7DWQ

Photosystem I from a chlorophyll d-containing cyanobacterium Acaryochloris marina


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 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

A unique photosystem I reaction center from a chlorophyll d-containing cyanobacterium Acaryochloris marina.

Xu, C.Zhu, Q.Chen, J.H.Shen, L.Yi, X.Huang, Z.Wang, W.Chen, M.Kuang, T.Shen, J.R.Zhang, X.Han, G.

(2021) J Integr Plant Biol 63: 1740-1752

  • DOI: https://doi.org/10.1111/jipb.13113
  • Primary Citation of Related Structures:  
    7DWQ

  • PubMed Abstract: 

    Photosystem I (PSI) is a large protein supercomplex that catalyzes the light-dependent oxidation of plastocyanin (or cytochrome c 6 ) and the reduction of ferredoxin. This catalytic reaction is realized by a transmembrane electron transfer chain consisting of primary electron donor (a special chlorophyll (Chl) pair) and electron acceptors A 0 , A 1 , and three Fe 4 S 4 clusters, F X , F A , and F B . Here we report the PSI structure from a Chl d-dominated cyanobacterium Acaryochloris marina at 3.3 Å resolution obtained by single-particle cryo-electron microscopy. The A. marina PSI exists as a trimer with three identical monomers. Surprisingly, the structure reveals a unique composition of electron transfer chain in which the primary electron acceptor A 0 is composed of two pheophytin a rather than Chl a found in any other well-known PSI structures. A novel subunit Psa27 is observed in the A. marina PSI structure. In addition, 77 Chls, 13 α-carotenes, two phylloquinones, three Fe-S clusters, two phosphatidyl glycerols, and one monogalactosyl-diglyceride were identified in each PSI monomer. Our results provide a structural basis for deciphering the mechanism of photosynthesis in a PSI complex with Chl d as the dominating pigments and absorbing far-red light.


  • Organizational Affiliation

    Department of Biophysics and Department of Pathology of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I protein PsaDA [auth D]139Acaryochloris marina MBIC11017Mutation(s): 0 
UniProt
Find proteins for B0C8F1 (Acaryochloris marina (strain MBIC 11017))
Explore B0C8F1 
Go to UniProtKB:  B0C8F1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0C8F1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P740 chlorophyll a apoprotein A1B [auth A]753Acaryochloris marina MBIC11017Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for B0C474 (Acaryochloris marina (strain MBIC 11017))
Explore B0C474 
Go to UniProtKB:  B0C474
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0C474
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P740 chlorophyll a apoprotein A2C [auth B]736Acaryochloris marina MBIC11017Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for B0C475 (Acaryochloris marina (strain MBIC 11017))
Explore B0C475 
Go to UniProtKB:  B0C475
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0C475
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerD [auth C]81Acaryochloris marina MBIC11017Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for B0CB42 (Acaryochloris marina (strain MBIC 11017))
Explore B0CB42 
Go to UniProtKB:  B0CB42
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0CB42
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 IV89Acaryochloris marina MBIC11017Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B0C5D5 (Acaryochloris marina (strain MBIC 11017))
Explore B0C5D5 
Go to UniProtKB:  B0C5D5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0C5D5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I protein PsaF167Acaryochloris marina MBIC11017Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B0C7S7 (Acaryochloris marina (strain MBIC 11017))
Explore B0C7S7 
Go to UniProtKB:  B0C7S7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0C7S7
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 IXG [auth J]51Acaryochloris marina MBIC11017Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B0C7S6 (Acaryochloris marina (strain MBIC 11017))
Explore B0C7S6 
Go to UniProtKB:  B0C7S6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0C7S6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I protein PsaLH [auth L]153Acaryochloris marina MBIC11017Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B0C7S4 (Acaryochloris marina (strain MBIC 11017))
Explore B0C7S4 
Go to UniProtKB:  B0C7S4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0C7S4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIII [auth M]31Acaryochloris marina MBIC11017Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B0C4H4 (Acaryochloris marina (strain MBIC 11017))
Explore B0C4H4 
Go to UniProtKB:  B0C4H4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0C4H4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I protein Psa27J [auth W]34Acaryochloris marina MBIC11017Mutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
G9R (Subject of Investigation/LOI)
Query on G9R

Download Ideal Coordinates CCD File 
DB [auth A]CHLOROPHYLL D ISOMER
C54 H70 Mg N4 O6
QXWRYZIMSXOOPY-WXWFEFDWSA-M
CL7 (Subject of Investigation/LOI)
Query on CL7

Download Ideal Coordinates CCD File 
AA [auth A]
AC [auth B]
BA [auth A]
BC [auth B]
CA [auth A]
AA [auth A],
AC [auth B],
BA [auth A],
BC [auth B],
CA [auth A],
CC [auth B],
DA [auth A],
DC [auth B],
DD [auth W],
EA [auth A],
EC [auth B],
FA [auth A],
FC [auth B],
GA [auth A],
GC [auth B],
HA [auth A],
HC [auth B],
IA [auth A],
IB [auth B],
IC [auth B],
JA [auth A],
JB [auth B],
JC [auth B],
K [auth A],
KA [auth A],
KB [auth B],
KC [auth B],
L [auth A],
LA [auth A],
LB [auth B],
M [auth A],
MA [auth A],
MB [auth B],
N [auth A],
NA [auth A],
NB [auth B],
O [auth A],
OA [auth A],
OB [auth B],
P [auth A],
PA [auth A],
PB [auth B],
Q [auth A],
QA [auth A],
QB [auth B],
R [auth A],
RA [auth A],
RB [auth B],
S [auth A],
SA [auth A],
SB [auth B],
T [auth A],
TA [auth A],
TB [auth B],
TC [auth F],
U [auth A],
UA [auth A],
UB [auth B],
UC [auth J],
V [auth A],
VA [auth A],
VB [auth B],
W [auth A],
WA [auth A],
WB [auth B],
X [auth A],
XA [auth A],
XB [auth B],
XC [auth L],
Y [auth A],
YA [auth A],
YB [auth B],
YC [auth L],
Z [auth A],
ZB [auth B],
ZC [auth L]
CHLOROPHYLL D
C54 H70 Mg N4 O6
FBCRYORFRGRJBC-ACDPFEIMSA-L
PHO (Subject of Investigation/LOI)
Query on PHO

Download Ideal Coordinates CCD File 
EB [auth A],
NC [auth B]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
LMG (Subject of Investigation/LOI)
Query on LMG

Download Ideal Coordinates CCD File 
MC [auth B]1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG
Query on LHG

Download Ideal Coordinates CCD File 
BB [auth A],
CB [auth A]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
8CT (Subject of Investigation/LOI)
Query on 8CT

Download Ideal Coordinates CCD File 
AD [auth L]
BD [auth L]
CD [auth M]
ED [auth W]
FB [auth A]
AD [auth L],
BD [auth L],
CD [auth M],
ED [auth W],
FB [auth A],
FD [auth W],
GB [auth A],
HB [auth A],
OC [auth B],
PC [auth B],
QC [auth B],
VC [auth J],
WC [auth J]
(6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene
C40 H56
ANVAOWXLWRTKGA-GZSHKXEASA-N
PQN (Subject of Investigation/LOI)
Query on PQN

Download Ideal Coordinates CCD File 
LC [auth B],
ZA [auth A]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4
Query on SF4

Download Ideal Coordinates CCD File 
AB [auth A],
RC [auth C],
SC [auth C]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC2.12

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-02
    Type: Initial release
  • Version 1.1: 2021-10-20
    Changes: Database references