50 m depth, where light is scarce and spectrally shifted; yet, the molecular basis of its photosynthetic adaptation remains unclear. Here, we report that P. oceanica genetically adapts for highly efficient photon use under dim light by enhancing photosystem antenna size and reducing exciton trapping time. We determine the structures of P. oceanica PSI supercomplexes by cryo-electron microscopy, revealing an expanded antenna system composed of PSI-LHCI, a trimeric phospho-LHCII, and an additional LHCI heterodimer. Low-energy chlorophyll forms associated with LHCI are lost. Ultrafast spectroscopy shows that this loss correlates with faster exciton trapping, which compensates for antenna expansion and enhances light-use efficiency under dim light. We identify key residues responsible for the loss of low-energy forms. Reversion to land-plant ortholog sequences restores red-shifted emission, providing strategies to enhance light-use efficiency in crops.


  • Organizational Affiliation
    • Laboratory of Photosynthesis and Bioenergy, Department of Biotechnology, University of Verona; Strada Le Grazie 15, Verona, Italy.

Macromolecule Content 

  • Total Structure Weight: 755.31 kDa 
  • Atom Count: 49,325 
  • Modeled Residue Count: 4,357 
  • Deposited Residue Count: 4,515 
  • Unique protein chains: 19

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 6 (Lhca1)A [auth 1],
E [auth 5]
200Posidonia oceanicaMutation(s): 0 
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I chlorophyll a/b-binding protein 2 (Lhca2)B [auth 2]211Posidonia oceanicaMutation(s): 0 
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I chlorophyll a/b-binding protein 3-1 (Lhca3)C [auth 3]232Posidonia oceanicaMutation(s): 0 
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 4 (Lhca4)D [auth 4],
F [auth 6]
200Posidonia oceanicaMutation(s): 0 
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1 (PsaA)G [auth A]750Posidonia oceanicaMutation(s): 0 
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2 (PsaB)H [auth B]734Posidonia oceanicaMutation(s): 0 
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center (PsaC)I [auth C]81Posidonia oceanicaMutation(s): 0 
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II-1, chloroplastic (PsaD1)J [auth D]155Posidonia oceanicaMutation(s): 0 
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV B (PsaE2)K [auth E]93Posidonia oceanicaMutation(s): 0 
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III (PsaF)L [auth F]159Posidonia oceanicaMutation(s): 0 
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit V (PsaG)M [auth G]100Posidonia oceanicaMutation(s): 0 
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VI-1 (PsaH)N [auth H]95Posidonia oceanicaMutation(s): 0 
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIII (PsaI)O [auth I]36Posidonia oceanicaMutation(s): 0 
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXP [auth J]42Posidonia oceanicaMutation(s): 0 
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit psaK (PsaK)Q [auth K]84Posidonia oceanicaMutation(s): 0 
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Reference Sequence
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XI (PsaL)R [auth L]170Posidonia oceanicaMutation(s): 0 
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Reference Sequence
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem I subunit O (PsaO)S [auth O]89Posidonia oceanicaMutation(s): 0 
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Reference Sequence
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 1 (Lhcb1)T [auth X],
V [auth Z]
228Posidonia oceanicaMutation(s): 0 
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Reference Sequence
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 2 (Lhcb2)U [auth Y]228Posidonia oceanicaMutation(s): 0 
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Reference Sequence

Small Molecules

Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
(Subject of Investigation/LOI)

Query on DGD



Download:Ideal Coordinates CCD File
JI [auth B]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL
(Subject of Investigation/LOI)

Query on CHL



Download:Ideal Coordinates CCD File
AD [auth 5]
AK [auth X]
AL [auth Y]
BA [auth 1]
EE [auth 6]
AD [auth 5],
AK [auth X],
AL [auth Y],
BA [auth 1],
EE [auth 6],
EK [auth X],
FB [auth 2],
FC [auth 4],
FK [auth X],
GC [auth 4],
GK [auth X],
HC [auth 4],
HK [auth X],
KL [auth Y],
LL [auth Z],
ML [auth Z],
PC [auth 4],
QL [auth Z],
RL [auth Z],
SA [auth 2],
SB [auth 3],
SK [auth Y],
SL [auth Z],
TL [auth Z],
UD [auth 6],
VC [auth 5],
VD [auth 6],
W [auth 1],
WA [auth 2],
WD [auth 6],
WK [auth Y],
XA [auth 2],
XK [auth Y],
YA [auth 2],
YK [auth Y],
ZK [auth Y]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA
(Subject of Investigation/LOI)

Query on CLA



Download:Ideal Coordinates CCD File
AA [auth 1]
AB [auth 2]
AE [auth 6]
AF [auth A]
AG [auth A]
AA [auth 1],
AB [auth 2],
AE [auth 6],
AF [auth A],
AG [auth A],
AH [auth B],
AI [auth B],
AJ [auth H],
BB [auth 2],
BC [auth 3],
BD [auth 5],
BE [auth 6],
BF [auth A],
BG [auth A],
BH [auth B],
BK [auth X],
BL [auth Y],
CA [auth 1],
CB [auth 2],
CC [auth 4],
CD [auth 5],
CE [auth 6],
CF [auth A],
CH [auth B],
CJ [auth J],
CK [auth X],
CL [auth Y],
DA [auth 1],
DB [auth 2],
DC [auth 4],
DD [auth 5],
DE [auth 6],
DF [auth A],
DH [auth B],
DJ [auth J],
DK [auth X],
DL [auth Y],
EA [auth 1],
EB [auth 2],
EC [auth 4],
ED [auth 5],
EF [auth A],
EH [auth B],
EL [auth Y],
FA [auth 1],
FD [auth 5],
FF [auth A],
FH [auth B],
FJ [auth K],
FL [auth Y],
GA [auth 1],
GD [auth 5],
GF [auth A],
GH [auth B],
GJ [auth K],
HA [auth 1],
HD [auth 5],
HF [auth A],
HH [auth B],
HJ [auth K],
IA [auth 1],
IC [auth 4],
ID [auth 5],
IF [auth A],
IH [auth B],
IJ [auth K],
IK [auth X],
JA [auth 1],
JB [auth 2],
JC [auth 4],
JF [auth A],
JH [auth B],
JK [auth X],
KC [auth 4],
KF [auth A],
KH [auth B],
KJ [auth L],
KK [auth X],
LC [auth 4],
LE [auth A],
LF [auth A],
LH [auth B],
LK [auth X],
MB [auth 3],
MC [auth 4],
ME [auth A],
MF [auth A],
MH [auth B],
MJ [auth L],
MK [auth X],
NB [auth 3],
NC [auth 4],
NE [auth A],
NF [auth A],
NG [auth B],
NH [auth B],
NJ [auth L],
NL [auth Z],
OB [auth 3],
OC [auth 4],
OE [auth A],
OF [auth A],
OG [auth B],
OH [auth B],
OJ [auth L],
OL [auth Z],
PB [auth 3],
PE [auth A],
PF [auth A],
PG [auth B],
PH [auth B],
PL [auth Z],
QB [auth 3],
QD [auth 6],
QE [auth A],
QF [auth A],
QG [auth B],
QH [auth B],
QI [auth F],
RB [auth 3],
RD [auth 6],
RE [auth A],
RF [auth A],
RG [auth B],
RH [auth B],
RK [auth X],
SD [auth 6],
SE [auth A],
SF [auth A],
SG [auth B],
SH [auth B],
TA [auth 2],
TB [auth 3],
TD [auth 6],
TE [auth A],
TF [auth A],
TG [auth B],
TH [auth B],
TJ [auth O],
TK [auth Y],
UA [auth 2],
UB [auth 3],
UE [auth A],
UF [auth A],
UG [auth B],
UH [auth B],
UJ [auth O],
UK [auth Y],
UL [auth Z],
VA [auth 2],
VB [auth 3],
VE [auth A],
VF [auth A],
VG [auth B],
VH [auth B],
VI [auth G],
VK [auth Y],
VL [auth Z],
WB [auth 3],
WC [auth 5],
WE [auth A],
WF [auth A],
WG [auth B],
WH [auth B],
WI [auth G],
WL [auth Z],
X [auth 1],
XB [auth 3],
XC [auth 5],
XD [auth 6],
XE [auth A],
XF [auth A],
XG [auth B],
XH [auth B],
XI [auth G],
XJ [auth O],
XL [auth Z],
Y [auth 1],
YB [auth 3],
YC [auth 5],
YD [auth 6],
YE [auth A],
YF [auth A],
YG [auth B],
YH [auth B],
YJ [auth O],
Z [auth 1],
ZA [auth 2],
ZC [auth 5],
ZD [auth 6],
ZE [auth A],
ZF [auth A],
ZG [auth B],
ZH [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG

Query on LMG



Download:Ideal Coordinates CCD File
IE [auth 6]
KI [auth B]
OA [auth 1]
OD [auth 5]
PD [auth 5]
IE [auth 6],
KI [auth B],
OA [auth 1],
OD [auth 5],
PD [auth 5],
QA [auth 1],
SI [auth F],
TC [auth 4],
TI [auth F],
ZI [auth G]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
(Subject of Investigation/LOI)

Query on LHG



Download:Ideal Coordinates CCD File
BM [auth Z]
IB [auth 2]
JG [auth A]
JL [auth Y]
LG [auth A]
BM [auth Z],
IB [auth 2],
JG [auth A],
JL [auth Y],
LG [auth A],
MD [auth 5],
NA [auth 1],
PA [auth 1],
QK [auth X],
RA [auth 1]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
NEX
(Subject of Investigation/LOI)

Query on NEX



Download:Ideal Coordinates CCD File
AM [auth Z],
IL [auth Y],
PK [auth X]
(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
(Subject of Investigation/LOI)

Query on XAT



Download:Ideal Coordinates CCD File
AC [auth 3]
GE [auth 6]
HB [auth 2]
KD [auth 5]
LA [auth 1]
AC [auth 3],
GE [auth 6],
HB [auth 2],
KD [auth 5],
LA [auth 1],
RC [auth 4],
ZJ [auth O]
(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
LUT
(Subject of Investigation/LOI)

Query on LUT



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FE [auth 6]
GB [auth 2]
GL [auth Y]
HL [auth Y]
JD [auth 5]
FE [auth 6],
GB [auth 2],
GL [auth Y],
HL [auth Y],
JD [auth 5],
KA [auth 1],
ND [auth 5],
NI [auth F],
NK [auth X],
OK [auth X],
QC [auth 4],
YL [auth Z],
ZB [auth 3],
ZL [auth Z]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR
(Subject of Investigation/LOI)

Query on BCR



Download:Ideal Coordinates CCD File
BJ [auth I]
CI [auth B]
DG [auth A]
DI [auth B]
EG [auth A]
BJ [auth I],
CI [auth B],
DG [auth A],
DI [auth B],
EG [auth A],
EI [auth B],
EJ [auth J],
FG [auth A],
FI [auth B],
GG [auth A],
GI [auth B],
HE [auth 6],
HG [auth A],
HI [auth B],
II [auth B],
JE [auth 6],
JJ [auth K],
KB [auth 2],
LB [auth 3],
LD [auth 5],
LJ [auth L],
MA [auth 1],
MG [auth A],
OI [auth F],
PJ [auth L],
QJ [auth L],
RI [auth F],
RJ [auth L],
SC [auth 4],
SJ [auth O],
VJ [auth O],
WJ [auth O],
YI [auth G]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT

Query on LMT



Download:Ideal Coordinates CCD File
KE [auth 6],
KG [auth A],
PI [auth F],
UC [auth 4],
UI [auth G]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
(Subject of Investigation/LOI)

Query on PQN



Download:Ideal Coordinates CCD File
BI [auth B],
CG [auth A]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
(Subject of Investigation/LOI)

Query on SF4



Download:Ideal Coordinates CCD File
IG [auth A],
LI [auth C],
MI [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
TPO
Query on TPO
U [auth Y]L-PEPTIDE LINKINGC4 H10 N O6 PTHR

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.31 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.2_5419
RECONSTRUCTIONcryoSPARC4.6.2

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union101053983-GrInSun

Revision History  (Full details and data files)

  • Version 1.0: 2026-07-29
    Type: Initial release