6KMW

Structure of PSI from H. hongdechloris grown under white light condition


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.35 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
View more details

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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A [auth aA],
I [auth bA],
Q [auth cA]
764Halomicronema hongdechloris C2206Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A1Z3HRW4 (Halomicronema hongdechloris C2206)
Explore A0A1Z3HRW4 
Go to UniProtKB:  A0A1Z3HRW4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Z3HRW4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2B [auth aB],
J [auth bB],
R [auth cB]
742Halomicronema hongdechloris C2206Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A1Z3HRY4 (Halomicronema hongdechloris C2206)
Explore A0A1Z3HRY4 
Go to UniProtKB:  A0A1Z3HRY4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Z3HRY4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerC [auth aC],
K [auth bC],
S [auth cC]
81Halomicronema hongdechloris C2206Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A1Z3HPE3 (Halomicronema hongdechloris C2206)
Explore A0A1Z3HPE3 
Go to UniProtKB:  A0A1Z3HPE3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Z3HPE3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IID [auth aD],
L [auth bD],
T [auth cD]
142Halomicronema hongdechloris C2206Mutation(s): 0 
EC: 1.97.1.12
UniProt
Find proteins for A0A1Z3HHI7 (Halomicronema hongdechloris C2206)
Explore A0A1Z3HHI7 
Go to UniProtKB:  A0A1Z3HHI7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Z3HHI7
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVE [auth aE],
M [auth bE],
U [auth cE]
68Halomicronema hongdechloris C2206Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1Z3HI16 (Halomicronema hongdechloris C2206)
Explore A0A1Z3HI16 
Go to UniProtKB:  A0A1Z3HI16
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Z3HI16
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIF [auth aI],
N [auth bI],
V [auth cI]
38Halomicronema hongdechloris C2206Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A1Z3HSF0 (Halomicronema hongdechloris C2206)
Explore A0A1Z3HSF0 
Go to UniProtKB:  A0A1Z3HSF0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Z3HSF0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIG [auth aL],
O [auth bL],
W [auth cL]
159Halomicronema hongdechloris C2206Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for A0A1Z3HS05 (Halomicronema hongdechloris C2206)
Explore A0A1Z3HS05 
Go to UniProtKB:  A0A1Z3HS05
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1Z3HS05
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIH [auth aM],
P [auth bM],
X [auth cM]
31Halomicronema hongdechloris C2206Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 10 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL0
Query on CL0

Download Ideal Coordinates CCD File 
IJ [auth cA],
QE [auth bA],
Y [auth aA]
CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
CLA
Query on CLA

Download Ideal Coordinates CCD File 
AA [auth aA]
AB [auth aA]
AD [auth aB]
AF [auth bA]
AG [auth bA]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
LMG
Query on LMG

Download Ideal Coordinates CCD File 
HN [auth cB],
PI [auth bB],
XD [auth aB]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

Download Ideal Coordinates CCD File 
AC [auth aA]
HL [auth cA]
KL [auth cA]
PG [auth bA]
SG [auth bA]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR
Query on BCR

Download Ideal Coordinates CCD File 
BE [auth aI]
BJ [auth bL]
BL [auth cA]
CE [auth aI]
CJ [auth bL]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

Download Ideal Coordinates CCD File 
IL [auth cA],
QG [auth bA],
YB [auth aA]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PQN
Query on PQN

Download Ideal Coordinates CCD File 
BN [auth cB]
HG [auth bA]
JI [auth bB]
PB [auth aA]
RD [auth aB]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
AE [auth aC]
AL [auth cA]
IG [auth bA]
JN [auth cC]
KN [auth cC]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
DJ [auth bL],
LE [auth aL],
VN [auth cL]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
UNL
Query on UNL

Download Ideal Coordinates CCD File 
DE [auth aI]
EE [auth aL]
EJ [auth bL]
FJ [auth bL]
GJ [auth bL]
Unknown ligand
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.35 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: Database references
  • Version 2.0: 2024-03-27
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description