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 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 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 hongdechlor ...

    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

    Faculty of Science, Tokyo University of Science, Tokyo, 162-8601, Japan. tomo@rs.tus.ac.jp.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1aA, bA, cA784Halomicronema hongdechloris C2206Mutation(s): 0 
Gene Names: psaA_1psaAXM38_010910
EC: 1.97.1.12
Find proteins for A0A1Z3HIN6 (Halomicronema hongdechloris C2206)
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2aB, bB, cB743Halomicronema hongdechloris C2206Mutation(s): 0 
Gene Names: psaB_1psaBXM38_010920
EC: 1.97.1.12
Find proteins for A0A1Z3HIL0 (Halomicronema hongdechloris C2206)
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centeraC, bC, cC81Halomicronema hongdechloris C2206Mutation(s): 0 
Gene Names: psaCXM38_031380
EC: 1.97.1.12
Find proteins for A0A1Z3HPE3 (Halomicronema hongdechloris C2206)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIaD, bD, cD142Halomicronema hongdechloris C2206Mutation(s): 0 
Gene Names: psaDXM38_006600
EC: 1.97.1.12
Find proteins for A0A1Z3HHI7 (Halomicronema hongdechloris C2206)
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVaE, bE, cE68Halomicronema hongdechloris C2206Mutation(s): 0 
Gene Names: psaEXM38_008840
Find proteins for A0A1Z3HI16 (Halomicronema hongdechloris C2206)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIaI, bI, cI63Halomicronema hongdechloris C2206Mutation(s): 0 
Gene Names: psaI_2XM38_010940
EC: 1.97.1.12
Find proteins for A0A1Z3HIL5 (Halomicronema hongdechloris C2206)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaKaK, bK, cK96Halomicronema hongdechloris C2206Mutation(s): 0 
Gene Names: psaKXM38_037430
Find proteins for A0A1Z3HR36 (Halomicronema hongdechloris C2206)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIaL, bL, cL189Halomicronema hongdechloris C2206Mutation(s): 0 
Gene Names: psaL_1XM38_010930
EC: 1.97.1.12
Find proteins for A0A1Z3HIQ7 (Halomicronema hongdechloris C2206)
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIaM, bM, cM31Halomicronema hongdechloris C2206Mutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 11 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
F6C
Query on F6C

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aA, aB, aL, bA, bB, bL, cA, cB, cL
Chlorophyll F
C55 H68 Mg N4 O6
YUTLCKLMRUVWDE-FOFJUSMOSA-M
 Ligand Interaction
CL0
Query on CL0

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

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aA, aB, aK, aL, bA, bB, bK, bL, cA, cB, cK, cL
CHLOROPHYLL A
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-AENOIHSZSA-M
 Ligand Interaction
LMG
Query on LMG

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aB, bB, cB
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
 Ligand Interaction
LHG
Query on LHG

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aA, bA, cA
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
 Ligand Interaction
BCR
Query on BCR

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aA, aB, aI, aK, aL, aM, bA, bB, bI, bK, bL, bM, cA, cB, cI, cK, cL, cM
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
 Ligand Interaction
LMT
Query on LMT

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aA, bA, cA
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
PQN
Query on PQN

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aA, aB, bA, bB, cA, cB
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
 Ligand Interaction
SF4
Query on SF4

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aA, aC, bA, bC, cA, cC
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
CA
Query on CA

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aL, bL, cL
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
UNL
Query on UNL

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aI, aL, bI, bL, cI, cL
Unknown ligand
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

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

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-01-15
    Type: Initial release
  • Version 1.1: 2020-01-29
    Changes: Data collection, Database references