9MH0 | pdb_00009mh0

Dunaliella salina PSI-LHCI supercomplex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 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 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]256Dunaliella salinaMutation(s): 0 
UniProt
Find proteins for A0A6I8WFT9 (Dunaliella salina)
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UniProt GroupA0A6I8WFT9
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
LHCA8E [auth 8]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]751Dunaliella 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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UniProt GroupD0FXZ0
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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
PSAI1O [auth I]109Dunaliella salinaMutation(s): 0 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXP [auth J]41Dunaliella salinaMutation(s): 0 
UniProt
Find proteins for D0FXW0 (Dunaliella salina)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
PSAK1Q [auth K]123Dunaliella salinaMutation(s): 0 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
PSAL1R [auth L]202Dunaliella salinaMutation(s): 0 
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Small Molecules
Ligands 18 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD (Subject of Investigation/LOI)
Query on DGD

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AJ [auth B],
DD [auth 7],
WK [auth L],
XE [auth A]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL (Subject of Investigation/LOI)
Query on CHL

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IE [auth 9]
KC [auth 7]
LB [auth 3]
LD [auth 8]
MD [auth 8]
IE [auth 9],
KC [auth 7],
LB [auth 3],
LD [auth 8],
MD [auth 8],
ND [auth 8],
OC [auth 7],
PA [auth 2],
PC [auth 7],
QC [auth 7],
S [auth 1],
UA [auth 2],
X [auth 1]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CL0 (Subject of Investigation/LOI)
Query on CL0

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

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AA [auth 1]
AB [auth 2]
AF [auth A]
AG [auth A]
AI [auth B]
AA [auth 1],
AB [auth 2],
AF [auth A],
AG [auth A],
AI [auth B],
BA [auth 1],
BB [auth 2],
BF [auth A],
BG [auth A],
BI [auth B],
CA [auth 1],
CF [auth A],
CG [auth A],
CI [auth B],
DA [auth 1],
DE [auth 9],
DF [auth A],
DG [auth A],
DI [auth B],
EA [auth 1],
EE [auth 9],
EF [auth A],
EG [auth A],
EI [auth B],
EK [auth J],
FA [auth 1],
FE [auth 9],
FF [auth A],
FG [auth A],
FH [auth B],
FI [auth B],
GD [auth 7],
GE [auth 9],
GF [auth A],
GG [auth A],
GH [auth B],
GI [auth B],
HE [auth 9],
HF [auth A],
HG [auth A],
HH [auth B],
HI [auth B],
HJ [auth F],
HK [auth K],
IF [auth A],
IG [auth A],
IH [auth B],
II [auth B],
IK [auth K],
JD [auth 8],
JE [auth 9],
JF [auth A],
JG [auth A],
JH [auth B],
JI [auth B],
JJ [auth F],
JK [auth K],
KB [auth 2],
KD [auth 8],
KE [auth 9],
KF [auth A],
KG [auth A],
KH [auth B],
KI [auth B],
KJ [auth F],
KK [auth K],
LC [auth 7],
LE [auth 9],
LF [auth A],
LG [auth A],
LH [auth B],
LI [auth B],
LJ [auth F],
MB [auth 3],
MC [auth 7],
ME [auth 9],
MF [auth A],
MG [auth A],
MH [auth B],
MI [auth B],
MJ [auth F],
MK [auth L],
NB [auth 3],
NC [auth 7],
NE [auth 9],
NF [auth A],
NG [auth A],
NH [auth B],
NI [auth B],
NK [auth L],
OB [auth 3],
OD [auth 8],
OE [auth 9],
OF [auth A],
OH [auth B],
OI [auth B],
PB [auth 3],
PD [auth 8],
PF [auth A],
PH [auth B],
PI [auth B],
PK [auth L],
QA [auth 2],
QB [auth 3],
QD [auth 8],
QF [auth A],
QH [auth B],
QI [auth B],
QK [auth L],
RA [auth 2],
RB [auth 3],
RC [auth 7],
RD [auth 8],
RF [auth A],
RH [auth B],
RI [auth B],
RJ [auth G],
RK [auth L],
SA [auth 2],
SB [auth 3],
SC [auth 7],
SD [auth 8],
SF [auth A],
SH [auth B],
SI [auth B],
SJ [auth G],
SK [auth L],
T [auth 1],
TA [auth 2],
TB [auth 3],
TC [auth 7],
TD [auth 8],
TF [auth A],
TH [auth B],
TI [auth B],
TJ [auth G],
U [auth 1],
UB [auth 3],
UC [auth 7],
UD [auth 8],
UF [auth A],
UH [auth B],
V [auth 1],
VA [auth 2],
VB [auth 3],
VC [auth 7],
VF [auth A],
VH [auth B],
W [auth 1],
WA [auth 2],
WB [auth 3],
WC [auth 7],
WF [auth A],
WH [auth B],
XA [auth 2],
XB [auth 3],
XC [auth 7],
XF [auth A],
XH [auth B],
Y [auth 1],
YA [auth 2],
YB [auth 3],
YF [auth A],
YH [auth B],
Z [auth 1],
ZA [auth 2],
ZE [auth A],
ZF [auth A],
ZH [auth B],
ZJ [auth H]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
4RF (Subject of Investigation/LOI)
Query on 4RF

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

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BJ [auth B],
FC [auth 3],
HB [auth 2],
HC [auth 3],
UE [auth 9]
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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BD [auth 7],
FJ [auth F],
ID [auth 8],
JC [auth 7],
WE [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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BE [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
Query on PTY

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DH [auth B]
ED [auth 7]
GC [auth 3]
NA [auth 1]
OA [auth 1]
DH [auth B],
ED [auth 7],
GC [auth 3],
NA [auth 1],
OA [auth 1],
OJ [auth F],
VK [auth L],
WJ [auth H],
XJ [auth H],
YD [auth 8],
ZD [auth 8]
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
LHG (Subject of Investigation/LOI)
Query on LHG

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AE [auth 8]
BK [auth I]
CD [auth 7]
CE [auth 8]
CJ [auth B]
AE [auth 8],
BK [auth I],
CD [auth 7],
CE [auth 8],
CJ [auth B],
EC [auth 3],
FD [auth 7],
GB [auth 2],
GJ [auth F],
GK [auth J],
HD [auth 7],
IC [auth 3],
JA [auth 1],
JB [auth 2],
KA [auth 1],
LA [auth 1],
MA [auth 1],
PJ [auth F],
TE [auth 9],
VE [auth 9],
VJ [auth G],
WG [auth A],
XG [auth A],
YJ [auth H]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
3PH (Subject of Investigation/LOI)
Query on 3PH

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

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AC [auth 3]
HA [auth 1]
QE [auth 9]
RE [auth 9]
WD [auth 8]
AC [auth 3],
HA [auth 1],
QE [auth 9],
RE [auth 9],
WD [auth 8],
ZC [auth 7]
(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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CB [auth 2]
DB [auth 2]
EB [auth 2]
FB [auth 2]
GA [auth 1]
CB [auth 2],
DB [auth 2],
EB [auth 2],
FB [auth 2],
GA [auth 1],
PE [auth 9],
VD [auth 8],
YC [auth 7],
ZB [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 (Subject of Investigation/LOI)
Query on BCR

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AD [auth 7]
AK [auth H]
BC [auth 3]
BH [auth A]
CC [auth 3]
AD [auth 7],
AK [auth H],
BC [auth 3],
BH [auth A],
CC [auth 3],
CK [auth I],
DC [auth 3],
DK [auth J],
EH [auth B],
FK [auth J],
IA [auth 1],
IJ [auth F],
LK [auth K],
NJ [auth F],
OK [auth L],
QG [auth A],
QJ [auth G],
RG [auth A],
SG [auth A],
TG [auth A],
TK [auth L],
UG [auth A],
UJ [auth G],
UK [auth L],
VG [auth A],
VI [auth B],
WI [auth B],
XD [auth 8],
XI [auth B],
YI [auth B],
ZI [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMU
Query on LMU

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AH [auth A],
SE [auth 9],
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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DJ [auth C],
EJ [auth C],
PG [auth A]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
OCD (Subject of Investigation/LOI)
Query on OCD

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YG [auth A]octadecanal
C18 H36 O
FWWQKRXKHIRPJY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21.1
RECONSTRUCTIONRELION

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