6SL5

Dunaliella Photosystem I Supercomplex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


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 : 148253-148253

  • DOI: 10.1016/j.bbabio.2020.148253
  • Structures With Same Primary Citation

  • 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 o ...

    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. Electronic address: nelson@tauex.tau.ac.il.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photosystem I P700 chlorophyll a apoprotein A1
A
740Dunaliella salinaMutation(s): 0 
Gene Names: psaA
EC: 1.97.1.12
Find proteins for D0FXV2 (Dunaliella salina)
Go to UniProtKB:  D0FXV2
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Photosystem I P700 chlorophyll a apoprotein A2
B
733Dunaliella salinaMutation(s): 0 
Gene Names: psaB
EC: 1.97.1.12
Find proteins for D0FXZ0 (Dunaliella salina)
Go to UniProtKB:  D0FXZ0
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Photosystem I iron-sulfur center
C
80Dunaliella salinaMutation(s): 0 
Gene Names: psaC
EC: 1.97.1.12
Find proteins for D0FXW7 (Dunaliella salina)
Go to UniProtKB:  D0FXW7
Protein Feature View
  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
PsaD
D
144Dunaliella salinaMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
PsaE
E
64Dunaliella salinaMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
PsaF
F
162Dunaliella salinaMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
Photosystem I reaction center subunit IX
J
41Dunaliella salinaMutation(s): 0 
Gene Names: psaJ
Find proteins for D0FXW0 (Dunaliella salina)
Go to UniProtKB:  D0FXW0
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
PsaI
I
39Dunaliella salinaMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
PsaK
K
84Dunaliella salinaMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
PsaO
O
86Dunaliella salinaMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
Chlorophyll a-b binding protein, chloroplastic
1
197Dunaliella salinaMutation(s): 0 
Gene Names: Lhca2
Find proteins for C1K003 (Dunaliella salina)
Go to UniProtKB:  C1K003
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Chlorophyll a-b binding protein, chloroplastic
3
228Dunaliella salinaMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
Lhca4
4
211Dunaliella salinaMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Lhca5
5
202Dunaliella salinaMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Lhca6
6
178Dunaliella salinaMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
PsaL
L
155Dunaliella salinaMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Lhca2
2
208Dunaliella salinaMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
PsaG
G
101Dunaliella salinaMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
PsaH
H
92Dunaliella salinaMutation(s): 0 
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Small Molecules
Ligands 20 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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2, 3, B
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
 Ligand Interaction
CHL
Query on CHL

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1, 2, 3, 4, 5, 6
CHLOROPHYLL B
C55 H70 Mg N4 O6
MWVCRINOIIOUAU-UYSPMESUSA-M
 Ligand Interaction
CL0
Query on CL0

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A
CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
 Ligand Interaction
CLA
Query on CLA

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1, 2, 3, 4, 5, 6, A, B, F, G, H, J, K, L, O
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
4RF
Query on 4RF

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5, L
Tripalmitoylglycerol
C51 H98 O6
PVNIQBQSYATKKL-UHFFFAOYSA-N
 Ligand Interaction
SQD
Query on SQD

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2, 3, 6
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
 Ligand Interaction
LMG
Query on LMG

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1, 2, 3, 4, 6, F
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
LMK
Query on LMK

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2, 4
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
 Ligand Interaction
PTY
Query on PTY

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1, 3, 4, 5, 6, L, O
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
 Ligand Interaction
LHG
Query on LHG

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1, 2, 3, 4, 5, 6, A, B, F
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
P3H
Query on P3H

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2, 5
[(2~{R})-1-nonanoyloxy-3-[oxidanyl-[(2~{R},3~{S},5~{R},6~{R})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl]oxy-phosphoryl]oxy-propan-2-yl] (5~{Z},8~{Z})-heptadeca-5,8-dienoate
C35 H63 O13 P
YESDZPSNSSEMJX-BCWHKXFCSA-N
 Ligand Interaction
3PH
Query on 3PH

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5, B, F
1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE
C39 H77 O8 P
YFWHNAWEOZTIPI-DIPNUNPCSA-N
 Ligand Interaction
XAT
Query on XAT

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1, 2, 3, 4, 6
(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
 Ligand Interaction
LUT
Query on LUT

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1, 2, 3, 4, 5, 6
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
C40 H56 O2
KBPHJBAIARWVSC-NSIPBSJQSA-N
 Ligand Interaction
BCR
Query on BCR

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1, 2, 3, 4, A, B, F, G, H, I, J, K, L, O
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
LMU
Query on LMU

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6, A, B
DODECYL-ALPHA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-YHBSTRCHSA-N
 Ligand Interaction
PQN
Query on PQN

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A, B
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
 Ligand Interaction
SF4
Query on SF4

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A, C
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
OCD
Query on OCD

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A
octadecanal
C18 H36 O
FWWQKRXKHIRPJY-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.84 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 

  • Version 1.0: 2020-06-24
    Type: Initial release
  • Version 1.1: 2020-07-01
    Changes: Database references