6K33

Structure of PSI-isiA supercomplex from Thermosynechococcus vulcanus


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.74 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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This is version 2.0 of the entry. See complete history


Literature

Structure of a cyanobacterial photosystem I surrounded by octadecameric IsiA antenna proteins.

Akita, F.Nagao, R.Kato, K.Nakajima, Y.Yokono, M.Ueno, Y.Suzuki, T.Dohmae, N.Shen, J.R.Akimoto, S.Miyazaki, N.

(2020) Commun Biol 3: 232-232

  • DOI: https://doi.org/10.1038/s42003-020-0949-6
  • Primary Citation of Related Structures:  
    6K33

  • PubMed Abstract: 

    Iron-stress induced protein A (IsiA) is a chlorophyll-binding membrane-spanning protein in photosynthetic prokaryote cyanobacteria, and is associated with photosystem I (PSI) trimer cores, but its structural and functional significance in light harvesting remains unclear. Here we report a 2.7-Å resolution cryo-electron microscopic structure of a supercomplex between PSI core trimer and IsiA from a thermophilic cyanobacterium Thermosynechococcus vulcanus. The structure showed that 18 IsiA subunits form a closed ring surrounding a PSI trimer core. Detailed arrangement of pigments within the supercomplex, as well as molecular interactions between PSI and IsiA and among IsiAs, were resolved. Time-resolved fluorescence spectra of the PSI-IsiA supercomplex showed clear excitation-energy transfer from IsiA to PSI, strongly indicating that IsiA functions as an energy donor, but not an energy quencher, in the supercomplex. These structural and spectroscopic findings provide important insights into the excitation-energy-transfer and subunit assembly mechanisms in the PSI-IsiA supercomplex.


  • Organizational Affiliation

    Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan. fusamichi_a@okayama-u.ac.jp.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A [auth aA],
KA [auth cA],
S [auth bA]
755Thermostichus vulcanusMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P25936 (Thermostichus vulcanus)
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UniProt GroupP25936
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2B [auth aB],
LA [auth cB],
T [auth bB]
740Thermostichus vulcanusMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P0A409 (Thermostichus vulcanus)
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UniProt GroupP0A409
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerC [auth aC],
MA [auth cC],
U [auth bC]
80Thermostichus vulcanusMutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P0A417 (Thermostichus vulcanus)
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UniProt GroupP0A417
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IID [auth aD],
NA [auth cD],
V [auth bD]
138Thermostichus vulcanusMutation(s): 0 
UniProt
Find proteins for P0A422 (Thermostichus vulcanus)
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UniProt GroupP0A422
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVE [auth aE],
OA [auth cE],
W [auth bE]
75Thermostichus vulcanusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIF [auth aF],
PA [auth cF],
X [auth bF]
164Thermostichus vulcanusMutation(s): 0 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIG [auth aI],
QA [auth cI],
Y [auth bI]
38Thermostichus vulcanusMutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXH [auth aJ],
RA [auth cJ],
Z [auth bJ]
41Thermostichus vulcanusMutation(s): 0 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaKAA [auth bK],
I [auth aK],
SA [auth cK]
85Thermostichus vulcanusMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P23318 (Thermostichus vulcanus)
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIBA [auth bL],
J [auth aL],
TA [auth cL]
154Thermostichus vulcanusMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIICA [auth bM],
K [auth aM],
UA [auth cM]
31Thermostichus vulcanusMutation(s): 0 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit psaXDA [auth bX],
L [auth aX],
VA [auth cX]
35Thermostichus vulcanusMutation(s): 0 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Iron stress in-duced protein A358Thermostichus vulcanusMutation(s): 0 
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Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA
Query on CLA

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AAA [auth c1]
AC [auth aA]
ACA [auth c4]
ADA [auth c5]
AE [auth aB]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0
Query on CL0

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CB [auth aA],
SU [auth cA],
YK [auth bA]
CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG
Query on LMG

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BF [auth aB],
QY [auth cB],
ZO [auth bB]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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AN [auth bA]
CD [auth aA]
DD [auth aA]
LZ [auth cX]
RW [auth cA]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR
Query on BCR

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ABA [auth c2]
AD [auth aA]
AF [auth aB]
AK [auth a5]
AT [auth b4]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN
Query on PQN

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JY [auth cB]
KW [auth cA]
RM [auth bA]
RO [auth bB]
UE [auth aB]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

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AP [auth bC]
BP [auth bC]
CF [auth aC]
DF [auth aC]
LW [auth cA]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CA
Query on CA

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SP [auth bL],
UF [auth aL],
WF [auth aL]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.74 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3
MODEL REFINEMENTPHENIX1.13_2998

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-20
    Type: Initial release
  • Version 1.1: 2020-05-27
    Changes: Database references
  • Version 2.0: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description, Structure summary