8EQM

Structure of a dimeric photosystem II complex acclimated to far-red light


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.2 of the entry. See complete history


Literature

Structure of a dimeric photosystem II complex from a cyanobacterium acclimated to far-red light.

Gisriel, C.J.Shen, G.Flesher, D.A.Kurashov, V.Golbeck, J.H.Brudvig, G.W.Amin, M.Bryant, D.A.

(2022) J Biol Chem 299: 102815-102815

  • DOI: https://doi.org/10.1016/j.jbc.2022.102815
  • Primary Citation of Related Structures:  
    8EQM

  • PubMed Abstract: 

    Photosystem II (PSII) is the water-splitting enzyme central to oxygenic photosynthesis. To drive water oxidation, light is harvested by accessory pigments, mostly chlorophyll (Chl) a molecules, which absorb visible light (400-700 nm). Some cyanobacteria facultatively acclimate to shaded environments by altering their photosynthetic machinery to additionally absorb far-red light (FRL, 700-800 nm), a process termed far-red light photoacclimation or FaRLiP. During far-red light photoacclimation, FRL-PSII is assembled with FRL-specific isoforms of the subunits PsbA, PsbB, PsbC, PsbD, and PsbH, and some Chl-binding sites contain Chls d or f instead of the usual Chl a. The structure of an apo-FRL-PSII monomer lacking the FRL-specific PsbH subunit has previously been determined, but visualization of the dimeric complex has remained elusive. Here, we report the cryo-EM structure of a dimeric FRL-PSII complex. The site assignments for Chls d and f are consistent with those assigned in the previous apo-FRL-PSII monomeric structure. All sites that bind Chl d or Chl f at high occupancy exhibit a FRL-specific interaction of the formyl moiety of the Chl d or Chl f with the protein environment, which in some cases involves a phenylalanine sidechain. The structure retains the FRL-specific PsbH2 subunit, which appears to alter the energetic landscape of FRL-PSII, redirecting energy transfer from the phycobiliprotein complex to a Chl f molecule bound by PsbB2 that acts as a bridge for energy transfer to the electron transfer chain. Collectively, these observations extend our previous understanding of the structure-function relationship that allows PSII to function using lower energy FRL.


  • Organizational Affiliation

    Department of Chemistry, Yale University, New Haven, Connecticut, USA. Electronic address: christopher.gisriel@yale.edu.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II protein D1A,
Q [auth a]
359Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
R [auth b]
509Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
S [auth c]
482Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupB4WKI2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
T [auth d]
352Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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UniProt GroupB4WKI3
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
U [auth e]
80Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
V [auth f]
44Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HG [auth H],
W [auth h]
66Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IH [auth I],
X [auth i]
38Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KI [auth K],
Y [auth k]
45Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LJ [auth L],
Z [auth l]
40Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MAA [auth m],
K [auth M]
36Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II manganese-stabilizing polypeptideBA [auth o],
L [auth O]
274Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TCA [auth t],
M [auth T]
32Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II 12 kDa extrinsic proteinDA [auth u],
N [auth U]
160Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
Cytochrome c-550EA [auth v],
O [auth V]
172Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem II reaction center X proteinFA [auth x],
P [auth X]
39Synechococcus sp. PCC 7335Mutation(s): 0 
Membrane Entity: Yes 
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Small Molecules
Ligands 17 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD
Query on DGD

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AC [auth C]
LC [auth D]
NE [auth c]
OE [auth c]
ZB [auth C]
AC [auth C],
LC [auth D],
NE [auth c],
OE [auth c],
ZB [auth C],
ZE [auth d]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
F6C (Subject of Investigation/LOI)
Query on F6C

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EB [auth B]
FE [auth c]
JD [auth b]
MD [auth b]
RB [auth C]
EB [auth B],
FE [auth c],
JD [auth b],
MD [auth b],
RB [auth C],
SD [auth b],
VA [auth B],
YA [auth B]
Chlorophyll F
C55 H68 Mg N4 O6
YUTLCKLMRUVWDE-FOFJUSMOSA-M
CL7 (Subject of Investigation/LOI)
Query on CL7

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CC [auth D],
QE [auth d]
CHLOROPHYLL D
C54 H70 Mg N4 O6
FBCRYORFRGRJBC-ACDPFEIMSA-L
CLA
Query on CLA

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AB [auth B]
AD [auth a]
AE [auth c]
BB [auth B]
BE [auth c]
AB [auth B],
AD [auth a],
AE [auth c],
BB [auth B],
BE [auth c],
BF [auth h],
CB [auth B],
CE [auth c],
DB [auth B],
DE [auth c],
EC [auth D],
EE [auth c],
FB [auth B],
FC [auth D],
GB [auth B],
GD [auth b],
GE [auth c],
HD [auth b],
HE [auth c],
ID [auth b],
IE [auth c],
JA [auth A],
JE [auth c],
KA [auth A],
KD [auth b],
KE [auth c],
LB [auth C],
LD [auth b],
LE [auth c],
MA [auth A],
MB [auth C],
NB [auth C],
NC [auth H],
ND [auth b],
OB [auth C],
OD [auth b],
PB [auth C],
PD [auth b],
QB [auth C],
QD [auth b],
RD [auth b],
SA [auth B],
SB [auth C],
SE [auth d],
TA [auth B],
TB [auth C],
TD [auth b],
TE [auth d],
UA [auth B],
UB [auth C],
UD [auth b],
VB [auth C],
WA [auth B],
WB [auth C],
XA [auth B],
XB [auth C],
XC [auth a],
YC [auth a],
ZA [auth B],
ZD [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO
Query on PHO

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DC [auth D],
LA [auth A],
RE [auth d],
ZC [auth a]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD
Query on SQD

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CD [auth a],
EF [auth l],
OA [auth A],
QC [auth L]
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
C41 H78 O12 S
RVUUQPKXGDTQPG-JUDHQOGESA-N
LMG
Query on LMG

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FF [auth m],
KC [auth D],
RC [auth M],
YE [auth d]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9
Query on PL9

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DD [auth a],
HC [auth D],
PA [auth A],
VE [auth d]
2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
C53 H80 O2
FKUYMLZIRPABFK-UHFFFAOYSA-N
LHG
Query on LHG

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DF [auth l]
FD [auth a]
IC [auth D]
JC [auth D]
PC [auth L]
DF [auth l],
FD [auth a],
IC [auth D],
JC [auth D],
PC [auth L],
RA [auth A],
WE [auth d],
XE [auth d]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM
Query on HEM

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AF [auth e],
HF [auth v],
MC [auth E],
TC [auth V]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
RRX
Query on RRX

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CF [auth h],
OC [auth H]
(3R)-beta,beta-caroten-3-ol
C40 H56 O
DMASLKHVQRHNES-FKKUPVFPSA-N
BCR
Query on BCR

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BC [auth C]
BD [auth a]
GC [auth D]
HB [auth B]
IB [auth B]
BC [auth C],
BD [auth a],
GC [auth D],
HB [auth B],
IB [auth B],
JB [auth B],
ME [auth c],
NA [auth A],
PE [auth c],
UE [auth d],
VD [auth b],
WD [auth b],
XD [auth b],
YB [auth C]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
LMT
Query on LMT

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GF [auth m],
SC [auth M]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
OEX
Query on OEX

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GA [auth A],
UC [auth a]
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
BCT
Query on BCT

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ED [auth a],
QA [auth A]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
FE2
Query on FE2

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HA [auth A],
VC [auth a]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL
Query on CL

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IA [auth A],
KB [auth C],
WC [auth a],
YD [auth c]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesK99GM140174
National Science Foundation (NSF, United States)United StatesMCB-1613022
Department of Energy (DOE, United States)United StatesDE-FG02-05ER15646

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-28
    Type: Initial release
  • Version 1.1: 2023-01-04
    Changes: Database references
  • Version 1.2: 2023-01-25
    Changes: Database references