9MGZ | pdb_00009mgz

Dunaliella tertiolecta PSI-LHCI-TIDI1 supercomplex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


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],
N [auth a]		228Dunaliella tertiolectaMutation(s): 0 
UniProt
Find proteins for A0A7S3VHS4 (Dunaliella tertiolecta)
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UniProt GroupA0A7S3VHS4
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
LHCA3B [auth 3]286Dunaliella tertiolectaMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticC [auth 7],
P [auth c]		255Dunaliella tertiolectaMutation(s): 0 
UniProt
Find proteins for A0A7S3R4R1 (Dunaliella tertiolecta)
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UniProt GroupA0A7S3R4R1
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticD [auth 8],
O [auth b]		254Dunaliella tertiolectaMutation(s): 0 
UniProt
Find proteins for A0A7S3VSS7 (Dunaliella tertiolecta)
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UniProt GroupA0A7S3VSS7
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1E [auth A]751Dunaliella tertiolectaMutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for K7NU01 (Dunaliella tertiolecta)
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UniProt GroupK7NU01
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2F [auth B]735Dunaliella tertiolectaMutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for K7NU68 (Dunaliella tertiolecta)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerG [auth C]81Dunaliella tertiolectaMutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for K7NRF9 (Dunaliella tertiolecta)
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UniProt GroupK7NRF9
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II, chloroplasticH [auth D]193Dunaliella tertiolectaMutation(s): 0 
UniProt
Find proteins for A0A7S3VQN8 (Dunaliella tertiolecta)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVI [auth E]111Dunaliella tertiolectaMutation(s): 0 
UniProt
Find proteins for A0A7S3VNZ8 (Dunaliella tertiolecta)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
PSAF1J [auth F]227Dunaliella tertiolectaMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXK [auth J]41Dunaliella tertiolectaMutation(s): 0 
UniProt
Find proteins for K7NVH8 (Dunaliella tertiolecta)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
PSI-KL [auth K]123Dunaliella tertiolectaMutation(s): 0 
UniProt
Find proteins for A0A6S8PC30 (Dunaliella tertiolecta)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
TIDI1M [auth T]350Dunaliella tertiolectaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
PSAL1Q [auth L]198Dunaliella tertiolectaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIR [auth I]108Dunaliella tertiolectaMutation(s): 0 
UniProt
Find proteins for A0A7S3R9S7 (Dunaliella tertiolecta)
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Small Molecules
Ligands 15 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD
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CC [auth 8],
FB [auth 3],
VG [auth B]		DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL (Subject of Investigation/LOI)
Query on CHL
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GB [auth 3]
GJ [auth b]
HC [auth 8]
HJ [auth b]
IC [auth 8]
GB [auth 3],
GJ [auth b],
HC [auth 8],
HJ [auth b],
IC [auth 8],
II [auth T],
IJ [auth b],
JC [auth 8],
JI [auth a],
LA [auth 3],
NB [auth 7],
OB [auth 7],
OI [auth a],
PB [auth 7],
S [auth 1],
TH [auth T],
X [auth 1],
XJ [auth c],
YJ [auth c],
ZJ [auth c]
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]
AD [auth A]
AE [auth A]
AG [auth B]
AI [auth T]
AA [auth 1],
AD [auth A],
AE [auth A],
AG [auth B],
AI [auth T],
AK [auth c],
BA [auth 1],
BD [auth A],
BE [auth A],
BF [auth B],
BG [auth B],
BI [auth T],
BK [auth c],
CA [auth 1],
CD [auth A],
CE [auth A],
CF [auth B],
CG [auth B],
CH [auth F],
CI [auth T],
CJ [auth b],
CK [auth c],
DA [auth 1],
DC [auth 8],
DD [auth A],
DE [auth A],
DF [auth B],
DG [auth B],
DI [auth T],
DJ [auth b],
DK [auth c],
EA [auth 1],
EC [auth 8],
ED [auth A],
EE [auth A],
EF [auth B],
EG [auth B],
EH [auth F],
EI [auth T],
EJ [auth b],
EK [auth c],
FA [auth 1],
FC [auth 8],
FD [auth A],
FE [auth A],
FF [auth B],
FG [auth B],
FH [auth F],
FJ [auth b],
FK [auth c],
GC [auth 8],
GD [auth A],
GE [auth A],
GF [auth B],
GG [auth B],
GH [auth F],
GK [auth c],
HB [auth 3],
HD [auth A],
HE [auth A],
HF [auth B],
HG [auth B],
HH [auth F],
IB [auth 3],
ID [auth A],
IE [auth A],
IF [auth B],
IG [auth B],
JD [auth A],
JE [auth A],
JF [auth B],
JG [auth B],
JJ [auth b],
KB [auth 7],
KC [auth 8],
KD [auth A],
KE [auth A],
KF [auth B],
KG [auth B],
KI [auth a],
KJ [auth b],
LB [auth 7],
LC [auth 8],
LD [auth A],
LE [auth A],
LF [auth B],
LG [auth B],
LH [auth J],
LI [auth a],
LJ [auth b],
LK [auth L],
MA [auth 3],
MB [auth 7],
MC [auth 8],
MD [auth A],
ME [auth A],
MF [auth B],
MG [auth B],
MI [auth a],
MJ [auth b],
MK [auth L],
NA [auth 3],
NC [auth 8],
ND [auth A],
NE [auth A],
NF [auth B],
NG [auth B],
NI [auth a],
NJ [auth b],
OA [auth 3],
OC [auth 8],
OD [auth A],
OE [auth A],
OF [auth B],
OG [auth B],
OH [auth K],
OJ [auth b],
PA [auth 3],
PC [auth 8],
PD [auth A],
PF [auth B],
PH [auth K],
PI [auth a],
PJ [auth b],
QA [auth 3],
QB [auth 7],
QC [auth 8],
QD [auth A],
QF [auth B],
QH [auth K],
QI [auth a],
RA [auth 3],
RB [auth 7],
RD [auth A],
RF [auth B],
RH [auth K],
RI [auth a],
SA [auth 3],
SB [auth 7],
SD [auth A],
SF [auth B],
SI [auth a],
T [auth 1],
TA [auth 3],
TB [auth 7],
TD [auth A],
TF [auth B],
TI [auth a],
U [auth 1],
UA [auth 3],
UB [auth 7],
UD [auth A],
UF [auth B],
UH [auth T],
UI [auth a],
UJ [auth c],
V [auth 1],
VA [auth 3],
VB [auth 7],
VD [auth A],
VF [auth B],
VH [auth T],
VI [auth a],
VJ [auth c],
W [auth 1],
WA [auth 3],
WB [auth 7],
WD [auth A],
WF [auth B],
WH [auth T],
WI [auth a],
WJ [auth c],
XA [auth 3],
XD [auth A],
XF [auth B],
XH [auth T],
Y [auth 1],
YA [auth 3],
YD [auth A],
YF [auth B],
YH [auth T],
Z [auth 1],
ZD [auth A],
ZF [auth B],
ZH [auth T]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0 (Subject of Investigation/LOI)
Query on CL0
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ZC [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
SQD (Subject of Investigation/LOI)
Query on SQD
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EB [auth 3]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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JB [auth 7],
JH [auth F],
XC [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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KH [auth J]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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AH [auth F],
BH [auth F],
UC [auth 8],
VC [auth 8]		PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
LHG (Subject of Investigation/LOI)
Query on LHG
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AC [auth 7]
AJ [auth a]
BJ [auth a]
JA [auth 1]
KA [auth 1]
AC [auth 7],
AJ [auth a],
BJ [auth a],
JA [auth 1],
KA [auth 1],
KK [auth c],
TJ [auth b],
WC [auth 8],
XE [auth A],
YC [auth A],
ZE [auth A],
ZG [auth F]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
XAT
Query on XAT
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AB [auth 3]
GI [auth T]
HA [auth 1]
IK [auth c]
RJ [auth b]
AB [auth 3],
GI [auth T],
HA [auth 1],
IK [auth c],
RJ [auth b],
SC [auth 8],
YB [auth 7],
YI [auth a]
(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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FI [auth T]
GA [auth 1]
HK [auth c]
QJ [auth b]
RC [auth 8]
FI [auth T],
GA [auth 1],
HK [auth c],
QJ [auth b],
RC [auth 8],
XB [auth 7],
XI [auth a],
ZA [auth 3]
(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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AF [auth B]
BB [auth 3]
CB [auth 3]
DB [auth 3]
DH [auth F]
AF [auth B],
BB [auth 3],
CB [auth 3],
DB [auth 3],
DH [auth F],
HI [auth T],
IA [auth 1],
IH [auth F],
JK [auth c],
MH [auth J],
NH [auth J],
NK [auth L],
OK [auth L],
PK [auth I],
QG [auth B],
RE [auth A],
RG [auth B],
SE [auth A],
SG [auth B],
SH [auth K],
SJ [auth b],
TC [auth 8],
TE [auth A],
TG [auth B],
UE [auth A],
UG [auth B],
VE [auth A],
WE [auth A],
WG [auth B],
ZB [auth 7],
ZI [auth a]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU
Query on LMU
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BC [auth 7],
YE [auth A]		DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
PQN
Query on PQN
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PE [auth A],
PG [auth B]		PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4
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QE [auth A],
XG [auth C],
YG [auth C]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1
RECONSTRUCTIONRELION

Structure Validation

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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