9KC5 | pdb_00009kc5

PSI-LHCI of the red alga Galdieria sulphuraria NIES-3638


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.19 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure of a photosystem I supercomplex from Galdieria sulphuraria close to an ancestral red alga.

Kato, K.Kumazawa, M.Nakajima, Y.Suzuki, T.Dohmae, N.Shen, J.R.Ifuku, K.Nagao, R.

(2025) Sci Adv 11: eadv7488-eadv7488

  • DOI: https://doi.org/10.1126/sciadv.adv7488
  • Primary Citation of Related Structures:  
    9KC5

  • PubMed Abstract: 

    Red algae exhibit unique photosynthetic adaptations, characterized by photosystem I (PSI) supercomplexes containing light-harvesting complexes (LHCs), forming PSI-LHCI supercomplexes. In this study, we solved the PSI-LHCI structure of Galdieria sulphuraria NIES-3638 at 2.19-angstrom resolution using cryo-electron microscopy, revealing a PSI monomer core associated with seven LHCI subunits. Structural analysis uncovered the absence of phylloquinones, the common secondary electron acceptor in PSI of photosynthetic organisms, suggesting adaptation to a benzoquinone-like molecule. Phylogenetic analysis suggests that G. sulphuraria retains traits characteristic of an ancestral red alga, including distinctive LHCI binding and interaction patterns. Variations in LHCI composition and interactions across red algae, particularly in red-lineage chlorophyll a / b -binding-like protein and red algal LHCs, highlight evolutionary divergence and specialization. These findings not only deepen our understanding of red algal PSI-LHCI diversification but also enable us to predict features of an ancestral red algal PSI-LHCI supercomplex, providing a framework to explore evolutionary adaptations from an ancestral red alga.


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

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1739Galdieria sulphurariaMutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for E3UIU0 (Galdieria sulphuraria)
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UniProt GroupE3UIU0
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2732Galdieria sulphurariaMutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for E3UIU1 (Galdieria sulphuraria)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur center80Galdieria sulphurariaMutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for E3UIU2 (Galdieria sulphuraria)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II138Galdieria sulphurariaMutation(s): 0 
UniProt
Find proteins for E3UIU3 (Galdieria sulphuraria)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I subunit IV64Galdieria sulphurariaMutation(s): 0 
UniProt
Find proteins for A0A075W2R1 (Galdieria sulphuraria)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III161Galdieria sulphurariaMutation(s): 0 
UniProt
Find proteins for E3UIU5 (Galdieria sulphuraria)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIG [auth I]34Galdieria sulphurariaMutation(s): 0 
UniProt
Find proteins for E3UIU6 (Galdieria sulphuraria)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXH [auth J]42Galdieria sulphurariaMutation(s): 0 
UniProt
Find proteins for E3UIU7 (Galdieria sulphuraria)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
PSI-KI [auth K]65Galdieria sulphurariaMutation(s): 0 
UniProt
Find proteins for E3UIU8 (Galdieria sulphuraria)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIJ [auth L]139Galdieria sulphurariaMutation(s): 0 
UniProt
Find proteins for E3UIU9 (Galdieria sulphuraria)
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UniProt GroupE3UIU9
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIK [auth M]28Galdieria sulphurariaMutation(s): 0 
UniProt
Find proteins for E3UIV0 (Galdieria sulphuraria)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I subunit OL [auth O]95Galdieria sulphurariaMutation(s): 0 
UniProt
Find proteins for M2XWX3 (Galdieria sulphuraria)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Psa28M [auth Z]84Galdieria sulphurariaMutation(s): 0 
UniProt
Find proteins for M2Y646 (Galdieria sulphuraria)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
RedCAPN [auth 1]177Galdieria sulphurariaMutation(s): 0 
UniProt
Find proteins for M2XW22 (Galdieria sulphuraria)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting complex proteinO [auth 2]162Galdieria sulphurariaMutation(s): 0 
UniProt
Find proteins for M2X4C9 (Galdieria sulphuraria)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting complex proteinP [auth 3]131Galdieria sulphurariaMutation(s): 0 
UniProt
Find proteins for M2XR49 (Galdieria sulphuraria)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting complex proteinQ [auth 4]178Galdieria sulphurariaMutation(s): 0 
UniProt
Find proteins for M2X090 (Galdieria sulphuraria)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting complex proteinR [auth 5]178Galdieria sulphurariaMutation(s): 0 
UniProt
Find proteins for M2VTV2 (Galdieria sulphuraria)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting complex proteinS [auth 6]178Galdieria sulphurariaMutation(s): 0 
UniProt
Find proteins for M2X4U9 (Galdieria sulphuraria)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting complex proteinT [auth 7]168Galdieria sulphurariaMutation(s): 0 
UniProt
Find proteins for M2Y652 (Galdieria sulphuraria)
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

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

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AA [auth A]
AB [auth A]
AC [auth A]
AD [auth B]
AF [auth K]
AA [auth A],
AB [auth A],
AC [auth A],
AD [auth B],
AF [auth K],
AI [auth 4],
AJ [auth 5],
AK [auth 6],
BA [auth A],
BB [auth A],
BD [auth B],
BG [auth Z],
BI [auth 4],
BJ [auth 5],
BK [auth 6],
CA [auth A],
CB [auth A],
CD [auth B],
CE [auth B],
CI [auth 4],
CJ [auth 5],
DA [auth A],
DB [auth A],
DD [auth B],
DE [auth B],
DH [auth 2],
DI [auth 4],
EA [auth A],
EB [auth A],
ED [auth B],
EH [auth 2],
EI [auth 4],
FA [auth A],
FB [auth A],
FD [auth B],
FF [auth L],
FH [auth 2],
FI [auth 4],
GA [auth A],
GB [auth A],
GC [auth B],
GD [auth B],
GF [auth L],
GH [auth 2],
GI [auth 4],
HA [auth A],
HC [auth B],
HD [auth B],
HF [auth L],
HH [auth 2],
HI [auth 4],
IA [auth A],
IC [auth B],
ID [auth B],
IH [auth 2],
II [auth 4],
JA [auth A],
JC [auth B],
JD [auth B],
JG [auth 1],
JH [auth 2],
KA [auth A],
KC [auth B],
KD [auth B],
KE [auth F],
KG [auth 1],
KH [auth 2],
LA [auth A],
LC [auth B],
LD [auth B],
LE [auth F],
LG [auth 1],
LH [auth 2],
MA [auth A],
MC [auth B],
MD [auth B],
ME [auth F],
MG [auth 1],
MH [auth 2],
NA [auth A],
NC [auth B],
ND [auth B],
NG [auth 1],
OA [auth A],
OC [auth B],
OD [auth B],
OG [auth 1],
OK [auth 7],
PA [auth A],
PB [auth A],
PC [auth B],
PD [auth B],
PG [auth 1],
PK [auth 7],
QA [auth A],
QC [auth B],
QD [auth B],
QF [auth O],
QG [auth 1],
QJ [auth 6],
QK [auth 7],
RA [auth A],
RC [auth B],
RD [auth B],
RF [auth O],
RG [auth 1],
RH [auth 3],
RJ [auth 6],
RK [auth 7],
SA [auth A],
SC [auth B],
SD [auth B],
SF [auth O],
SH [auth 3],
SI [auth 5],
SJ [auth 6],
SK [auth 7],
TA [auth A],
TC [auth B],
TF [auth O],
TH [auth 3],
TI [auth 5],
TJ [auth 6],
TK [auth 7],
UA [auth A],
UC [auth B],
UE [auth J],
UH [auth 3],
UI [auth 5],
UJ [auth 6],
UK [auth 7],
V [auth A],
VA [auth A],
VC [auth B],
VH [auth 3],
VI [auth 5],
VJ [auth 6],
VK [auth 7],
W [auth A],
WA [auth A],
WC [auth B],
WI [auth 5],
WJ [auth 6],
WK [auth 7],
X [auth A],
XA [auth A],
XC [auth B],
XI [auth 5],
XJ [auth 6],
XK [auth 7],
Y [auth A],
YA [auth A],
YB [auth A],
YC [auth B],
YF [auth Z],
YH [auth 4],
YI [auth 5],
YJ [auth 6],
YK [auth 7],
Z [auth A],
ZA [auth A],
ZB [auth A],
ZC [auth B],
ZE [auth K],
ZH [auth 4],
ZI [auth 5],
ZJ [auth 6]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0 (Subject of Investigation/LOI)
Query on CL0

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U [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LHG (Subject of Investigation/LOI)
Query on LHG

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BC [auth A]
GK [auth 6]
HJ [auth 5]
IB [auth A]
JB [auth A]
BC [auth A],
GK [auth 6],
HJ [auth 5],
IB [auth A],
JB [auth A],
OI [auth 4],
QH [auth 2],
YE [auth J],
YG [auth 1],
ZD [auth B]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
5X6 (Subject of Investigation/LOI)
Query on 5X6

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AL [auth 7]
BL [auth 7]
CK [auth 6]
CL [auth 7]
DG [auth Z]
AL [auth 7],
BL [auth 7],
CK [auth 6],
CL [auth 7],
DG [auth Z],
DJ [auth 5],
DK [auth 6],
DL [auth 7],
EE [auth B],
EJ [auth 5],
EK [auth 6],
FJ [auth 5],
JI [auth 4],
KI [auth 4],
LI [auth 4],
MF [auth M],
MJ [auth 5],
NH [auth 2],
OH [auth 2],
PH [auth 2],
SG [auth 1],
TG [auth 1],
UF [auth O],
UG [auth 1],
VF [auth O],
VG [auth 1],
WE [auth J],
WH [auth 3],
XG [auth 1],
ZK [auth 7]
Zeaxanthin
C40 H56 O2
JKQXZKUSFCKOGQ-AYORJBSZSA-N
RRX (Subject of Investigation/LOI)
Query on RRX

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FK [auth 6],
NI [auth 4],
NJ [auth 5],
WG [auth 1]
(3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
BCR (Subject of Investigation/LOI)
Query on BCR

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BF [auth K]
CC [auth A]
CG [auth Z]
CH [auth 2]
DC [auth A]
BF [auth K],
CC [auth A],
CG [auth Z],
CH [auth 2],
DC [auth A],
DF [auth L],
EF [auth L],
GJ [auth 5],
HE [auth F],
IF [auth L],
IG [auth 1],
KB [auth A],
LB [auth A],
MB [auth A],
MI [auth 4],
NB [auth A],
NE [auth F],
RE [auth I],
UD [auth B],
VD [auth B],
VE [auth J],
WD [auth B],
XD [auth B],
ZF [auth Z]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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IE [auth F],
LJ [auth 5],
OF [auth O],
PI [auth 4]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
A1L64 (Subject of Investigation/LOI)
Query on A1L64

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HB [auth A],
TD [auth B]
Coenzyme Q4
C29 H42 O4
XGCJRRDNIMSYNC-INVBOZNNSA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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FE [auth C],
GE [auth C],
OB [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
UNL
Query on UNL

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AE [auth B]
AG [auth Z]
AH [auth 1]
BE [auth B]
BH [auth 1]
AE [auth B],
AG [auth Z],
AH [auth 1],
BE [auth B],
BH [auth 1],
CF [auth K],
EC [auth A],
EG [auth Z],
EL [auth 7],
FC [auth A],
FG [auth Z],
FL [auth 7],
GG [auth Z],
HG [auth Z],
HK [auth 6],
IJ [auth 5],
IK [auth 6],
JE [auth F],
JF [auth L],
JJ [auth 5],
JK [auth 6],
KF [auth L],
KJ [auth 5],
KK [auth 6],
LF [auth L],
LK [auth 6],
MK [auth 7],
NF [auth M],
NK [auth 7],
OE [auth F],
OJ [auth 6],
PE [auth F],
PF [auth O],
PJ [auth 6],
QB [auth A],
QE [auth I],
QI [auth 4],
RB [auth A],
RI [auth 4],
SB [auth A],
SE [auth I],
TB [auth A],
TE [auth J],
UB [auth A],
VB [auth A],
WB [auth A],
WF [auth O],
XB [auth A],
XE [auth J],
XF [auth O],
XH [auth 4],
ZG [auth 1]
Unknown ligand
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.19 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION4.0
MODEL REFINEMENTServalcat0.4.32
MODEL REFINEMENTREFMAC5.8.0419
MODEL REFINEMENTPHENIX1.20.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)JapanJP23K14211
Japan Society for the Promotion of Science (JSPS)JapanJP22H04916
Japan Society for the Promotion of Science (JSPS)JapanJP23H02423

Revision History  (Full details and data files)

  • Version 1.0: 2025-04-23
    Type: Initial release
  • Version 1.1: 2025-05-28
    Changes: Data collection, Database references