8WGH

Cryo-EM structure of the red-shifted Fittonia albivenis PSI-LHCI


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 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 the red-shifted Fittonia albivenis photosystem I.

Li, X.Huang, G.Zhu, L.Hao, C.Sui, S.F.Qin, X.

(2024) Nat Commun 15: 6325-6325

  • DOI: https://doi.org/10.1038/s41467-024-50655-9
  • Primary Citation of Related Structures:  
    8WGH

  • PubMed Abstract: 

    Photosystem I (PSI) from Fittonia albivenis, an Acanthaceae ornamental plant, is notable among green plants for its red-shifted emission spectrum. Here, we solved the structure of a PSI-light harvesting complex I (LHCI) supercomplex from F. albivenis at 2.46-Å resolution using cryo-electron microscopy. The supercomplex contains a core complex of 14 subunits and an LHCI belt with four antenna subunits (Lhca1-4) similar to previously reported angiosperm PSI-LHCI structures; however, Lhca3 differs in three regions surrounding a dimer of low-energy chlorophylls (Chls) termed red Chls, which absorb far-red beyond visible light. The unique amino acid sequences within these regions are exclusively shared by plants with strongly red-shifted fluorescence emission, suggesting candidate structural elements for regulating the energy state of red Chls. These results provide a structural basis for unraveling the mechanisms of light harvest and transfer in PSI-LHCI of under canopy plants and for designing Lhc to harness longer-wavelength light in the far-red spectral range.


  • Organizational Affiliation

    School of Chemistry and Chemical Engineering, School of Biological Science and Technology, University of Jinan, Jinan, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 1A [auth 1]246Fittonia albivenisMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 2B [auth 2]265Fittonia albivenisMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 3C [auth 3]272Fittonia albivenisMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein 4D [auth 4]248Fittonia albivenisMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1E [auth A]750Fittonia albivenisMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2F [auth B]734Fittonia albivenisMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerG [auth C]81Fittonia albivenisMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIH [auth D]190Fittonia albivenisMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVI [auth E]151Fittonia albivenisMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III, chloroplasticJ [auth F]221Fittonia albivenisMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIK [auth G]145Fittonia albivenisMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIL [auth H]145Fittonia albivenisMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIM [auth I]36Fittonia albivenisMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXN [auth J]44Fittonia albivenisMutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit psaKO [auth K]132Fittonia albivenisMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIP [auth L]217Fittonia albivenisMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit NQ [auth N]173Fittonia albivenisMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit OR [auth O]144Fittonia albivenisMutation(s): 0 
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Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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PG [auth B]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL (Subject of Investigation/LOI)
Query on CHL

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CB [auth 2]
CC [auth 4]
DC [auth 4]
EC [auth 4]
MB [auth 3]
CB [auth 2],
CC [auth 4],
DC [auth 4],
EC [auth 4],
MB [auth 3],
MC [auth 4],
PA [auth 2],
S [auth 1],
TA [auth 2],
UA [auth 2],
VA [auth 2],
X [auth 1]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CLA (Subject of Investigation/LOI)
Query on CLA

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AA [auth 1]
AB [auth 2]
AC [auth 4]
AD [auth A]
AE [auth A]
AA [auth 1],
AB [auth 2],
AC [auth 4],
AD [auth A],
AE [auth A],
AF [auth B],
AG [auth B],
AI [auth L],
BA [auth 1],
BB [auth 2],
BC [auth 4],
BD [auth A],
BE [auth A],
BF [auth B],
BG [auth B],
CA [auth 1],
CD [auth A],
CE [auth A],
CF [auth B],
CG [auth B],
CI [auth N],
DA [auth 1],
DD [auth A],
DE [auth A],
DF [auth B],
DG [auth B],
DI [auth N],
EA [auth 1],
ED [auth A],
EE [auth A],
EF [auth B],
EG [auth B],
EH [auth G],
EI [auth O],
FA [auth 1],
FC [auth 4],
FD [auth A],
FE [auth A],
FF [auth B],
FG [auth B],
FH [auth G],
FI [auth O],
GC [auth 4],
GD [auth A],
GE [auth A],
GF [auth B],
GG [auth B],
GH [auth G],
GI [auth O],
HB [auth 3],
HC [auth 4],
HD [auth A],
HF [auth B],
IB [auth 3],
IC [auth 4],
ID [auth A],
IF [auth B],
IH [auth H],
JB [auth 3],
JC [auth 4],
JD [auth A],
JF [auth B],
KB [auth 3],
KC [auth 4],
KD [auth A],
KF [auth B],
KH [auth J],
LB [auth 3],
LC [auth 4],
LD [auth A],
LF [auth B],
MA [auth 1],
MD [auth A],
MF [auth B],
MH [auth J],
NB [auth 3],
ND [auth A],
NF [auth B],
OB [auth 3],
OD [auth A],
OF [auth B],
PB [auth 3],
PD [auth A],
PF [auth B],
PH [auth K],
QA [auth 2],
QB [auth 3],
QD [auth A],
QE [auth A],
QF [auth B],
QH [auth K],
RA [auth 2],
RB [auth 3],
RD [auth A],
RF [auth B],
RH [auth K],
SA [auth 2],
SB [auth 3],
SC [auth A],
SD [auth A],
SE [auth A],
SF [auth B],
T [auth 1],
TB [auth 3],
TC [auth A],
TD [auth A],
TF [auth B],
TH [auth K],
U [auth 1],
UB [auth 3],
UC [auth A],
UD [auth A],
UE [auth B],
UF [auth B],
V [auth 1],
VC [auth A],
VD [auth A],
VE [auth B],
VF [auth B],
VH [auth L],
W [auth 1],
WA [auth 2],
WC [auth A],
WD [auth A],
WE [auth B],
WF [auth B],
WG [auth F],
WH [auth L],
XA [auth 2],
XC [auth A],
XD [auth A],
XE [auth B],
XF [auth B],
XH [auth L],
Y [auth 1],
YA [auth 2],
YB [auth 4],
YC [auth A],
YD [auth A],
YE [auth B],
YF [auth B],
YG [auth F],
Z [auth 1],
ZA [auth 2],
ZB [auth 4],
ZC [auth A],
ZD [auth A],
ZE [auth B],
ZF [auth B],
ZG [auth F]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG (Subject of Investigation/LOI)
Query on LMG

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LA [auth 1],
OA [auth 1],
QC [auth 4]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG (Subject of Investigation/LOI)
Query on LHG

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GB [auth 2],
IE [auth A],
JA [auth 1],
JE [auth A],
QG [auth B]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
XAT
Query on XAT

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EB [auth 2],
HA [auth 1],
OC [auth 4],
WB [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
Query on LUT

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DB [auth 2]
GA [auth 1]
HI [auth O]
II [auth O]
KA [auth 1]
DB [auth 2],
GA [auth 1],
HI [auth O],
II [auth O],
KA [auth 1],
NC [auth 4],
VB [auth 3]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR
Query on BCR

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AH [auth F]
FB [auth 2]
HH [auth G]
IA [auth 1]
IG [auth B]
AH [auth F],
FB [auth 2],
HH [auth G],
IA [auth 1],
IG [auth B],
JG [auth B],
JH [auth I],
KE [auth A],
KG [auth B],
LE [auth A],
LG [auth B],
LH [auth J],
ME [auth A],
MG [auth B],
NE [auth A],
NG [auth B],
NH [auth J],
OE [auth A],
PC [auth 4],
SH [auth K],
TE [auth A],
UH [auth L],
VG [auth F],
XB [auth 3],
YH [auth L],
ZH [auth L]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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CH [auth G],
OG [auth B]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
Query on PQN

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

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PE [auth A],
TG [auth C],
UG [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
HTG
Query on HTG

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BH [auth F]
BI [auth N]
DH [auth G]
NA [auth 1]
OH [auth J]
BH [auth F],
BI [auth N],
DH [auth G],
NA [auth 1],
OH [auth J],
RC [auth 4],
RE [auth A],
RG [auth B],
SG [auth B],
XG [auth F]
heptyl 1-thio-beta-D-glucopyranoside
C13 H26 O5 S
HPEGNLMTTNTJSP-LBELIVKGSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-10
    Type: Initial release
  • Version 1.1: 2024-08-07
    Changes: Data collection, Database references