9VFJ | pdb_00009vfj

PSI-LHCI of Euglena gracilis strain Z


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into the divergent evolution of a photosystem I supercomplex in Euglena gracilis.

Kato, K.Nakajima, Y.Sakamoto, R.Kumazawa, M.Ifuku, K.Ishikawa, T.Shen, J.R.Takabayashi, A.Nagao, R.

(2025) Sci Adv 11: eaea6241-eaea6241

  • DOI: https://doi.org/10.1126/sciadv.aea6241
  • Primary Citation of Related Structures:  
    9VFJ

  • PubMed Abstract: 

    Photosystem I (PSI) forms supercomplexes with light-harvesting complexes (LHCs) to perform oxygenic photosynthesis. Here, we report a 2.82-angstrom cryo-electron microscopy structure of the PSI-LHCI supercomplex from Euglena gracilis , a eukaryotic alga with secondary green alga-derived plastids. The structure reveals a PSI monomer core with eight subunits and 13 asymmetrically arranged LHCI proteins. Euglena LHCIs bind diadinoxanthin, which is one of the carotenoids typically associated with red-lineage LHCs and is not present in the canonical LHCI belt found in green-lineage PSI-LHCI structures. Phylogenetic analysis shows that the Euglena LHCIs originated from LHCII-related clades rather than from the green-lineage LHCI group and that the nuclear-encoded PSI subunit PsaD likely originated from cyanobacteria via horizontal gene transfer. These observations indicate a mosaic origin of the Euglena PSI-LHCI. Our findings uncover a noncanonical light-harvesting architecture and highlight the structural and evolutionary plasticity of photosynthetic systems, illustrating how endosymbiotic acquisition and lineage-specific adaptation shape divergent light-harvesting strategies.


  • Organizational Affiliation
    • Research Institute for Interdisciplinary Science, Advanced Research Field, and Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, Okayama, Okayama 700-8530, Japan.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1760Euglena gracilisMutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for P19430 (Euglena gracilis)
Explore P19430 
Go to UniProtKB:  P19430
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19430
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2734Euglena gracilisMutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for P19431 (Euglena gracilis)
Explore P19431 
Go to UniProtKB:  P19431
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP19431
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center81Euglena gracilisMutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for P31556 (Euglena gracilis)
Explore P31556 
Go to UniProtKB:  P31556
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31556
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II698Euglena gracilisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV161Euglena gracilisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III333Euglena gracilisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXG [auth J]37Euglena gracilisMutation(s): 0 
UniProt
Find proteins for P30394 (Euglena gracilis)
Explore P30394 
Go to UniProtKB:  P30394
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30394
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIH [auth M]31Euglena gracilisMutation(s): 0 
UniProt
Find proteins for P31479 (Euglena gracilis)
Explore P31479 
Go to UniProtKB:  P31479
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP31479
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
LHCI-1I [auth 1]492Euglena gracilisMutation(s): 0 
UniProt
Find proteins for A8HPH1 (Euglena gracilis)
Explore A8HPH1 
Go to UniProtKB:  A8HPH1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8HPH1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
LHCI-2J [auth 2]620Euglena gracilisMutation(s): 0 
UniProt
Find proteins for Q39725 (Euglena gracilis)
Explore Q39725 
Go to UniProtKB:  Q39725
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ39725
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
LHCI-3K [auth 3]431Euglena gracilisMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
LHCI-4L [auth 4]411Euglena gracilisMutation(s): 0 
UniProt
Find proteins for A8HPE4 (Euglena gracilis)
Explore A8HPE4 
Go to UniProtKB:  A8HPE4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8HPE4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Chloroplast light-harvesting complex I proteinM [auth 5]252Euglena gracilisMutation(s): 0 
UniProt
Find proteins for A8HPE4 (Euglena gracilis)
Explore A8HPE4 
Go to UniProtKB:  A8HPE4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8HPE4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
LHCI-6N [auth 6]889Euglena gracilisMutation(s): 0 
UniProt
Find proteins for A8HPC6 (Euglena gracilis)
Explore A8HPC6 
Go to UniProtKB:  A8HPC6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8HPC6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
LHCI-7O [auth 7]616Euglena gracilisMutation(s): 0 
UniProt
Find proteins for A8HPC6 (Euglena gracilis)
Explore A8HPC6 
Go to UniProtKB:  A8HPC6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8HPC6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
LHCI-8P [auth 8]828Euglena gracilisMutation(s): 0 
UniProt
Find proteins for A8HPC6 (Euglena gracilis)
Explore A8HPC6 
Go to UniProtKB:  A8HPC6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8HPC6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
LHCI-9Q [auth 9]873Euglena gracilisMutation(s): 0 
UniProt
Find proteins for A8HPC6 (Euglena gracilis)
Explore A8HPC6 
Go to UniProtKB:  A8HPC6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8HPC6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
LHCI-10R [auth 10]643Euglena gracilisMutation(s): 0 
UniProt
Find proteins for A8HPC6 (Euglena gracilis)
Explore A8HPC6 
Go to UniProtKB:  A8HPC6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8HPC6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
LHCI-11S [auth 11],
T [auth 12],
U [auth 13]
1,048Euglena gracilisMutation(s): 0 
UniProt
Find proteins for A8HPC6 (Euglena gracilis)
Explore A8HPC6 
Go to UniProtKB:  A8HPC6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA8HPC6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

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

Download Ideal Coordinates CCD File 
AA [auth A]
AB [auth A]
AD [auth B]
AF [auth 1]
AG [auth 2]
AA [auth A],
AB [auth A],
AD [auth B],
AF [auth 1],
AG [auth 2],
AH [auth 3],
AI [auth 5],
AL [auth 9],
AM [auth 11],
BA [auth A],
BB [auth A],
BD [auth B],
BF [auth 1],
BG [auth 2],
BH [auth 3],
BI [auth 5],
BL [auth 9],
BM [auth 11],
CA [auth A],
CB [auth A],
CD [auth B],
CF [auth 1],
CG [auth 2],
CH [auth 3],
CI [auth 5],
CL [auth 9],
CM [auth 11],
DA [auth A],
DB [auth A],
DD [auth B],
DF [auth 1],
DG [auth 2],
DH [auth 3],
DI [auth 5],
DK [auth 8],
DL [auth 9],
DM [auth 11],
EA [auth A],
EB [auth A],
EC [auth A],
ED [auth B],
EF [auth 1],
EG [auth 2],
EH [auth 3],
EI [auth 5],
EK [auth 8],
EL [auth 9],
EM [auth 11],
FA [auth A],
FB [auth A],
FC [auth B],
FD [auth B],
FF [auth 1],
FG [auth 2],
FH [auth 3],
FI [auth 5],
FK [auth 8],
FL [auth 9],
FM [auth 11],
GA [auth A],
GB [auth A],
GC [auth B],
GD [auth B],
GF [auth 1],
GG [auth 2],
GI [auth 5],
GJ [auth 7],
GK [auth 8],
GL [auth 9],
GM [auth 11],
HA [auth A],
HB [auth A],
HC [auth B],
HD [auth B],
HF [auth 1],
HG [auth 2],
HI [auth 5],
HJ [auth 7],
HK [auth 8],
HL [auth 9],
HM [auth 11],
IA [auth A],
IB [auth A],
IC [auth B],
ID [auth B],
IF [auth 1],
IG [auth 2],
II [auth 5],
IJ [auth 7],
IK [auth 8],
IM [auth 11],
JA [auth A],
JB [auth A],
JC [auth B],
JD [auth B],
JE [auth F],
JF [auth 1],
JG [auth 2],
JJ [auth 7],
JK [auth 8],
KA [auth A],
KB [auth A],
KC [auth B],
KD [auth B],
KF [auth 1],
KH [auth 4],
KJ [auth 7],
KK [auth 8],
LA [auth A],
LB [auth A],
LC [auth B],
LD [auth B],
LE [auth F],
LF [auth 1],
LH [auth 4],
LJ [auth 7],
LK [auth 8],
MA [auth A],
MB [auth A],
MC [auth B],
MD [auth B],
ME [auth F],
MF [auth 1],
MH [auth 4],
MJ [auth 7],
MK [auth 8],
MM [auth 12],
NA [auth A],
NC [auth B],
ND [auth B],
NH [auth 4],
NJ [auth 7],
NK [auth 8],
NL [auth 10],
NM [auth 12],
OA [auth A],
OC [auth B],
OD [auth B],
OH [auth 4],
OI [auth 6],
OJ [auth 7],
OK [auth 8],
OL [auth 10],
OM [auth 12],
PA [auth A],
PC [auth B],
PD [auth B],
PE [auth J],
PH [auth 4],
PI [auth 6],
PJ [auth 7],
PL [auth 10],
PM [auth 12],
QA [auth A],
QC [auth B],
QD [auth B],
QH [auth 4],
QI [auth 6],
QJ [auth 7],
QL [auth 10],
QM [auth 12],
RA [auth A],
RC [auth B],
RD [auth B],
RG [auth 3],
RH [auth 4],
RI [auth 6],
RJ [auth 7],
RL [auth 10],
RM [auth 12],
SA [auth A],
SC [auth B],
SG [auth 3],
SH [auth 4],
SI [auth 6],
SJ [auth 7],
SL [auth 10],
SM [auth 12],
TA [auth A],
TC [auth B],
TG [auth 3],
TH [auth 4],
TI [auth 6],
TL [auth 10],
TM [auth 12],
UA [auth A],
UC [auth B],
UG [auth 3],
UH [auth 4],
UI [auth 6],
UL [auth 10],
VA [auth A],
VC [auth B],
VF [auth 2],
VG [auth 3],
VI [auth 6],
VK [auth 9],
VL [auth 10],
W [auth A],
WA [auth A],
WC [auth B],
WE [auth 1],
WF [auth 2],
WG [auth 3],
WI [auth 6],
WK [auth 9],
WL [auth 10],
WM [auth 13],
X [auth A],
XA [auth A],
XC [auth B],
XF [auth 2],
XG [auth 3],
XI [auth 6],
XK [auth 9],
XM [auth 13],
Y [auth A],
YA [auth A],
YC [auth B],
YF [auth 2],
YG [auth 3],
YH [auth 5],
YI [auth 6],
YK [auth 9],
YL [auth 11],
YM [auth 13],
Z [auth A],
ZA [auth A],
ZC [auth B],
ZE [auth 1],
ZF [auth 2],
ZG [auth 3],
ZH [auth 5],
ZI [auth 6],
ZK [auth 9],
ZL [auth 11]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0 (Subject of Investigation/LOI)
Query on CL0

Download Ideal Coordinates CCD File 
V [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LHG (Subject of Investigation/LOI)
Query on LHG

Download Ideal Coordinates CCD File 
AE [auth B]
CJ [auth 6]
JH [auth 3]
KL [auth 9]
LI [auth 5]
AE [auth B],
CJ [auth 6],
JH [auth 3],
KL [auth 9],
LI [auth 5],
LM [auth 11],
NG [auth 2],
QF [auth 1],
RK [auth 8],
VB [auth A],
VJ [auth 7],
WB [auth A],
XH [auth 4],
XL [auth 10]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
DD6 (Subject of Investigation/LOI)
Query on DD6

Download Ideal Coordinates CCD File 
AJ [auth 6]
BJ [auth 6]
GH [auth 3]
HH [auth 3]
IH [auth 3]
AJ [auth 6],
BJ [auth 6],
GH [auth 3],
HH [auth 3],
IH [auth 3],
IL [auth 9],
JI [auth 5],
JL [auth 9],
JM [auth 11],
KG [auth 2],
KI [auth 5],
KM [auth 11],
LG [auth 2],
MG [auth 2],
NF [auth 1],
OF [auth 1],
PF [auth 1],
PK [auth 8],
QK [auth 8],
SE [auth J],
TJ [auth 7],
UJ [auth 7],
UM [auth 12],
VH [auth 4],
VM [auth 12],
WH [auth 4]
(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
BCR (Subject of Investigation/LOI)
Query on BCR

Download Ideal Coordinates CCD File 
KE [auth F]
NE [auth F]
PB [auth A]
QB [auth A]
QE [auth J]
KE [auth F],
NE [auth F],
PB [auth A],
QB [auth A],
QE [auth J],
RB [auth A],
RE [auth J],
SB [auth A],
TB [auth A],
TD [auth B],
UB [auth A],
UD [auth B],
UE [auth M],
VD [auth B],
WD [auth B],
XD [auth B],
YD [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN (Subject of Investigation/LOI)
Query on PQN

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

Download Ideal Coordinates CCD File 
GE [auth C],
HE [auth C],
OB [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
UNL (Subject of Investigation/LOI)
Query on UNL

Download Ideal Coordinates CCD File 
AC [auth A]
AK [auth 7]
BC [auth A]
BE [auth B]
BK [auth 8]
AC [auth A],
AK [auth 7],
BC [auth A],
BE [auth B],
BK [auth 8],
CC [auth A],
CE [auth B],
CK [auth 8],
DC [auth A],
DE [auth B],
DJ [auth 6],
EE [auth B],
EJ [auth 6],
FE [auth B],
FJ [auth 7],
IE [auth D],
LL [auth 10],
MI [auth 6],
ML [auth 10],
NI [auth 6],
OE [auth F],
OG [auth 2],
PG [auth 2],
QG [auth 2],
RF [auth 1],
SF [auth 1],
SK [auth 8],
TE [auth M],
TF [auth 2],
TK [auth 8],
UF [auth 2],
UK [auth 9],
VE [auth M],
WJ [auth 7],
XB [auth A],
XE [auth 1],
XJ [auth 7],
YB [auth A],
YE [auth 1],
YJ [auth 7],
ZB [auth A],
ZJ [auth 7]
Unknown ligand
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTServalcat0.4.32
MODEL REFINEMENTREFMAC5.8.0419
MODEL REFINEMENTPHENIX1.20.1
RECONSTRUCTIONRELION3.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP23K14211, JP22H04916, and JP23H02423

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-08
    Type: Initial release
  • Version 1.1: 2025-11-12
    Changes: Data collection, Database references