9M4F | pdb_00009m4f

Photosystem I from the eukaryotic filamentous algae

  • Classification: PHOTOSYNTHESIS
  • Organism(s): Tribonema minus
  • Mutation(s): No 

  • Deposited: 2025-03-04 Released: 2025-08-27 
  • Deposition Author(s): Shao, R.Q., Pan, X.W.
  • Funding Organization(s): Ministry of Science and Technology (MoST, China), National Natural Science Foundation of China (NSFC), Chinese Academy of Sciences

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.82 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

Architecture of photosystem I-light-harvesting complex from the eukaryotic filamentous yellow-green alga Tribonema minus.

Shao, R.Zou, Y.Shang, H.Qiu, Y.Liang, Z.Su, X.Zhang, S.Li, M.Pan, X.

(2025) J Integr Plant Biol 67: 3014-3031

  • DOI: https://doi.org/10.1111/jipb.70010
  • Primary Citation of Related Structures:  
    9M4F

  • PubMed Abstract: 

    Eukaryotic photosystem I (PSI) is a multi-subunit pigment-protein supercomplex that consists of a core complex and multiple peripheral light-harvesting complexes I (LHCIs), which increases the light absorption capacity of the core complex. Throughout the evolution of oxygenic photoautotrophs, the core subunits of PSI have remained highly conserved, while LHCIs exhibit significant variability, presumably to adapt to diverse environments. This study presents a 2.82 Å resolution structure of PSI from the filamentous yellow-green alga Tribonema minus (Tm), a member of the class Xanthophyceae that evolved from red algae through endosymbiosis and is considered a promising candidate for biofuel production due to its high biomass and lipid content. Our structure reveals a supramolecular organization consisting of 12 core subunits and 13 LHCIs, here referred to as Xanthophyceae light-harvesting complexes (XLHs), along with the arrangement of pigments within the TmPSI-XLH supercomplex. A structural comparison between TmPSI-XLH and PSI-LHCI from various red lineages highlights distinctive features of TmPSI-XLH, suggesting that it represents a unique intermediate state in the PSI assembly process during the evolutionary transition from red algae to diatoms. Our findings advance the understanding of the molecular mechanisms responsible for energy transfer in Xanthophyceae PSI-XLH and the evolutionary adaptation of red lineages.


  • Organizational Affiliation
    • Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, College of Life Science, Capital Normal University, Beijing, 100048, China.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting protein XLH1A [auth 1]220Tribonema minusMutation(s): 0 
UniProt
Find proteins for A0A835Z6M5 (Tribonema minus)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
light-harvesting protein XLH2B [auth 2]194Tribonema minusMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
light-harvesting protein XLH3C [auth 3]205Tribonema minusMutation(s): 0 
UniProt
Find proteins for A0A835YRG9 (Tribonema minus)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
light-harvesting protein XLH4D [auth 4]231Tribonema minusMutation(s): 0 
UniProt
Find proteins for A0A836CGA6 (Tribonema minus)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
light-harvesting protein XLH5E [auth 5]216Tribonema minusMutation(s): 0 
UniProt
Find proteins for A0A835Z6T4 (Tribonema minus)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
light-harvesting protein XLH6/10F [auth 6],
J [auth h]
212Tribonema minusMutation(s): 0 
UniProt
Find proteins for A0A836CK85 (Tribonema minus)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
light-harvesting protein XLH7G [auth 7]207Tribonema minusMutation(s): 0 
UniProt
Find proteins for A0A835Z4D2 (Tribonema minus)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
light-harvesting protein XLH8H [auth 8]179Tribonema minusMutation(s): 0 
UniProt
Find proteins for A0A836CLY0 (Tribonema minus)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
light-harvesting protein XLH9/13I [auth 9],
M [auth k]
215Tribonema minusMutation(s): 0 
UniProt
Find proteins for A0A835Z019 (Tribonema minus)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
light-harvesting protein XLH11K [auth c]210Tribonema minusMutation(s): 0 
UniProt
Find proteins for A0A835YIY2 (Tribonema minus)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
light-harvesting protein XLH12L [auth t]228Tribonema minusMutation(s): 0 
EC: 4.2.1.19
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
PsaAN [auth A]749Tribonema minusMutation(s): 0 
EC: 1.97.1.12
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
PsaBO [auth B]734Tribonema minusMutation(s): 0 
EC: 1.97.1.12
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
PsaCP [auth C]81Tribonema minusMutation(s): 0 
EC: 1.97.1.12
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
PsaDQ [auth D]139Tribonema minusMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
PsaER [auth E]61Tribonema minusMutation(s): 0 
UniProt
Find proteins for A0T0F3 (Phaeodactylum tricornutum (strain CCAP 1055/1))
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
PsaFS [auth F]185Tribonema minusMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
PsaIT [auth I]36Tribonema minusMutation(s): 0 
UniProt
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
PsaJU [auth J]42Tribonema minusMutation(s): 0 
UniProt
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
PsaLV [auth L]149Tribonema minusMutation(s): 0 
UniProt
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
PsaMW [auth M]30Tribonema minusMutation(s): 0 
UniProt
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
PsaRX [auth R]87Tribonema minusMutation(s): 0 
UniProt
Find proteins for A0A836C871 (Tribonema minus)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
PsaSY [auth S]134Tribonema minusMutation(s): 0 
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Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA (Subject of Investigation/LOI)
Query on CLA

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AA [auth 1]
AC [auth 4]
AD [auth 6]
AF [auth 9]
AI [auth A]
AA [auth 1],
AC [auth 4],
AD [auth 6],
AF [auth 9],
AI [auth A],
AJ [auth A],
AL [auth B],
BA [auth 1],
BC [auth 4],
BD [auth 6],
BF [auth 9],
BG [auth c],
BI [auth A],
BJ [auth A],
BK [auth A],
BL [auth B],
BM [auth F],
CA [auth 1],
CC [auth 4],
CD [auth 6],
CF [auth 9],
CG [auth c],
CI [auth A],
CJ [auth A],
CK [auth B],
CL [auth B],
CM [auth F],
DA [auth 1],
DC [auth 4],
DD [auth 6],
DF [auth 9],
DG [auth c],
DI [auth A],
DJ [auth A],
DK [auth B],
DL [auth B],
DM [auth F],
EA [auth 1],
EC [auth 4],
ED [auth 6],
EG [auth c],
EH [auth k],
EI [auth A],
EJ [auth A],
EK [auth B],
EL [auth B],
FA [auth 1],
FC [auth 4],
FD [auth 6],
FG [auth c],
FH [auth k],
FI [auth A],
FJ [auth A],
FK [auth B],
FL [auth B],
GA [auth 1],
GB [auth 3],
GC [auth 4],
GD [auth 6],
GE [auth 8],
GG [auth c],
GH [auth k],
GI [auth A],
GK [auth B],
GL [auth B],
HA [auth 1],
HB [auth 3],
HC [auth 4],
HD [auth 6],
HE [auth 8],
HG [auth c],
HH [auth k],
HI [auth A],
HJ [auth A],
HK [auth B],
HL [auth B],
IB [auth 3],
ID [auth 6],
IE [auth 8],
IG [auth c],
IH [auth k],
II [auth A],
IK [auth B],
IL [auth B],
JB [auth 3],
JE [auth 8],
JG [auth c],
JH [auth k],
JI [auth A],
JK [auth B],
JL [auth B],
KB [auth 3],
KE [auth 8],
KF [auth h],
KG [auth c],
KH [auth k],
KI [auth A],
KK [auth B],
KL [auth B],
KM [auth J],
LB [auth 3],
LE [auth 8],
LF [auth h],
LG [auth c],
LH [auth k],
LI [auth A],
LK [auth B],
LL [auth B],
MB [auth 3],
ME [auth 8],
MF [auth h],
MH [auth k],
MI [auth A],
MK [auth B],
ML [auth B],
NB [auth 3],
NE [auth 8],
NF [auth h],
NH [auth k],
NI [auth A],
NK [auth B],
NL [auth B],
OB [auth 3],
OC [auth 5],
OD [auth 7],
OE [auth 8],
OF [auth h],
OH [auth k],
OI [auth A],
OJ [auth A],
OK [auth B],
PA [auth 1],
PC [auth 5],
PD [auth 7],
PF [auth h],
PI [auth A],
PK [auth B],
PM [auth L],
QC [auth 5],
QD [auth 7],
QF [auth h],
QG [auth t],
QI [auth A],
QK [auth B],
QM [auth L],
RA [auth 2],
RC [auth 5],
RD [auth 7],
RF [auth h],
RG [auth t],
RI [auth A],
RK [auth B],
RM [auth L],
SA [auth 2],
SC [auth 5],
SD [auth 7],
SF [auth h],
SG [auth t],
SI [auth A],
SK [auth B],
TA [auth 2],
TC [auth 5],
TD [auth 7],
TE [auth 9],
TF [auth h],
TG [auth t],
TI [auth A],
TK [auth B],
UA [auth 2],
UC [auth 5],
UD [auth 7],
UE [auth 9],
UF [auth h],
UG [auth t],
UH [auth A],
UI [auth A],
UJ [auth A],
UK [auth B],
VA [auth 2],
VB [auth 4],
VD [auth 7],
VE [auth 9],
VF [auth h],
VG [auth t],
VH [auth A],
VI [auth A],
VK [auth B],
VL [auth B],
WA [auth 2],
WB [auth 4],
WD [auth 7],
WE [auth 9],
WG [auth t],
WH [auth A],
WI [auth A],
WK [auth B],
WL [auth B],
WM [auth R],
XA [auth 2],
XB [auth 4],
XC [auth 6],
XD [auth 7],
XE [auth 9],
XG [auth t],
XH [auth A],
XI [auth A],
XJ [auth A],
XK [auth B],
XL [auth B],
XM [auth R],
YA [auth 2],
YB [auth 4],
YC [auth 6],
YD [auth 7],
YE [auth 9],
YG [auth t],
YH [auth A],
YI [auth A],
YJ [auth A],
YK [auth B],
Z [auth 1],
ZA [auth 2],
ZB [auth 4],
ZC [auth 6],
ZD [auth 7],
ZE [auth 9],
ZG [auth t],
ZH [auth A],
ZI [auth A],
ZK [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG (Subject of Investigation/LOI)
Query on LMG

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DH [auth t],
EB [auth 2],
WJ [auth A]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG (Subject of Investigation/LOI)
Query on LHG

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FB [auth 2]
HM [auth I]
IJ [auth A]
JJ [auth A]
MM [auth J]
FB [auth 2],
HM [auth I],
IJ [auth A],
JJ [auth A],
MM [auth J],
NC [auth 4],
NM [auth L],
QA [auth 1],
QJ [auth A],
SE [auth 8],
TJ [auth A],
TL [auth B],
UB [auth 3],
UL [auth B]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
A1L1G (Subject of Investigation/LOI)
Query on A1L1G

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BE [auth 7],
DB [auth 2],
EF [auth 9],
PB [auth 3],
PH [auth k]
(1~{R},3~{S})-6-[(3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{Z},17~{E})-16-(hydroxymethyl)-3,7,12-trimethyl-18-[(1~{S},4~{S},6~{R})-2,2,6-trimethyl-4-oxidanyl-7-oxabicyclo[4.1.0]heptan-1-yl]octadeca-1,3,5,7,9,11,13,15,17-nonaenylidene]-1,5,5-trimethyl-cyclohexane-1,3-diol
C40 H56 O5
OWWSPDNLRSCPIS-XZHZJERWSA-N
DD6 (Subject of Investigation/LOI)
Query on DD6

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AB [auth 2]
AE [auth 7]
AH [auth t]
CB [auth 2]
CE [auth 7]
AB [auth 2],
AE [auth 7],
AH [auth t],
CB [auth 2],
CE [auth 7],
CH [auth t],
DE [auth 7],
FE [auth 7],
FF [auth 9],
GF [auth 9],
HF [auth 9],
IC [auth 4],
JA [auth 1],
JC [auth 4],
JD [auth 6],
JF [auth 9],
JM [auth J],
KA [auth 1],
KC [auth 4],
KD [auth 6],
LA [auth 1],
LC [auth 4],
LD [auth 6],
MD [auth 6],
MG [auth c],
ND [auth 6],
NG [auth c],
OG [auth c],
PE [auth 8],
PJ [auth A],
QB [auth 3],
QE [auth 8],
QH [auth k],
RB [auth 3],
RE [auth 8],
RH [auth k],
SB [auth 3],
SH [auth k],
VC [auth 5],
WC [auth 5],
WF [auth h],
XF [auth h],
YF [auth h],
YM [auth R],
ZF [auth h]
(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

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AK [auth A]
BB [auth 2]
BH [auth t]
EE [auth 7]
EM [auth F]
AK [auth A],
BB [auth 2],
BH [auth t],
EE [auth 7],
EM [auth F],
FM [auth I],
GM [auth I],
IA [auth 1],
IF [auth 9],
IM [auth J],
KJ [auth A],
LJ [auth A],
LM [auth J],
MA [auth 1],
MC [auth 4],
MJ [auth A],
NJ [auth A],
OM [auth L],
PG [auth c],
PL [auth B],
QL [auth B],
RL [auth B],
SL [auth B],
SM [auth L],
TH [auth k],
TM [auth M],
UM [auth R],
VM [auth R],
YL [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT (Subject of Investigation/LOI)
Query on LMT

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AG [auth h]
NA [auth 1]
OA [auth 1]
RJ [auth A]
SJ [auth A]
AG [auth h],
NA [auth 1],
OA [auth 1],
RJ [auth A],
SJ [auth A],
TB [auth 3],
VJ [auth A]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN (Subject of Investigation/LOI)
Query on PQN

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GJ [auth A],
OL [auth B]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

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AM [auth C],
ZJ [auth A],
ZL [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.82 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2022YFC2804400
National Natural Science Foundation of China (NSFC)China32371269
National Natural Science Foundation of China (NSFC)China32470247
Chinese Academy of SciencesChina2024kf05

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-27
    Type: Initial release
  • Version 1.1: 2025-11-19
    Changes: Data collection, Database references