8ZEH | pdb_00008zeh

PSI-FCPI-L in Thalassiosira pseudonana


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.78 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

Structures of PSI-FCPI from Thalassiosira pseudonana grown under high light provide evidence for convergent evolution and light-adaptive strategies in diatom FCPIs.

Feng, Y.Li, Z.Yang, Y.Shen, L.Li, X.Liu, X.Zhang, X.Zhang, J.Ren, F.Wang, Y.Liu, C.Han, G.Wang, X.Kuang, T.Shen, J.R.Wang, W.

(2025) J Integr Plant Biol 67: 949-966

  • DOI: https://doi.org/10.1111/jipb.13816
  • Primary Citation of Related Structures:  
    8ZEH, 8ZET

  • PubMed Abstract: 

    Diatoms rely on fucoxanthin chlorophyll a/c-binding proteins (FCPs) for light harvesting and energy quenching under marine environments. Here we report two cryo-electron microscopic structures of photosystem I (PSI) with either 13 or five fucoxanthin chlorophyll a/c-binding protein Is (FCPIs) at 2.78 and 3.20 Å resolutions from Thalassiosira pseudonana grown under high light (HL) conditions. Among them, five FCPIs are stably associated with the PSI core, these include Lhcr3, RedCAP, Lhcq8, Lhcf10, and FCP3. The eight additional Lhcr-type FCPIs are loosely associated with the PSI core and detached under the present purification conditions. The pigments of this centric diatom showed a higher proportion of chlorophylls a, diadinoxanthins, and diatoxanthins; some of the chlorophyll as and diadinoxanthins occupy the locations of fucoxanthins found in the huge PSI-FCPI from another centric diatom Chaetoceros gracilis grown under low-light conditions. These additional chlorophyll as may form more energy transfer pathways and additional diadinoxanthins may form more energy dissipation sites relying on the diadinoxanthin-diatoxanthin cycle. These results reveal the assembly mechanism of FCPIs and corresponding light-adaptive strategies of T. pseudonana PSI-FCPI, as well as the convergent evolution of the diatom PSI-FCPI structures.


  • Organizational Affiliation

    Key Laboratory of Photobiology, Photosynthesis Research Center, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tp-Lhcr18148Thalassiosira pseudonana CCMP1335Mutation(s): 0 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c-binding protein Lhcq8165Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chl a/c light-harvesting protein, major type170Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Tp-RedCAPD [auth E]185Thalassiosira pseudonana CCMP1335Mutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Tp-Lhcr20E [auth F]170Thalassiosira pseudonana CCMP1335Mutation(s): 0 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chl a/c light-harvesting protein, lhcr typeF [auth G]174Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chl a/c light-harvesting proteinG [auth H]168Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chl a/c light-harvesting proteinH [auth I]172Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chl a/c light-harvesting proteinI [auth J]183Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c light-harvesting proteinJ [auth K]176Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c light-harvesting proteinK [auth L]217Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Fucoxanthin chlorophyll a/c light-harvesting protein, lhcr typeL [auth M]171Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1M [auth a]743Thalassiosira pseudonana CCMP1335Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIN [auth d]132Thalassiosira pseudonana CCMP1335Mutation(s): 0 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVO [auth e]62Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIP [auth f]160Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit Psa29Q [auth g]131Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIR [auth i]33Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0T0S9 (Thalassiosira pseudonana)
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UniProt GroupA0T0S9
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXS [auth j]40Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0T0V1 (Thalassiosira pseudonana)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIT [auth l]146Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0T0U5 (Thalassiosira pseudonana)
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIU [auth m]29Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
Tp-PsaRV [auth r]89Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
Pt17531-like proteinW [auth D]164Thalassiosira pseudonana CCMP1335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2X [auth b]732Thalassiosira pseudonana CCMP1335Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
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Entity ID: 25
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerY [auth c]80Thalassiosira pseudonana CCMP1335Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
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Small Molecules
Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

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

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AB [auth B]
AD [auth F]
AE [auth H]
AF [auth I]
AH [auth L]
AB [auth B],
AD [auth F],
AE [auth H],
AF [auth I],
AH [auth L],
AI [auth M],
AJ [auth a],
AK [auth a],
AL [auth l],
AM [auth D],
AN [auth b],
BA [auth A],
BD [auth F],
BE [auth H],
BH [auth L],
BI [auth M],
BJ [auth a],
BL [auth l],
BM [auth b],
BN [auth b],
CA [auth A],
CC [auth E],
CD [auth F],
CE [auth H],
CI [auth M],
CJ [auth a],
CK [auth a],
CN [auth b],
DA [auth A],
DC [auth E],
DD [auth F],
DE [auth H],
DG [auth K],
DH [auth L],
DI [auth M],
DJ [auth a],
DK [auth a],
DL [auth l],
DM [auth b],
DN [auth b],
EA [auth A],
EC [auth E],
EE [auth H],
EG [auth K],
EH [auth L],
EI [auth M],
EJ [auth a],
EK [auth a],
EM [auth b],
EN [auth b],
FA [auth A],
FC [auth E],
FG [auth K],
FH [auth L],
FJ [auth a],
FM [auth b],
FN [auth b],
GA [auth A],
GC [auth E],
GE [auth H],
GG [auth K],
GH [auth L],
GJ [auth a],
GM [auth b],
HB [auth C],
HC [auth E],
HE [auth H],
HG [auth K],
HH [auth L],
HJ [auth a],
HL [auth r],
HM [auth b],
IA [auth A],
IB [auth C],
IC [auth E],
IE [auth H],
IG [auth K],
IJ [auth a],
IK [auth a],
IM [auth b],
JA [auth A],
JC [auth E],
JD [auth G],
JF [auth J],
JH [auth L],
JI [auth a],
JJ [auth a],
JK [auth a],
JM [auth b],
KB [auth C],
KD [auth G],
KF [auth J],
KG [auth K],
KI [auth a],
KJ [auth a],
KK [auth a],
KM [auth b],
LB [auth C],
LD [auth G],
LF [auth J],
LG [auth K],
LI [auth a],
LK [auth f],
LM [auth b],
MB [auth C],
MD [auth G],
MF [auth J],
MG [auth K],
MI [auth a],
MJ [auth a],
MK [auth f],
MM [auth b],
MN [auth b],
NB [auth C],
ND [auth G],
NF [auth J],
NG [auth K],
NI [auth a],
NK [auth f],
NM [auth b],
NN [auth b],
OD [auth G],
OE [auth I],
OF [auth J],
OI [auth a],
OM [auth b],
PB [auth C],
PD [auth G],
PE [auth I],
PF [auth J],
PI [auth a],
PM [auth b],
PN [auth b],
QB [auth C],
QE [auth I],
QF [auth J],
QI [auth a],
QK [auth i],
QL [auth D],
QM [auth b],
QN [auth b],
RB [auth C],
RC [auth F],
RD [auth G],
RE [auth I],
RF [auth J],
RI [auth a],
RL [auth D],
RM [auth b],
RN [auth b],
SA [auth B],
SB [auth C],
SC [auth F],
SD [auth G],
SE [auth I],
SH [auth M],
SI [auth a],
SJ [auth a],
SL [auth D],
SM [auth b],
SN [auth b],
TA [auth B],
TB [auth C],
TC [auth F],
TD [auth G],
TE [auth I],
TH [auth M],
TI [auth a],
TJ [auth a],
TL [auth D],
TM [auth b],
TN [auth b],
UA [auth B],
UC [auth F],
UD [auth G],
UE [auth I],
UH [auth M],
UI [auth a],
UJ [auth a],
UL [auth D],
UM [auth b],
UN [auth b],
VA [auth B],
VC [auth F],
VG [auth L],
VH [auth M],
VI [auth a],
VJ [auth a],
VL [auth D],
VM [auth b],
VN [auth b],
WA [auth B],
WC [auth F],
WE [auth I],
WG [auth L],
WH [auth M],
WI [auth a],
WJ [auth a],
WK [auth j],
WL [auth D],
WM [auth b],
XA [auth B],
XC [auth F],
XE [auth I],
XG [auth L],
XH [auth M],
XI [auth a],
XJ [auth a],
XL [auth D],
XM [auth b],
XN [auth b],
YA [auth B],
YD [auth H],
YE [auth I],
YG [auth L],
YH [auth M],
YI [auth a],
YJ [auth a],
YL [auth D],
YM [auth b],
YN [auth b],
ZC [auth F],
ZD [auth H],
ZE [auth I],
ZG [auth L],
ZI [auth a],
ZJ [auth a],
ZL [auth D],
ZM [auth b]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
SQD (Subject of Investigation/LOI)
Query on SQD

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UF [auth J]1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG (Subject of Investigation/LOI)
Query on LMG

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CB [auth C]
CF [auth I]
GI [auth M]
GK [auth a]
KA [auth A]
CB [auth C],
CF [auth I],
GI [auth M],
GK [auth a],
KA [auth A],
LC [auth E],
LH [auth L],
LL [auth D],
MA [auth A],
TF [auth J],
UB [auth C],
VK [auth j],
YK [auth l]
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 B]
BF [auth I]
FI [auth M]
HI [auth a]
II [auth a]
BB [auth B],
BF [auth I],
FI [auth M],
HI [auth a],
II [auth a],
JE [auth H],
KC [auth E],
KL [auth D],
KN [auth b],
MC [auth E],
NJ [auth a],
OG [auth K],
OJ [auth a],
RJ [auth a],
UK [auth j]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
A86 (Subject of Investigation/LOI)
Query on A86

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AG [auth K]
BG [auth K]
DB [auth C]
DF [auth J]
FB [auth C]
AG [auth K],
BG [auth K],
DB [auth C],
DF [auth J],
FB [auth C],
FD [auth G],
FL [auth m],
GB [auth C],
GF [auth J],
IL [auth r],
KE [auth I],
LA [auth A],
ME [auth I],
ML [auth D],
NA [auth B],
NC [auth F],
NH [auth M],
NL [auth D],
OA [auth B],
OH [auth M],
PL [auth D],
QA [auth B],
QC [auth F],
QG [auth L],
QH [auth M],
RA [auth B],
SF [auth J],
SG [auth L],
TG [auth L],
UG [auth L],
VB [auth E],
VD [auth H],
VF [auth K],
WF [auth K],
WN [auth b],
XD [auth H],
YF [auth K],
ZF [auth K]
(3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate
C42 H58 O6
SJWWTRQNNRNTPU-XJUZQKKNSA-N
KC1 (Subject of Investigation/LOI)
Query on KC1

Download Ideal Coordinates CCD File 
CG [auth K]
CH [auth L]
FE [auth H]
HA [auth A]
IF [auth J]
CG [auth K],
CH [auth L],
FE [auth H],
HA [auth A],
IF [auth J],
IH [auth L],
JB [auth C],
JG [auth K],
KH [auth L],
OB [auth C],
QD [auth G],
VE [auth I],
YC [auth F],
ZA [auth B],
ZH [auth M]
Chlorophyll c1
C35 H30 Mg N4 O5
DGNIJJSSARBJSH-QIEHNWLWSA-L
DD6 (Subject of Investigation/LOI)
Query on DD6

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AA [auth A]
AC [auth E]
BC [auth E]
EB [auth C]
ED [auth G]
AA [auth A],
AC [auth E],
BC [auth E],
EB [auth C],
ED [auth G],
EF [auth J],
FF [auth J],
GD [auth G],
HD [auth G],
HF [auth J],
ID [auth G],
LE [auth I],
MH [auth M],
NE [auth I],
OC [auth F],
OL [auth D],
PA [auth B],
PC [auth F],
PG [auth L],
PH [auth M],
RG [auth L],
RH [auth M],
WB [auth E],
WD [auth H],
XB [auth E],
XF [auth K],
Z [auth A]
(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
ET4 (Subject of Investigation/LOI)
Query on ET4

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EL [auth l](1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol
C40 H54 O2
HNYJHQMUSVNWPV-DRCJTWAYSA-N
BCR (Subject of Investigation/LOI)
Query on BCR

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BK [auth a]
CL [auth l]
FK [auth a]
GL [auth m]
HK [auth a]
BK [auth a],
CL [auth l],
FK [auth a],
GL [auth m],
HK [auth a],
HN [auth b],
IN [auth b],
JL [auth r],
LN [auth b],
OK [auth f],
ON [auth b],
PJ [auth a],
PK [auth f],
QJ [auth a],
RK [auth i],
SK [auth i],
TK [auth j],
XK [auth j],
YB [auth E],
ZB [auth E],
ZK [auth l]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN (Subject of Investigation/LOI)
Query on PQN

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GN [auth b],
LJ [auth a]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
AO [auth c],
CM [auth b],
ZN [auth c]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.78 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChina2020081

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-25
    Type: Initial release
  • Version 1.1: 2025-04-30
    Changes: Data collection, Database references