9MGW | pdb_00009mgw

Dunaliella salina PSI-LHCI-TIDI1 supercomplex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 1.0 of the entry. See complete history


Literature

A distinct LHCI arrangement is recruited to photosystem I in Fe-starved green algae.

Liu, H.W.Khera, R.Grob, P.Gallaher, S.D.Purvine, S.O.Nicora, C.D.Lipton, M.S.Niyogi, K.K.Nogales, E.Iwai, M.Merchant, S.S.

(2025) Proc Natl Acad Sci U S A 122: e2500621122-e2500621122

  • DOI: https://doi.org/10.1073/pnas.2500621122
  • Primary Citation of Related Structures:  
    9MGW, 9MGZ, 9MH0, 9MH1

  • PubMed Abstract: 

    Iron (Fe) availability limits photosynthesis at a global scale where Fe-rich photosystem (PS) I abundance is drastically reduced in Fe-poor environments. We used single-particle cryoelectron microscopy to reveal a unique Fe starvation-dependent arrangement of light-harvesting chlorophyll (LHC) proteins where Fe starvation-induced TIDI1 is found in an additional tetramer of LHC proteins associated with PSI in Dunaliella tertiolecta and Dunaliella salina . These cosmopolitan green algae are resilient to poor Fe nutrition. TIDI1 is a distinct LHC protein that co-occurs in diverse algae with flavodoxin (an Fe-independent replacement for the Fe-containing ferredoxin). The antenna expansion in eukaryotic algae we describe here is reminiscent of the iron-starvation induced ( isiA- encoding) antenna ring in cyanobacteria, which typically co-occurs with isiB , encoding flavodoxin. Our work showcases the convergent strategies that evolved after the Great Oxidation Event to maintain PSI capacity.


  • Organizational Affiliation
    • Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticA [auth 1],
R [auth a]
228Dunaliella salinaMutation(s): 0 
UniProt
Find proteins for C1K003 (Dunaliella salina)
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
LHCA2B [auth 2]263Dunaliella salinaMutation(s): 0 
UniProt
Find proteins for Q2TLM8 (Dunaliella salina)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
LHCA3C [auth 3]320Dunaliella salinaMutation(s): 0 
UniProt
Find proteins for C1K004 (Dunaliella salina)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
LHCA7D [auth 7],
T [auth c]
256Dunaliella salinaMutation(s): 0 
UniProt
Find proteins for A0A6I8WFT9 (Dunaliella salina)
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
LHCA8E [auth 8],
S [auth b]
254Dunaliella salinaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
LHCA9F [auth 9]222Dunaliella salinaMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1G [auth A]750Dunaliella salinaMutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for D0FXV2 (Dunaliella salina)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2H [auth B]735Dunaliella salinaMutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for D0FXZ0 (Dunaliella salina)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerI [auth C]81Dunaliella salinaMutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for D0FXW7 (Dunaliella salina)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
PSAD1J [auth D]202Dunaliella salinaMutation(s): 0 
UniProt
Find proteins for A0A6I8WFU1 (Dunaliella salina)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
PSAE1K [auth E]125Dunaliella salinaMutation(s): 0 
UniProt
Find proteins for A0A6I8WFU2 (Dunaliella salina)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
PSAF1L [auth F]232Dunaliella salinaMutation(s): 0 
UniProt
Find proteins for A0A6I8WFT8 (Dunaliella salina)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
PSAG1M [auth G]141Dunaliella salinaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
PSAH1N [auth H]135Dunaliella salinaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXO [auth J]41Dunaliella salinaMutation(s): 0 
UniProt
Find proteins for D0FXW0 (Dunaliella salina)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
PSAL1P [auth L]202Dunaliella salinaMutation(s): 0 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
PSAO1Q [auth O]129Dunaliella salinaMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
PSAI1U [auth I]109Dunaliella salinaMutation(s): 0 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
PSAK1V [auth K]123Dunaliella salinaMutation(s): 0 
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
TIDI1W [auth T]365Dunaliella salinaMutation(s): 0 
UniProt
Find proteins for Q56D18 (Dunaliella salina)
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Small Molecules
Ligands 17 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

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LD [auth 8],
MC [auth 7],
YE [auth A],
ZI [auth B]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL (Subject of Investigation/LOI)
Query on CHL

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BA [auth 1]
EN [auth T]
FN [auth T]
GM [auth c]
HM [auth c]
BA [auth 1],
EN [auth T],
FN [auth T],
GM [auth c],
HM [auth c],
IM [auth c],
KD [auth 8],
KL [auth b],
LE [auth 9],
OB [auth 3],
OC [auth 7],
PD [auth 8],
PL [auth b],
QD [auth 8],
QL [auth b],
RD [auth 8],
RL [auth b],
SC [auth 7],
TC [auth 7],
UA [auth 2],
UC [auth 7],
VK [auth a],
ZA [auth 2]
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 3]
AD [auth 7]
AF [auth A]
AA [auth 1],
AB [auth 2],
AC [auth 3],
AD [auth 7],
AF [auth A],
AG [auth A],
AH [auth A],
AI [auth B],
AL [auth a],
AN [auth K],
BB [auth 2],
BC [auth 3],
BD [auth 7],
BF [auth A],
BG [auth A],
BI [auth B],
BL [auth a],
BN [auth K],
CA [auth 1],
CB [auth 2],
CF [auth A],
CG [auth A],
CI [auth B],
CK [auth L],
CL [auth a],
CM [auth c],
CN [auth K],
DA [auth 1],
DB [auth 2],
DF [auth A],
DG [auth A],
DI [auth B],
DL [auth a],
DM [auth c],
EA [auth 1],
EB [auth 2],
EF [auth A],
EG [auth A],
EI [auth B],
EK [auth L],
EM [auth c],
FA [auth 1],
FB [auth 2],
FE [auth 8],
FF [auth A],
FG [auth A],
FH [auth B],
FI [auth B],
FK [auth L],
FM [auth c],
GA [auth 1],
GB [auth 2],
GE [auth 9],
GF [auth A],
GG [auth A],
GI [auth B],
GK [auth L],
GN [auth T],
HA [auth 1],
HE [auth 9],
HF [auth A],
HG [auth A],
HH [auth B],
HI [auth B],
HK [auth L],
HN [auth T],
IA [auth 1],
ID [auth 7],
IE [auth 9],
IF [auth A],
IG [auth A],
IH [auth B],
II [auth B],
IJ [auth F],
IN [auth T],
JA [auth 1],
JE [auth 9],
JF [auth A],
JG [auth A],
JH [auth B],
JI [auth B],
JJ [auth F],
JM [auth c],
JN [auth T],
KE [auth 9],
KF [auth A],
KG [auth A],
KH [auth B],
KI [auth B],
KJ [auth F],
KM [auth c],
KN [auth T],
LF [auth A],
LG [auth A],
LH [auth B],
LI [auth B],
LK [auth O],
LM [auth c],
LN [auth T],
MD [auth 8],
ME [auth 9],
MF [auth A],
MG [auth A],
MH [auth B],
MI [auth B],
MK [auth O],
ML [auth b],
MM [auth c],
MN [auth T],
ND [auth 8],
NE [auth 9],
NF [auth A],
NG [auth A],
NH [auth B],
NI [auth B],
NJ [auth G],
NK [auth O],
NL [auth b],
NM [auth c],
NN [auth T],
OD [auth 8],
OE [auth 9],
OF [auth A],
OH [auth B],
OI [auth B],
OL [auth b],
OM [auth c],
ON [auth T],
PB [auth 3],
PC [auth 7],
PE [auth 9],
PF [auth A],
PH [auth B],
PI [auth B],
PJ [auth G],
PM [auth c],
PN [auth T],
QB [auth 3],
QC [auth 7],
QE [auth 9],
QF [auth A],
QH [auth B],
QI [auth B],
QJ [auth G],
QN [auth T],
RA [auth 1],
RB [auth 3],
RC [auth 7],
RE [auth 9],
RF [auth A],
RH [auth B],
RI [auth B],
RJ [auth G],
RK [auth a],
RN [auth T],
SB [auth 3],
SD [auth 8],
SF [auth A],
SH [auth B],
SI [auth B],
SK [auth a],
SL [auth b],
TB [auth 3],
TD [auth 8],
TF [auth A],
TH [auth B],
TI [auth B],
TK [auth a],
TL [auth b],
UB [auth 3],
UD [auth 8],
UF [auth A],
UH [auth B],
UK [auth a],
UL [auth b],
VA [auth 2],
VB [auth 3],
VC [auth 7],
VD [auth 8],
VF [auth A],
VH [auth B],
VL [auth b],
WA [auth 2],
WB [auth 3],
WC [auth 7],
WD [auth 8],
WF [auth A],
WH [auth B],
WJ [auth H],
WK [auth a],
WL [auth b],
X [auth 1],
XA [auth 2],
XB [auth 3],
XC [auth 7],
XD [auth 8],
XF [auth A],
XH [auth B],
XJ [auth H],
XK [auth a],
XL [auth b],
Y [auth 1],
YA [auth 2],
YB [auth 3],
YC [auth 7],
YD [auth 8],
YF [auth A],
YH [auth B],
YK [auth a],
YL [auth b],
Z [auth 1],
ZB [auth 3],
ZC [auth 7],
ZF [auth A],
ZH [auth B],
ZJ [auth J],
ZK [auth a],
ZM [auth K]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0 (Subject of Investigation/LOI)
Query on CL0

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ZE [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
4RF (Subject of Investigation/LOI)
Query on 4RF

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BH [auth A]Tripalmitoylglycerol
C51 H98 O6
PVNIQBQSYATKKL-UHFFFAOYSA-N
SQD (Subject of Investigation/LOI)
Query on SQD

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JC [auth 3],
LB [auth 2]
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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FD [auth 7]
IC [auth 3]
MJ [auth F]
NA [auth 1]
TJ [auth G]
FD [auth 7],
IC [auth 3],
MJ [auth F],
NA [auth 1],
TJ [auth G],
XE [auth A]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LMK (Subject of Investigation/LOI)
Query on LMK

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EE [auth 8]trimethyl-[(2~{R})-1-oxidanyl-1-oxidanylidene-4-[(2~{S})-2-[(1~{S})-1-oxidanyloctadecoxy]-3-[(1~{R})-1-oxidanyloctadecoxy]propoxy]butan-2-yl]azanium
C46 H94 N O7
BUXLRCGOLVGJEI-LHQLQFMZSA-O
PTY (Subject of Investigation/LOI)
Query on PTY

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AJ [auth B]
CE [auth 8]
EH [auth B]
HD [auth 7]
IL [auth a]
AJ [auth B],
CE [auth 8],
EH [auth B],
HD [auth 7],
IL [auth a],
JK [auth L],
KC [auth 3],
NB [auth 2],
NC [auth 7],
QA [auth 1],
UJ [auth H],
UM [auth c],
VM [auth c],
WM [auth I],
YJ [auth J]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
LHG (Subject of Investigation/LOI)
Query on LHG

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DE [auth 8]
DH [auth B]
EJ [auth F]
GD [auth 7]
GJ [auth F]
DE [auth 8],
DH [auth B],
EJ [auth F],
GD [auth 7],
GJ [auth F],
HC [auth 3],
HL [auth a],
JD [auth 7],
JL [auth b],
KB [auth 2],
LC [auth 3],
LL [auth b],
PA [auth 1],
QK [auth a],
SA [auth 1],
TA [auth 1],
TM [auth c],
VJ [auth H],
WE [auth 9],
WG [auth A],
XG [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
3PH (Subject of Investigation/LOI)
Query on 3PH

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FJ [auth F],
MB [auth 2]
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
XAT
Query on XAT

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AE [auth 8]
AM [auth b]
DC [auth 3]
DD [auth 7]
FL [auth a]
AE [auth 8],
AM [auth b],
DC [auth 3],
DD [auth 7],
FL [auth a],
LA [auth 1],
RM [auth c],
TE [auth 9],
TN [auth T],
UE [auth 9]
(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 (Subject of Investigation/LOI)
Query on LUT

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CC [auth 3]
CD [auth 7]
CH [auth B]
EL [auth a]
HB [auth 2]
CC [auth 3],
CD [auth 7],
CH [auth B],
EL [auth a],
HB [auth 2],
IB [auth 2],
JB [auth 2],
KA [auth 1],
PK [auth O],
QM [auth c],
SE [auth 9],
SN [auth T],
ZD [auth 8],
ZL [auth b]
(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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AK [auth J]
BE [auth 8]
BJ [auth B]
BK [auth J]
BM [auth b]
AK [auth J],
BE [auth 8],
BJ [auth B],
BK [auth J],
BM [auth b],
DK [auth L],
DN [auth K],
EC [auth 3],
ED [auth 7],
FC [auth 3],
GC [auth 3],
GH [auth B],
GL [auth a],
HJ [auth F],
IK [auth L],
KK [auth L],
LJ [auth F],
MA [auth 1],
OJ [auth G],
OK [auth O],
QG [auth A],
RG [auth A],
SG [auth A],
SJ [auth G],
SM [auth c],
TG [auth A],
UG [auth A],
UN [auth T],
VG [auth A],
VI [auth B],
WI [auth B],
XI [auth B],
XM [auth I],
YI [auth B],
YM [auth I]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU
Query on LMU

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OA [auth 1],
VE [auth 9],
YG [auth A],
ZG [auth A]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
PQN
Query on PQN

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

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CJ [auth C],
DJ [auth C],
PG [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION
MODEL REFINEMENTPHENIX1.21.1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-SC0020627

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-25
    Type: Initial release