7COY

Structure of the far-red light utilizing photosystem I of Acaryochloris marina

• PDB DOI: https://doi.org/10.2210/pdb7COY/pdb
• EM Map EMD-30420: EMDB EMDataResource

• Classification: PHOTOSYNTHESIS
• Organism(s): Acaryochloris marina MBIC11017
• Mutation(s): No 
• Membrane Protein: Yes  OPMmpstruc


• Deposited: 2020-08-05 Released: 2021-03-31 
• Deposition Author(s): Kawakami, K., Yonekura, K., Hamaguchi, T., Kashino, Y., Shinzawa-Itoh, K., Inoue-Kashino, N., Itoh, S., Ifuku, K., Yamashita, E.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Japan Agency for Medical Research and Development (AMED)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of the far-red light utilizing photosystem I of Acaryochloris marina.

Hamaguchi, T., Kawakami, K., Shinzawa-Itoh, K., Inoue-Kashino, N., Itoh, S., Ifuku, K., Yamashita, E., Maeda, K., Yonekura, K., Kashino, Y.

(2021) Nat Commun 12: 2333-2333

• PubMed: 33879791 
• DOI: https://doi.org/10.1038/s41467-021-22502-8
• Primary Citation of Related Structures:  
  7COY


• PubMed Abstract: 
  

  Acaryochloris marina is one of the cyanobacterial species that can use far-red light to drive photochemical reactions for oxygenic photosynthesis. Here, we report the structure of A. marina photosystem I (PSI) reaction center, determined by cryo-electron microscopy at 2.58 Å resolution. The structure reveals an arrangement of electron carriers and light-harvesting pigments distinct from other type I reaction centers. The paired chlorophyll, or special pair (also referred to as P740 in this case), is a dimer of chlorophyll d and its epimer chlorophyll d'. The primary electron acceptor is pheophytin a, a metal-less chlorin. We show the architecture of this PSI reaction center is composed of 11 subunits and we identify key components that help explain how the low energy yield from far-red light is efficiently utilized for driving oxygenic photosynthesis.

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Organizational Affiliation: 

Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Sayo, Hyogo, Japan.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Hetero 33-mer - A3B3C3D3E3F3G3H3I3J3K3 Pseudo Symmetry: Cyclic - C3  (Explore in 3D)
Pseudo Stoichiometry: Hetero 33-mer - A6B6C3D3E3F3G3H3I3 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 971.74 kDa 
• Atom Count: 57,966 
• Modelled Residue Count: 6,096 
• Deposited Residue Count: 6,960 
• Unique protein chains: 11

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I P700 chlorophyll a apoprotein A1	A [auth aA], L [auth bA], W [auth cA]	753	Acaryochloris marina MBIC11017	Mutation(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 ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I P700 chlorophyll a apoprotein A2	B [auth aB], M [auth bB], X [auth cB]	736	Acaryochloris marina MBIC11017	Mutation(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 ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I iron-sulfur center	C [auth aC], N [auth bC], Y [auth cC]	81	Acaryochloris marina MBIC11017	Mutation(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 ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I protein PsaD	D [auth aD], O [auth bD], Z [auth cD]	139	Acaryochloris marina MBIC11017	Mutation(s): 0
UniProt
Find proteins for B0C8F1 (Acaryochloris marina (strain MBIC 11017)) Explore B0C8F1  Go to UniProtKB:  B0C8F1

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit IV	AA [auth cE], E [auth aE], P [auth bE]	89	Acaryochloris marina MBIC11017	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B0C5D5 (Acaryochloris marina (strain MBIC 11017)) Explore B0C5D5  Go to UniProtKB:  B0C5D5

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I protein PsaF	BA [auth cF], F [auth aF], Q [auth bF]	167	Acaryochloris marina MBIC11017	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B0C7S7 (Acaryochloris marina (strain MBIC 11017)) Explore B0C7S7  Go to UniProtKB:  B0C7S7

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I protein Psa27	CA [auth cI], G [auth aI], R [auth bI]	34	Acaryochloris marina MBIC11017	Mutation(s): 0

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit IX	DA [auth cJ], H [auth aJ], S [auth bJ]	51	Acaryochloris marina MBIC11017	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B0C7S6 (Acaryochloris marina (strain MBIC 11017)) Explore B0C7S6  Go to UniProtKB:  B0C7S6

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I reaction center subunit PsaK	EA [auth cK], I [auth aK], T [auth bK]	86	Acaryochloris marina MBIC11017	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B0CA71 (Acaryochloris marina (strain MBIC 11017)) Explore B0CA71  Go to UniProtKB:  B0CA71

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I protein PsaL	FA [auth cL], J [auth aL], U [auth bL]	153	Acaryochloris marina MBIC11017	Mutation(s): 0  Membrane Entity: Yes
UniProt
Find proteins for B0C7S4 (Acaryochloris marina (strain MBIC 11017)) Explore B0C7S4  Go to UniProtKB:  B0C7S4

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
Photosystem I protein PsaM	GA [auth cM], K [auth aM], V [auth bM]	31	Acaryochloris marina MBIC11017	Mutation(s): 0

Small Molecules

Ligands 8 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL7 (Subject of Investigation/LOI)	AB [auth aA], AC [auth aA], AD [auth aB], AE [auth bA], AF [auth bA], AG [auth bB], AH [auth bF], AI [auth cA], AJ [auth cA], AK [auth cB], BB [auth aA], BE [auth bA], BF [auth bA], BG [auth bB], BI [auth cA], BK [auth cB], CB [auth aA], CC [auth aB], CE [auth bA], CF [auth bA], CG [auth bB], CI [auth cA], CJ [auth cA], CK [auth cB], DB [auth aA], DC [auth aB], DE [auth bA], DG [auth bB], DH [auth bJ], DI [auth cA], DK [auth cB], EB [auth aA], ED [auth aB], EE [auth bA], EG [auth bB], EI [auth cA], FB [auth aA], FC [auth aB], FD [auth aB], FE [auth bA], FG [auth bB], FH [auth bK], FI [auth cA], FJ [auth cB], GB [auth aA], GC [auth aB], GD [auth aB], GE [auth bA], GG [auth bB], GI [auth cA], GJ [auth cB], HB [auth aA], HC [auth aB], HE [auth bA], HG [auth bB], HI [auth cA], HK [auth cB], IB [auth aA], IC [auth aB], IE [auth bA], IF [auth bA], IG [auth bB], IH [auth bL], II [auth cA], IJ [auth cB], IK [auth cB], JA [auth aA], JB [auth aA], JC [auth aB], JE [auth bA], JF [auth bA], JG [auth bB], JH [auth bL], JI [auth cA], JJ [auth cB], JK [auth cB], KA [auth aA], KB [auth aA], KC [auth aB], KE [auth bA], KF [auth bA], KG [auth bB], KH [auth bL], KI [auth cA], KJ [auth cB], LA [auth aA], LB [auth aA], LC [auth aB], LD [auth aF], LE [auth bA], LF [auth bA], LG [auth bB], LI [auth cA], LJ [auth cB], MA [auth aA], MB [auth aA], MC [auth aB], ME [auth bA], MG [auth bB], MH [auth cA], MI [auth cA], MJ [auth cB], NA [auth aA], NB [auth aA], NC [auth aB], NE [auth bA], NG [auth bB], NH [auth cA], NI [auth cA], NJ [auth cB], OA [auth aA], OB [auth aA], OC [auth aB], OD [auth aJ], OE [auth bA], OF [auth bA], OG [auth bB], OH [auth cA], OI [auth cA], OJ [auth cB], OK [auth cF], PA [auth aA], PC [auth aB], PE [auth bA], PG [auth bB], PH [auth cA], PI [auth cA], PJ [auth cB], QA [auth aA], QC [auth aB], QD [auth aK], QE [auth bA], QH [auth cA], QI [auth cA], QJ [auth cB], RA [auth aA], RC [auth aB], RE [auth bA], RF [auth bB], RH [auth cA], RI [auth cA], RJ [auth cB], SA [auth aA], SC [auth aB], SD [auth aL], SE [auth bA], SF [auth bB], SH [auth cA], SJ [auth cB], SK [auth cJ], TA [auth aA], TC [auth aB], TD [auth aL], TE [auth bA], TG [auth bB], TH [auth cA], TJ [auth cB], UA [auth aA], UB [auth aA], UC [auth aB], UD [auth aL], UE [auth bA], UF [auth bB], UG [auth bB], UH [auth cA], UJ [auth cB], UK [auth cK], VA [auth aA], VB [auth aA], VC [auth aB], VE [auth bA], VF [auth bB], VG [auth bB], VH [auth cA], VJ [auth cB], WA [auth aA], WB [auth aA], WC [auth aB], WE [auth bA], WF [auth bB], WH [auth cA], WJ [auth cB], XA [auth aA], XB [auth aA], XC [auth aB], XD [auth bA], XE [auth bA], XF [auth bB], XH [auth cA], XI [auth cA], XJ [auth cB], XK [auth cL], YA [auth aA], YC [auth aB], YD [auth bA], YE [auth bA], YF [auth bB], YH [auth cA], YI [auth cA], YJ [auth cB], YK [auth cL], ZA [auth aA], ZC [auth aB], ZD [auth bA], ZE [auth bA], ZF [auth bB], ZH [auth cA], ZI [auth cA], ZJ [auth cB], ZK [auth cL]	CHLOROPHYLL D C54 H70 Mg N4 O6 FBCRYORFRGRJBC-ACDPFEIMSA-L
G9R (Subject of Investigation/LOI)	HA [auth aA], LH [auth cA], WD [auth bA]	CHLOROPHYLL D ISOMER C54 H70 Mg N4 O6 QXWRYZIMSXOOPY-WXWFEFDWSA-M
PHO (Subject of Investigation/LOI)	DJ [auth cB], EC [auth aB], HJ [auth cB], IA [auth aA], PF [auth bB], TF [auth bB]	PHEOPHYTIN A C55 H74 N4 O5 CQIKWXUXPNUNDV-RCBXBCQGSA-N
LMG (Subject of Investigation/LOI)	DD [auth aB], GK [auth cB], SG [auth bB]	1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE C45 H86 O10 DCLTVZLYPPIIID-CVELTQQQSA-N
LHG (Subject of Investigation/LOI)	GF [auth bA], HF [auth bA], SB [auth aA], TB [auth aA], VI [auth cA], WI [auth cA]	1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE C38 H75 O10 P BIABMEZBCHDPBV-MPQUPPDSSA-N
PQN (Subject of Investigation/LOI)	BD [auth aB], BJ [auth cA], EK [auth cB], MF [auth bA], QG [auth bB], YB [auth aA]	PHYLLOQUINONE C31 H46 O2 MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4 (Subject of Investigation/LOI)	BC [auth aB], EJ [auth cB], JD [auth aC], KD [auth aC], MK [auth cC], NK [auth cC], QF [auth bB], YG [auth bC], ZG [auth bC]	IRON/SULFUR CLUSTER Fe4 S4 LJBDFODJNLIPKO-UHFFFAOYSA-N
UNL (Subject of Investigation/LOI)	BH [auth bI], CD [auth aB], CH [auth bI], DF [auth bA], EF [auth bA], EH [auth bJ], FF [auth bA], FK [auth cB], GH [auth bL], HD [auth aB], HH [auth bL], ID [auth aB], KK [auth cB], LK [auth cB], MD [auth aI], ND [auth aI], NF [auth bA], PB [auth aA], PD [auth aJ], PK [auth cF], QB [auth aA], QK [auth cI], RB [auth aA], RD [auth aL], RG [auth bB], RK [auth cI], SI [auth cA], TI [auth cA], TK [auth cJ], UI [auth cA], VD [auth aL], VK [auth cL], WG [auth bB], WK [auth cL], XG [auth bB], ZB [auth aA]	Unknown ligand LJBDFODJNLIPKO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-31 
Deposition Author(s): Kawakami, K., Yonekura, K., Hamaguchi, T., Kashino, Y., Shinzawa-Itoh, K., Inoue-Kashino, N., Itoh, S., Ifuku, K., Yamashita, E.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	18H05175
Japan Society for the Promotion of Science (JSPS)	Japan	16H04757
Japan Society for the Promotion of Science (JSPS)	Japan	16H06554
Japan Society for the Promotion of Science (JSPS)	Japan	20K06684
Japan Agency for Medical Research and Development (AMED)	Japan	--

Revision History  

• Version 1.0: 2021-03-31
  Type: Initial release
  
• Version 1.1: 2021-05-05
  Changes: Database references
• Version 1.2: 2024-11-13
  Changes: Data collection, Database references, Structure summary