9MH1 | pdb_00009mh1

Dunaliella tertiolecta PSI-LHCI supercomplex

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.10 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]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]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]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
LHCA9E [auth 9]222Dunaliella tertiolectaMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1F [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: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2G [auth B]735Dunaliella tertiolectaMutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for K7NU68 (Dunaliella tertiolecta)
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UniProt GroupK7NU68
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerH [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: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II, chloroplasticI [auth D]193Dunaliella tertiolectaMutation(s): 0 
UniProt
Find proteins for A0A7S3VQN8 (Dunaliella tertiolecta)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVJ [auth E]111Dunaliella tertiolectaMutation(s): 0 
UniProt
Find proteins for A0A7S3VNZ8 (Dunaliella tertiolecta)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
PSAF1K [auth F]227Dunaliella tertiolectaMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
PSAG1L [auth G]141Dunaliella tertiolectaMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
PSAH1M [auth H]134Dunaliella tertiolectaMutation(s): 0 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIN [auth I]109Dunaliella tertiolectaMutation(s): 0 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXO [auth J]41Dunaliella tertiolectaMutation(s): 0 
UniProt
Find proteins for K7NVH8 (Dunaliella tertiolecta)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
PSI-KP [auth K]123Dunaliella tertiolectaMutation(s): 0 
UniProt
Find proteins for A0A6S8PC30 (Dunaliella tertiolecta)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
PSAL1Q [auth L]198Dunaliella tertiolectaMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
LHCA2R [auth 2]261Dunaliella tertiolectaMutation(s): 0 
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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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FC [auth 7],
VH [auth B]		DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL (Subject of Investigation/LOI)
Query on CHL
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IB [auth 3]
LD [auth 9]
MA [auth 3]
NC [auth 8]
NJ [auth 2]
IB [auth 3],
LD [auth 9],
MA [auth 3],
NC [auth 8],
NJ [auth 2],
OC [auth 8],
PC [auth 8],
QB [auth 7],
RB [auth 7],
RJ [auth 2],
S [auth 1],
SB [auth 7],
X [auth 1]
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]
AE [auth A]
AF [auth A]
AH [auth B]
BA [auth 1]
AA [auth 1],
AE [auth A],
AF [auth A],
AH [auth B],
BA [auth 1],
BE [auth A],
BF [auth A],
BH [auth B],
BJ [auth K],
CA [auth 1],
CE [auth A],
CF [auth A],
CH [auth B],
CI [auth F],
CJ [auth K],
DA [auth 1],
DE [auth A],
DF [auth A],
DG [auth B],
DH [auth B],
DJ [auth K],
EA [auth 1],
ED [auth 8],
EE [auth A],
EF [auth A],
EG [auth B],
EH [auth B],
EJ [auth K],
FA [auth 1],
FE [auth A],
FF [auth A],
FG [auth B],
FH [auth B],
FI [auth F],
GD [auth 9],
GE [auth A],
GF [auth A],
GG [auth B],
GH [auth B],
GI [auth F],
GJ [auth L],
HC [auth 7],
HD [auth 9],
HE [auth A],
HF [auth A],
HG [auth B],
HH [auth B],
HI [auth F],
HJ [auth L],
ID [auth 9],
IE [auth A],
IF [auth A],
IG [auth B],
IH [auth B],
JB [auth 3],
JD [auth 9],
JE [auth A],
JF [auth A],
JG [auth B],
JH [auth B],
JJ [auth L],
KB [auth 3],
KC [auth 8],
KD [auth 9],
KE [auth A],
KF [auth A],
KG [auth B],
KH [auth B],
KJ [auth L],
LC [auth 8],
LE [auth A],
LF [auth A],
LG [auth B],
LH [auth B],
LI [auth G],
MC [auth 8],
MD [auth 9],
ME [auth A],
MF [auth A],
MG [auth B],
MH [auth B],
MI [auth G],
MJ [auth 2],
NA [auth 3],
NB [auth 7],
ND [auth 9],
NE [auth A],
NF [auth A],
NG [auth B],
NH [auth B],
NI [auth G],
OA [auth 3],
OB [auth 7],
OD [auth 9],
OE [auth A],
OF [auth A],
OG [auth B],
OI [auth G],
OJ [auth 2],
PA [auth 3],
PB [auth 7],
PD [auth 9],
PE [auth A],
PG [auth B],
PJ [auth 2],
QA [auth 3],
QC [auth 8],
QD [auth 9],
QE [auth A],
QG [auth B],
QJ [auth 2],
RA [auth 3],
RC [auth 8],
RD [auth 9],
RE [auth A],
RG [auth B],
RI [auth H],
SA [auth 3],
SC [auth 8],
SE [auth A],
SG [auth B],
SJ [auth 2],
T [auth 1],
TA [auth 3],
TB [auth 7],
TC [auth 8],
TE [auth A],
TG [auth B],
TJ [auth 2],
U [auth 1],
UA [auth 3],
UB [auth 7],
UC [auth 8],
UE [auth A],
UG [auth B],
UJ [auth 2],
V [auth 1],
VA [auth 3],
VB [auth 7],
VC [auth 8],
VE [auth A],
VG [auth B],
VJ [auth 2],
W [auth 1],
WA [auth 3],
WB [auth 7],
WC [auth 8],
WE [auth A],
WG [auth B],
WJ [auth 2],
XA [auth 3],
XB [auth 7],
XE [auth A],
XG [auth B],
XI [auth J],
XJ [auth 2],
Y [auth 1],
YA [auth 3],
YB [auth 7],
YE [auth A],
YG [auth B],
YJ [auth 2],
Z [auth 1],
ZA [auth 3],
ZB [auth 7],
ZE [auth A],
ZG [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0 (Subject of Investigation/LOI)
Query on CL0
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ZD [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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FB [auth 3]
GC [auth 7]
HB [auth 3]
KA [auth 1]
KI [auth F]
FB [auth 3],
GC [auth 7],
HB [auth 3],
KA [auth 1],
KI [auth F],
XH [auth B]
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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IC [auth 7],
LB [auth 7],
QI [auth G],
WI [auth J],
XD [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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UI [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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AI [auth F]
BG [auth B]
BI [auth F]
GB [auth 3]
JI [auth F]
AI [auth F],
BG [auth B],
BI [auth F],
GB [auth 3],
JI [auth F],
MB [auth 7]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
LHG (Subject of Investigation/LOI)
Query on LHG
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AD [auth 8]
AG [auth B]
BK [auth 2]
CD [auth 8]
DC [auth 7]
AD [auth 8],
AG [auth B],
BK [auth 2],
CD [auth 8],
DC [auth 7],
DD [auth 8],
EC [auth 7],
JA [auth 1],
LA [auth 1],
TI [auth I],
WD [auth 9],
WF [auth A],
WH [auth B],
YD [auth A],
YF [auth A],
ZF [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
XAT
Query on XAT
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BB [auth 3]
BC [auth 7]
HA [auth 1]
TD [auth 9]
UD [auth 9]
BB [auth 3],
BC [auth 7],
HA [auth 1],
TD [auth 9],
UD [auth 9],
YC [auth 8]
(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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AB [auth 3]
AC [auth 7]
AK [auth 2]
GA [auth 1]
SD [auth 9]
AB [auth 3],
AC [auth 7],
AK [auth 2],
GA [auth 1],
SD [auth 9],
XC [auth 8],
ZJ [auth 2]
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
BCR (Subject of Investigation/LOI)
Query on BCR
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AJ [auth K]
CB [auth 3]
CC [auth 7]
CG [auth B]
DB [auth 3]
AJ [auth K],
CB [auth 3],
CC [auth 7],
CG [auth B],
DB [auth 3],
DI [auth F],
EB [auth 3],
FJ [auth K],
IA [auth 1],
II [auth F],
IJ [auth L],
LJ [auth L],
PH [auth B],
PI [auth G],
QH [auth B],
RF [auth A],
RH [auth B],
SF [auth A],
SH [auth B],
SI [auth I],
TF [auth A],
TH [auth B],
UF [auth A],
UH [auth B],
VF [auth A],
VI [auth J],
YI [auth J],
ZC [auth 8],
ZI [auth J]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU (Subject of Investigation/LOI)
Query on LMU
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BD [auth 8]
EI [auth F]
FD [auth 8]
JC [auth 7]
VD [auth 9]
BD [auth 8],
EI [auth F],
FD [auth 8],
JC [auth 7],
VD [auth 9],
XF [auth A]
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
PQN
Query on PQN
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OH [auth B],
PF [auth A]		PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4
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QF [auth A],
YH [auth C],
ZH [auth C]		IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.10 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