6RHZ

Structure of a minimal photosystem I from a green alga


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.2 of the entry. See complete history


Literature

Structure of a minimal photosystem I from the green alga Dunaliella salina.

Perez-Boerema, A.Klaiman, D.Caspy, I.Netzer-El, S.Y.Amunts, A.Nelson, N.

(2020) Nat Plants 6: 321-327

  • DOI: https://doi.org/10.1038/s41477-020-0611-9
  • Primary Citation of Related Structures:  
    6QPH, 6RHZ

  • PubMed Abstract: 

    Solar energy harnessed by oxygenic photosynthesis supports most of the life forms on Earth. In eukaryotes, photosynthesis occurs in chloroplasts and is achieved by membrane-embedded macromolecular complexes that contain core and peripheral antennae with multiple pigments. The structure of photosystem I (PSI) comprises the core and light-harvesting (LHCI) complexes, which together form PSI-LHCI. Here we determined the structure of PSI-LHCI from the salt-tolerant green alga Dunaliella salina using X-ray crystallography and electron cryo-microscopy. Our results reveal a previously undescribed configuration of the PSI core. It is composed of only 7 subunits, compared with 14-16 subunits in plants and the alga Chlamydomonas reinhardtii, and forms the smallest known PSI. The LHCI is poorly conserved at the sequence level and binds to pigments that form new energy pathways, and the interactions between the individual Lhca1-4 proteins are weakened. Overall, the data indicate the PSI of D. salina represents a different type of the molecular organization that provides important information for reconstructing the plasticity and evolution of PSI.


  • Organizational Affiliation

    Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Solna, Sweden.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticA [auth 1]197Dunaliella salinaMutation(s): 0 
UniProt
Find proteins for C1K003 (Dunaliella salina)
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UniProt GroupC1K003
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, Lhca2B [auth 2]208Dunaliella salinaMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, chloroplasticC [auth 3]210Dunaliella salinaMutation(s): 0 
UniProt
Find proteins for C1K004 (Dunaliella salina)
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Chlorophyll a-b binding protein, Lhca4D [auth 4]211Dunaliella salinaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1E [auth A]739Dunaliella salinaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for D0FXV2 (Dunaliella salina)
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2F [auth B]730Dunaliella salinaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for D0FXZ0 (Dunaliella salina)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerG [auth C]80Dunaliella salinaMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for D0FXW7 (Dunaliella salina)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit II, PsaDH [auth D]141Dunaliella salinaMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IV, PsaEI [auth E]64Dunaliella salinaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit III, PsaFJ [auth F]163Dunaliella salinaMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXK [auth J]40Dunaliella salinaMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for D0FXW0 (Dunaliella salina)
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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LG [auth B]DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CHL
Query on CHL

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EC [auth 4]
FB [auth 3]
FC [auth 4]
HC [auth 4]
OA [auth 2]
EC [auth 4],
FB [auth 3],
FC [auth 4],
HC [auth 4],
OA [auth 2],
PA [auth 2],
QA [auth 2],
SA [auth 2],
W [auth 1],
X [auth 1]
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
CL0
Query on CL0

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KC [auth A]CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
CLA
Query on CLA

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AA [auth 1]
AC [auth 4]
AD [auth A]
AE [auth A]
AF [auth B]
AA [auth 1],
AC [auth 4],
AD [auth A],
AE [auth A],
AF [auth B],
AG [auth B],
BA [auth 1],
BC [auth 4],
BD [auth A],
BE [auth A],
BF [auth B],
BG [auth B],
CC [auth 4],
CD [auth A],
CF [auth B],
CG [auth B],
DB [auth 3],
DC [auth 4],
DD [auth A],
DF [auth B],
EB [auth 3],
ED [auth A],
EF [auth B],
FD [auth A],
FF [auth B],
GA [auth 2],
GB [auth 3],
GC [auth 4],
GD [auth A],
GF [auth B],
HA [auth 2],
HB [auth 3],
HD [auth A],
HF [auth B],
IA [auth 2],
IB [auth 3],
IC [auth 4],
ID [auth A],
IF [auth B],
JA [auth 2],
JB [auth 3],
JD [auth A],
JF [auth B],
KA [auth 2],
KB [auth 3],
KD [auth A],
KF [auth B],
LA [auth 2],
LB [auth 3],
LC [auth A],
LD [auth A],
LF [auth B],
MA [auth 2],
MB [auth 3],
MC [auth A],
MD [auth A],
MF [auth B],
NA [auth 2],
NB [auth 3],
NC [auth A],
ND [auth A],
NE [auth B],
NF [auth B],
O [auth 1],
OB [auth 3],
OC [auth A],
OD [auth A],
OE [auth B],
OF [auth B],
P [auth 1],
PB [auth 3],
PC [auth A],
PD [auth A],
PE [auth B],
PF [auth B],
PG [auth F],
Q [auth 1],
QB [auth 3],
QC [auth A],
QD [auth A],
QE [auth B],
QF [auth B],
QG [auth F],
R [auth 1],
RA [auth 2],
RC [auth A],
RD [auth A],
RE [auth B],
RF [auth B],
S [auth 1],
SC [auth A],
SD [auth A],
SE [auth B],
SF [auth B],
T [auth 1],
TA [auth 2],
TC [auth A],
TD [auth A],
TE [auth B],
TF [auth B],
TG [auth J],
U [auth 1],
UC [auth A],
UD [auth A],
UE [auth B],
UF [auth B],
V [auth 1],
VB [auth 4],
VC [auth A],
VD [auth A],
VE [auth B],
VF [auth B],
WB [auth 4],
WC [auth A],
WD [auth A],
WE [auth B],
WF [auth B],
XB [auth 4],
XC [auth A],
XD [auth A],
XE [auth B],
XF [auth B],
Y [auth 1],
YB [auth 4],
YC [auth A],
YD [auth A],
YE [auth B],
YF [auth B],
Z [auth 1],
ZB [auth 4],
ZC [auth A],
ZD [auth A],
ZE [auth B],
ZF [auth B]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG
Query on LMG

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JC [auth 4],
MG [auth B],
VA [auth 2],
WA [auth 2],
XA [auth 2]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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CA [auth 1]
KG [auth B]
LE [auth A]
ME [auth A]
RB [auth 3]
CA [auth 1],
KG [auth B],
LE [auth A],
ME [auth A],
RB [auth 3],
UA [auth 2]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
XAT
Query on XAT

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EA [auth 2],
M [auth 1],
TB [auth 4],
ZA [auth 3]
(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
Query on LUT

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DA [auth 2],
L [auth 1],
SB [auth 4],
YA [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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AB [auth 3]
BB [auth 3]
CB [auth 3]
EE [auth A]
EG [auth B]
AB [auth 3],
BB [auth 3],
CB [auth 3],
EE [auth A],
EG [auth B],
FA [auth 2],
FE [auth A],
FG [auth B],
GE [auth A],
GG [auth B],
HE [auth A],
HG [auth B],
IE [auth A],
IG [auth B],
JE [auth A],
JG [auth B],
KE [auth A],
N [auth 1],
RG [auth F],
SG [auth F],
UB [auth 4],
UG [auth J],
VG [auth J]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN
Query on PQN

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

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DE [auth A],
NG [auth C],
OG [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
RECONSTRUCTIONRELION2.1
MODEL REFINEMENTPHENIX1.14-3260

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael569/17
Swedish Research CouncilSwedenNT_2015-04107
European Research CouncilSwedenERC-2018-StG-805230

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2020-03-18
    Changes: Database references
  • Version 1.2: 2020-03-25
    Changes: Database references