7COY | pdb_00007coy

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

Experimental Data Snapshot

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

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


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

  • 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.

    • Organizational Affiliation: 
    • Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Sayo, Hyogo, Japan.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1A [auth aA],
L [auth bA],
W [auth cA]		753Acaryochloris marina MBIC11017Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for B0C474 (Acaryochloris marina (strain MBIC 11017))
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Go to UniProtKB:  B0C474
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UniProt GroupB0C474
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2B [auth aB],
M [auth bB],
X [auth cB]		736Acaryochloris marina MBIC11017Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for B0C475 (Acaryochloris marina (strain MBIC 11017))
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UniProt GroupB0C475
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerC [auth aC],
N [auth bC],
Y [auth cC]		81Acaryochloris marina MBIC11017Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for B0CB42 (Acaryochloris marina (strain MBIC 11017))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I protein PsaDD [auth aD],
O [auth bD],
Z [auth cD]		139Acaryochloris marina MBIC11017Mutation(s): 0 
UniProt
Find proteins for B0C8F1 (Acaryochloris marina (strain MBIC 11017))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVAA [auth cE],
E [auth aE],
P [auth bE]		89Acaryochloris marina MBIC11017Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B0C5D5 (Acaryochloris marina (strain MBIC 11017))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I protein PsaFBA [auth cF],
F [auth aF],
Q [auth bF]		167Acaryochloris marina MBIC11017Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B0C7S7 (Acaryochloris marina (strain MBIC 11017))
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I protein Psa27CA [auth cI],
G [auth aI],
R [auth bI]		34Acaryochloris marina MBIC11017Mutation(s): 0 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXDA [auth cJ],
H [auth aJ],
S [auth bJ]		51Acaryochloris marina MBIC11017Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B0C7S6 (Acaryochloris marina (strain MBIC 11017))
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaKEA [auth cK],
I [auth aK],
T [auth bK]		86Acaryochloris marina MBIC11017Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B0CA71 (Acaryochloris marina (strain MBIC 11017))
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I protein PsaLFA [auth cL],
J [auth aL],
U [auth bL]		153Acaryochloris marina MBIC11017Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for B0C7S4 (Acaryochloris marina (strain MBIC 11017))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I protein PsaMGA [auth cM],
K [auth aM],
V [auth bM]		31Acaryochloris marina MBIC11017Mutation(s): 0 
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Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CL7 (Subject of Investigation/LOI)
Query on CL7
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AB [auth aA]
AC [auth aA]
AD [auth aB]
AE [auth bA]
AF [auth bA]
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)
Query on G9R
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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)
Query on PHO
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DJ [auth cB]
EC [auth aB]
HJ [auth cB]
IA [auth aA]
PF [auth bB]
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)
Query on LMG
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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)
Query on LHG
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GF [auth bA]
HF [auth bA]
SB [auth aA]
TB [auth aA]
VI [auth cA]
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)
Query on PQN
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BD [auth aB]
BJ [auth cA]
EK [auth cB]
MF [auth bA]
QG [auth bB]
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)
Query on SF4
Download Ideal Coordinates CCD File 
BC [auth aB]
EJ [auth cB]
JD [auth aC]
KD [auth aC]
MK [auth cC]
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)
Query on UNL
Download Ideal Coordinates CCD File 
BH [auth bI]
CD [auth aB]
CH [auth bI]
DF [auth bA]
EF [auth bA]
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

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan18H05175
Japan Society for the Promotion of Science (JSPS)Japan16H04757
Japan Society for the Promotion of Science (JSPS)Japan16H06554
Japan Society for the Promotion of Science (JSPS)Japan20K06684
Japan Agency for Medical Research and Development (AMED)Japan--

Revision History  (Full details and data files)

  • 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