6YXR

Dunaliella Minimal Photosystem I


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Structure and energy transfer pathways of the Dunaliella Salina photosystem I supercomplex.

Caspy, I.Malavath, T.Klaiman, D.Fadeeva, M.Shkolnisky, Y.Nelson, N.

(2020) Biochim Biophys Acta Bioenerg 1861: 148253-148253

  • DOI: https://doi.org/10.1016/j.bbabio.2020.148253
  • Primary Citation of Related Structures:  
    6SL5, 6YXR

  • PubMed Abstract: 

    Oxygenic photosynthesis evolved more than 3 billion years ago in cyanobacteria. The increased complexity of photosystem I (PSI) became apparent from the high-resolution structures that were obtained for the complexes that were isolated from various organisms, ranging from cyanobacteria to plants. These complexes are all evolutionarily linked. In this paper, the researchers have uncovered the increased complexity of PSI in a single organism demonstrated by the coexistance of two distinct PSI compositions. The Large Dunaliella PSI contains eight additional subunits, six in PSI core and two light harvesting complexes. Two additional chlorophyll a molecules pertinent for efficient excitation energy transfer in state II transition were identified in PsaL and PsaO. Short distances between these newly identified chlorophylls correspond with fast excitation transfer rates previously reported during state II transition. The apparent PSI conformations could be a coping mechanism for the high salinity.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel.


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
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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UniProt GroupC1K004
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
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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UniProt GroupD0FXV2
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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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UniProt GroupD0FXZ0
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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
PsaDH [auth D]141Dunaliella salinaMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
PsaEI [auth E]64Dunaliella salinaMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
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 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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

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FB [auth 3]
FC [auth 4]
GC [auth 4]
IC [auth 4]
OA [auth 2]
FB [auth 3],
FC [auth 4],
GC [auth 4],
IC [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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LC [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],
CE [auth A],
CF [auth B],
CG [auth B],
DB [auth 3],
DC [auth 4],
DD [auth A],
DF [auth B],
DG [auth B],
EB [auth 3],
EC [auth 4],
ED [auth A],
EF [auth B],
FD [auth A],
FF [auth B],
GA [auth 2],
GB [auth 3],
GD [auth A],
GF [auth B],
HA [auth 2],
HB [auth 3],
HC [auth 4],
HD [auth A],
HF [auth B],
IA [auth 2],
IB [auth 3],
ID [auth A],
IF [auth B],
JA [auth 2],
JB [auth 3],
JC [auth 4],
JD [auth A],
JF [auth B],
KA [auth 2],
KB [auth 3],
KD [auth A],
KF [auth B],
LA [auth 2],
LB [auth 3],
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],
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],
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],
RG [auth F],
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],
U [auth 1],
UC [auth A],
UD [auth A],
UE [auth B],
UF [auth B],
UG [auth J],
V [auth 1],
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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KC [auth 4],
NG [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]
LG [auth B]
ME [auth A]
NE [auth A]
RB [auth 3]
CA [auth 1],
LG [auth B],
ME [auth A],
NE [auth A],
RB [auth 3],
UA [auth 2]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
3PH
Query on 3PH

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

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EA [auth 2],
M [auth 1],
UB [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],
TB [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]
FA [auth 2]
FE [auth A]
AB [auth 3],
BB [auth 3],
CB [auth 3],
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],
KG [auth B],
LE [auth A],
N [auth 1],
SG [auth F],
TG [auth F],
VB [auth 4],
VG [auth J],
WG [auth J]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN
Query on PQN

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

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONRELION3.0.7

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Israel Science FoundationIsrael569/17
European Research Council (ERC)Belgium723991

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2020-07-15
    Changes: Database references