9GC2 | pdb_00009gc2

Cryo-EM structure of Arabidopsis thaliana PSI-LHCI- a603-NH mutant


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural determinants for red-shifted absorption in higher-plants Photosystem I.

Capaldi, S.Guardini, Z.Montepietra, D.Pagliuca, V.F.Amelii, A.Betti, E.John, C.Pedraza-Gonzalez, L.Cupellini, L.Mennucci, B.Bonnet, D.M.V.Chaves-Sanjuan, A.Dall'Osto, L.Bassi, R.

(2025) New Phytol 248: 2331-2346

  • DOI: https://doi.org/10.1111/nph.70562
  • Primary Citation of Related Structures:  
    9GBI, 9GC2

  • PubMed Abstract: 

    Higher plants Photosystem I absorbs far-red light, enriched under vegetation canopies, through long-wavelength Chls to enhance photon capture. Far-red absorption originates from Chl pairs within the Lhca3 and Lhca4 subunits of the LHCI antenna, known as the 'red cluster', including Chls a603 and a609. We used reverse genetics to produce an Arabidopsis mutant devoid of red-shifted absorption, and we obtained high-resolution cryogenic electron microscopy structures of PSI-LHCI complexes from both wild-type and mutant plants. Computed excitonic coupling values suggested contributions from additional nearby pigment molecules, namely Chl a615 and violaxanthin in the L2 site, to far-red absorption. We investigated the structural determinants of far-red absorption by producing further Arabidopsis transgenic lines and analyzed the spectroscopic effects of mutations targeting these chromophores. The two structures solved were used for quantum mechanics calculations, revealing that excitonic interactions alone cannot explain far-red absorption, while charge transfer states were needed for accurate spectral simulations. Our findings demonstrate that the molecular mechanisms of light-harvesting under shaded conditions rely on very precise tuning of chromophore interactions, whose understanding is crucial for designing light-harvesting complexes with engineered absorption spectra.


  • Organizational Affiliation
    • Dipartimento di Biotecnologie, Università di Verona, Strada Le Grazie 15, 37134, Verona, Italy.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 6, chloroplasticA [auth 1]206Arabidopsis thalianaMutation(s): 0 
Gene Names: LHCA1CAB6At3g54890F28P10.130
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I chlorophyll a/b-binding protein 2, chloroplasticB [auth 2]214Arabidopsis thalianaMutation(s): 0 
Gene Names: LHCA2At3g61470F2A19.70
UniProt
Find proteins for Q9SYW8 (Arabidopsis thaliana)
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UniProt GroupQ9SYW8
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I chlorophyll a/b-binding protein 3-1, chloroplasticC [auth 3]234Arabidopsis thalianaMutation(s): 1 
Gene Names: LHCA3At1g61520T25B24.12
UniProt
Find proteins for Q9SY97 (Arabidopsis thaliana)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 4, chloroplasticD [auth 4]199Arabidopsis thalianaMutation(s): 1 
Gene Names: LHCA4CAB4At3g47470F1P2.20
UniProt
Find proteins for P27521 (Arabidopsis thaliana)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1E [auth A]750Arabidopsis thalianaMutation(s): 0 
Gene Names: psaA
EC: 1.97.1.12
UniProt
Find proteins for A0A8F5S1X0 (Arabidopsis thaliana)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2F [auth B]734Arabidopsis thalianaMutation(s): 0 
Gene Names: psaB
EC: 1.97.1.12
UniProt
Find proteins for A0A8F5P166 (Arabidopsis thaliana)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerG [auth C]81Arabidopsis thalianaMutation(s): 0 
Gene Names: psaCfrxAAtCg01060
EC: 1.97.1.12
UniProt
Find proteins for P62090 (Arabidopsis thaliana)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II-2, chloroplasticH [auth D]160Arabidopsis thalianaMutation(s): 0 
Gene Names: PSAD2At1g03130F10O3_4
UniProt
Find proteins for Q9SA56 (Arabidopsis thaliana)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV B, chloroplasticI [auth E]99Arabidopsis thalianaMutation(s): 0 
Gene Names: PSAE2At2g20260F11A3.19
UniProt
Find proteins for Q9S714 (Arabidopsis thaliana)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III, chloroplasticJ [auth F]154Arabidopsis thalianaMutation(s): 0 
Gene Names: PSAFAt1g31330T19E23.12
UniProt
Find proteins for Q9SHE8 (Arabidopsis thaliana)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit V, chloroplasticK [auth G]100Arabidopsis thalianaMutation(s): 0 
Gene Names: PSAGAt1g55670F20N2.21F20N2.33F20N2_3
UniProt
Find proteins for Q9S7N7 (Arabidopsis thaliana)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VI-1, chloroplasticL [auth H]95Arabidopsis thalianaMutation(s): 0 
Gene Names: PSAH1At3g16140MSL1.18
UniProt
Find proteins for Q9SUI7 (Arabidopsis thaliana)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIM [auth I]37Arabidopsis thalianaMutation(s): 0 
Gene Names: psaIAtCg00510
UniProt
Find proteins for P56768 (Arabidopsis thaliana)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXN [auth J]44Arabidopsis thalianaMutation(s): 0 
Gene Names: psaJ
UniProt
Find proteins for A0A8F5NZW2 (Arabidopsis thaliana)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XI, chloroplasticO [auth L]169Arabidopsis thalianaMutation(s): 0 
Gene Names: PSALAt4g12800T20K18.150
UniProt
Find proteins for Q9SUI4 (Arabidopsis thaliana)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit psaK, chloroplasticP [auth K]84Arabidopsis thalianaMutation(s): 0 
Gene Names: PSAKAt1g30380T4K22.2
UniProt
Find proteins for Q9SUI5 (Arabidopsis thaliana)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit N, chloroplasticQ [auth N]85Arabidopsis thalianaMutation(s): 0 
Gene Names: PSANAt5g64040MHJ24.2
UniProt
Find proteins for P49107 (Arabidopsis thaliana)
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

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

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AC [auth 4]
BC [auth 4]
IC [auth 4]
KB [auth 3]
LA [auth 2]
AC [auth 4],
BC [auth 4],
IC [auth 4],
KB [auth 3],
LA [auth 2],
PA [auth 2],
QA [auth 2],
R [auth 1],
RA [auth 2],
W [auth 1],
YA [auth 2],
ZB [auth 4]
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]
AD [auth A]
AE [auth A]
AF [auth B]
AG [auth B]
AA [auth 1],
AD [auth A],
AE [auth A],
AF [auth B],
AG [auth B],
AH [auth H],
BA [auth 1],
BD [auth A],
BF [auth B],
BG [auth B],
BH [auth H],
CA [auth 1],
CC [auth 4],
CD [auth A],
CF [auth B],
CG [auth B],
DA [auth 1],
DC [auth 4],
DD [auth A],
DF [auth B],
EA [auth 1],
EB [auth 3],
EC [auth 4],
ED [auth A],
EF [auth B],
EH [auth J],
FB [auth 3],
FC [auth 4],
FD [auth A],
FF [auth B],
GB [auth 3],
GC [auth 4],
GD [auth A],
GF [auth B],
HB [auth 3],
HC [auth 4],
HD [auth A],
HF [auth B],
HH [auth L],
IA [auth 1],
IB [auth 3],
ID [auth A],
IF [auth B],
IH [auth L],
JB [auth 3],
JD [auth A],
JF [auth B],
KD [auth A],
KF [auth B],
LB [auth 3],
LD [auth A],
LF [auth B],
MA [auth 2],
MB [auth 3],
MD [auth A],
ME [auth A],
MF [auth B],
MH [auth K],
NA [auth 2],
NB [auth 3],
NC [auth A],
ND [auth A],
NE [auth A],
NF [auth B],
NG [auth B],
NH [auth K],
OA [auth 2],
OB [auth 3],
OC [auth A],
OD [auth A],
OE [auth A],
OF [auth B],
OH [auth K],
PB [auth 3],
PC [auth A],
PD [auth A],
PE [auth B],
PF [auth B],
QB [auth 3],
QC [auth A],
QD [auth A],
QE [auth B],
QF [auth B],
QG [auth F],
RB [auth 3],
RC [auth A],
RD [auth A],
RE [auth B],
RF [auth B],
RG [auth F],
S [auth 1],
SA [auth 2],
SC [auth A],
SD [auth A],
SE [auth B],
SF [auth B],
T [auth 1],
TA [auth 2],
TC [auth A],
TD [auth A],
TE [auth B],
TF [auth B],
U [auth 1],
UA [auth 2],
UC [auth A],
UD [auth A],
UE [auth B],
UF [auth B],
V [auth 1],
VA [auth 2],
VB [auth 4],
VC [auth A],
VD [auth A],
VE [auth B],
VF [auth B],
WA [auth 2],
WB [auth 4],
WC [auth A],
WD [auth A],
WE [auth B],
WF [auth B],
WG [auth G],
X [auth 1],
XA [auth 2],
XB [auth 4],
XC [auth A],
XD [auth A],
XE [auth B],
XF [auth B],
XG [auth G],
Y [auth 1],
YB [auth 4],
YC [auth A],
YD [auth A],
YE [auth B],
YF [auth B],
YG [auth G],
Z [auth 1],
ZC [auth A],
ZD [auth A],
ZE [auth B],
ZF [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG (Subject of Investigation/LOI)
Query on LMG

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LG [auth B],
MC [auth 4],
UG [auth F]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG (Subject of Investigation/LOI)
Query on LHG

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BB [auth 2],
CE [auth A],
HA [auth 1],
KA [auth 1],
MG [auth B]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
XAT (Subject of Investigation/LOI)
Query on XAT

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AB [auth 2],
GA [auth 1],
KC [auth 4],
TB [auth 3]
(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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FA [auth 1],
JA [auth 1],
JC [auth 4],
SB [auth 3],
ZA [auth 2]
(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

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CH [auth I]
DB [auth 2]
DE [auth A]
DH [auth J]
EE [auth A]
CH [auth I],
DB [auth 2],
DE [auth A],
DH [auth J],
EE [auth A],
EG [auth B],
FE [auth A],
FG [auth B],
FH [auth J],
GE [auth A],
GG [auth B],
GH [auth J],
HE [auth A],
HG [auth B],
IE [auth A],
IG [auth B],
JE [auth A],
JG [auth B],
JH [auth L],
KH [auth L],
LC [auth 4],
LH [auth L],
SG [auth F],
TG [auth F],
UB [auth 3],
VG [auth G],
ZG [auth G]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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CB [auth 2],
LE [auth A]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN (Subject of Investigation/LOI)
Query on PQN

Download Ideal Coordinates CCD File 
BE [auth A],
DG [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
KE [auth A],
OG [auth C],
PG [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.29 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC4.4.1

Structure Validation

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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: 2025-08-13
    Type: Initial release
  • Version 1.1: 2025-09-24
    Changes: Data collection, Database references
  • Version 1.2: 2025-11-19
    Changes: Data collection, Database references