6KMX

Structure of PSI from H. hongdechloris grown under far-red light condition


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Structural basis for the adaptation and function of chlorophyll f in photosystem I.

Kato, K.Shinoda, T.Nagao, R.Akimoto, S.Suzuki, T.Dohmae, N.Chen, M.Allakhverdiev, S.I.Shen, J.R.Akita, F.Miyazaki, N.Tomo, T.

(2020) Nat Commun 11: 238-238

  • DOI: https://doi.org/10.1038/s41467-019-13898-5
  • Primary Citation of Related Structures:  
    6KMW, 6KMX

  • PubMed Abstract: 

    Chlorophylls (Chl) play pivotal roles in energy capture, transfer and charge separation in photosynthesis. Among Chls functioning in oxygenic photosynthesis, Chl f is the most red-shifted type first found in a cyanobacterium Halomicronema hongdechloris. The location and function of Chl f in photosystems are not clear. Here we analyzed the high-resolution structures of photosystem I (PSI) core from H. hongdechloris grown under white or far-red light by cryo-electron microscopy. The structure showed that, far-red PSI binds 83 Chl a and 7 Chl f, and Chl f are associated at the periphery of PSI but not in the electron transfer chain. The appearance of Chl f is well correlated with the expression of PSI genes induced under far-red light. These results indicate that Chl f functions to harvest the far-red light and enhance uphill energy transfer, and changes in the gene sequences are essential for the binding of Chl f.


  • Organizational Affiliation

    Research Institute for Interdisciplinary Science and Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A [auth aA],
J [auth bA],
S [auth cA]
784Halomicronema hongdechloris C2206Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A1Z3HIN6 (Halomicronema hongdechloris C2206)
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UniProt GroupA0A1Z3HIN6
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2B [auth aB],
K [auth bB],
T [auth cB]
743Halomicronema hongdechloris C2206Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A1Z3HIL0 (Halomicronema hongdechloris C2206)
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UniProt GroupA0A1Z3HIL0
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerC [auth aC],
L [auth bC],
U [auth cC]
81Halomicronema hongdechloris C2206Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A1Z3HPE3 (Halomicronema hongdechloris C2206)
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UniProt GroupA0A1Z3HPE3
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IID [auth aD],
M [auth bD],
V [auth cD]
142Halomicronema hongdechloris C2206Mutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for A0A1Z3HHI7 (Halomicronema hongdechloris C2206)
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UniProt GroupA0A1Z3HHI7
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVE [auth aE],
N [auth bE],
W [auth cE]
68Halomicronema hongdechloris C2206Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1Z3HI16 (Halomicronema hongdechloris C2206)
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UniProt GroupA0A1Z3HI16
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIF [auth aI],
O [auth bI],
X [auth cI]
63Halomicronema hongdechloris C2206Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A1Z3HIL5 (Halomicronema hongdechloris C2206)
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UniProt GroupA0A1Z3HIL5
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaKG [auth aK],
P [auth bK],
Y [auth cK]
96Halomicronema hongdechloris C2206Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1Z3HR36 (Halomicronema hongdechloris C2206)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIH [auth aL],
Q [auth bL],
Z [auth cL]
189Halomicronema hongdechloris C2206Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A1Z3HIQ7 (Halomicronema hongdechloris C2206)
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UniProt GroupA0A1Z3HIQ7
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIAA [auth cM],
I [auth aM],
R [auth bM]
31Halomicronema hongdechloris C2206Mutation(s): 0 
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Small Molecules
Ligands 11 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
F6C
Query on F6C

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AB [auth aA]
AL [auth cA]
BB [auth aA]
EB [auth aA]
GB [auth aA]
Chlorophyll F
C55 H68 Mg N4 O6
YUTLCKLMRUVWDE-FOFJUSMOSA-M
CLA
Query on CLA

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AD [auth aB]
AF [auth bA]
AG [auth bA]
AH [auth bB]
AI [auth bB]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0
Query on CL0

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BA [auth aA],
JJ [auth cA],
SE [auth bA]
CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG
Query on LMG

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EN [auth cB],
NI [auth bB],
WD [auth aB]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

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AC [auth aA],
IL [auth cA],
RG [auth bA]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR
Query on BCR

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AE [auth aI]
AN [auth cB]
BN [auth cB]
CJ [auth bL]
CN [auth cB]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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BC [auth aA],
JL [auth cA],
SG [auth bA]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
Query on PQN

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BL [auth cA]
HI [auth bB]
KG [auth bA]
QD [auth aB]
TB [auth aA]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

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CL [auth cA]
GN [auth cC]
HN [auth cC]
LG [auth bA]
PI [auth bC]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CA
Query on CA

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EJ [auth bL],
NE [auth aL],
WN [auth cL]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
UNL
Query on UNL

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BE [auth aI]
FE [auth aL]
FJ [auth bL]
GJ [auth bL]
HJ [auth bL]
Unknown ligand
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.41 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3
MODEL REFINEMENTPHENIX1.13_2998

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2020-01-29
    Changes: Data collection, Database references
  • Version 2.0: 2024-03-27
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description