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 31FD | pdb_000031fd

Photosystem II from Arabidopsis thaliana following high light and high temperature treatment


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.74 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.0 of the entry. See complete history. 

Literature

Effects of high light and elevated temperature on the structure of photosystem II isolated from Arabidopsis thaliana.

Forsman, J., Graca, A.T., Hall, M., Schroder, W.P., Messinger, J.

(2026) Photosynth Res 164

  • DOI: https://doi.org/10.1007/s11120-026-01238-w
  • Primary Citation Related Structures: 
    31FD

  • PubMed Abstract: 

    Photosystem II (PS II) is a large membrane-bound pigment-protein complex responsible for extracting electrons and protons from water during photosynthesis and releasing molecular oxygen into the atmosphere. While light is required to drive the photochemical reactions, high light and high temperature can be damaging to PS II. To gain insight into potential structural consequences of such conditions, we performed an exploratory study where isolated PS II complexes (C2S2) from Arabidopsis thaliana were exposed to high light and elevated temperature and employed cryo-electron microscopy for structural determination. This resulted in a 'high light' structure (2.74 Å global resolution) which is compared to the published 2.44 Å structure of intact Arabidopsis-PSII vitrified under dim light conditions (control). The high light structure is missing several of the subunits present in the control, including the strongly bound light-harvesting antenna complexes as well as several small transmembrane and extrinsic subunits. Beyond the loss of subunits, the clearest evidence of specific photodamage was found on the acceptor side of the D1 and D2 subunits near the non-heme iron, including the loss of the bicarbonate ligand of the non-heme iron. Finally, we were able to observe that high light/elevated temperature conditions result in the movement of the D1:His252 residue, potentially forming a serine protease triad that may trigger auto-proteolysis of the D1 subunit.


  • Organizational Affiliation: 
    • Department of Chemistry, Umeå University, Umeå, SE, 90187, Sweden. jack.forsman@umu.se.

Macromolecule Content 

  • Total Structure Weight: 672.75 kDa 
  • Atom Count: 39,296 
  • Modeled Residue Count: 4,174 
  • Deposited Residue Count: 5,270 
  • Unique protein chains: 15

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II protein D1A,
P [auth a]
353Arabidopsis thalianaMutation(s): 0 
EC: 1.10.3.9
UniProt
Find proteins for P83755 (Arabidopsis thaliana)
Explore P83755 
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UniProt GroupP83755
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP47 reaction center proteinB,
Q [auth b]
508Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P56777 (Arabidopsis thaliana)
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UniProt GroupP56777
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II CP43 reaction center proteinC,
R [auth c]
473Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P56778 (Arabidopsis thaliana)
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UniProt GroupP56778
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II D2 proteinD,
S [auth d]
353Arabidopsis thalianaMutation(s): 0 
EC: 1.10.3.9
UniProt
Find proteins for P56761 (Arabidopsis thaliana)
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UniProt GroupP56761
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit alphaE,
T [auth e]
83Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P56779 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Cytochrome b559 subunit betaF,
U [auth f]
39Arabidopsis thalianaMutation(s): 1 
UniProt
Find proteins for P62095 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein HG [auth H],
V [auth h]
73Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P56780 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein IH [auth I],
W [auth i]
36Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P62100 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein KI [auth K],
X [auth k]
61Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P56782 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein LJ [auth L],
Y [auth l]
38Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P60129 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein MK [auth M],
Z [auth m]
34Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P62109 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Oxygen-evolving enhancer protein 1-1, chloroplasticAA [auth o],
L [auth O]
332Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P23321 (Arabidopsis thaliana)
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UniProt GroupP23321
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Reference Sequence
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II reaction center protein TBA [auth t],
M [auth T]
33Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for P61839 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Photosystem II 5 kDa protein, chloroplasticCA [auth u],
N [auth U]
103Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q39195 (Arabidopsis thaliana)
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Reference Sequence
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Expressed proteinDA [auth x],
O [auth X]
116Arabidopsis thalianaMutation(s): 0 
UniProt
Find proteins for Q9SKI3 (Arabidopsis thaliana)
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Reference Sequence

Small Molecules

Ligands 12 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DGD

Query on DGD



Download:Ideal Coordinates CCD File
EE [auth c]
HB [auth B]
HE [auth c]
KB [auth C]
QD [auth b]
EE [auth c],
HB [auth B],
HE [auth c],
KB [auth C],
QD [auth b],
UB [auth C]
DIGALACTOSYL DIACYL GLYCEROL (DGDG)
C51 H96 O15
LDQFLSUQYHBXSX-HXXRYREZSA-N
CLA

Query on CLA



Download:Ideal Coordinates CCD File
AD [auth b]
AE [auth c]
BB [auth B]
BD [auth b]
BE [auth c]
AD [auth b],
AE [auth c],
BB [auth B],
BD [auth b],
BE [auth c],
CB [auth B],
CD [auth b],
CE [auth c],
DB [auth B],
DC [auth D],
DD [auth b],
DE [auth c],
EB [auth B],
EC [auth D],
ED [auth b],
FB [auth B],
FE [auth c],
GA [auth A],
GB [auth B],
GD [auth b],
GE [auth c],
HA [auth A],
HD [auth b],
IA [auth A],
ID [auth b],
JA [auth A],
JC [auth H],
JD [auth b],
KD [auth b],
LB [auth C],
LE [auth d],
MB [auth C],
MD [auth b],
NB [auth C],
OA [auth B],
OB [auth C],
OC [auth a],
OD [auth b],
PA [auth B],
PB [auth C],
PC [auth a],
PD [auth b],
PE [auth d],
QA [auth B],
QB [auth C],
QC [auth a],
RB [auth C],
SA [auth B],
SB [auth C],
SC [auth a],
TA [auth B],
TB [auth C],
TD [auth c],
UA [auth B],
UD [auth c],
VA [auth B],
VB [auth C],
VD [auth c],
WA [auth B],
WB [auth C],
WC [auth b],
WD [auth c],
XB [auth C],
XD [auth c],
YA [auth B],
YB [auth C],
YC [auth b],
YD [auth c],
ZC [auth b],
ZD [auth c]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
PHO

Query on PHO



Download:Ideal Coordinates CCD File
AC [auth D],
IE [auth d],
KA [auth A],
UC [auth a]
PHEOPHYTIN A
C55 H74 N4 O5
CQIKWXUXPNUNDV-RCBXBCQGSA-N
SQD

Query on SQD



Download:Ideal Coordinates CCD File
MA [auth A],
RC [auth a]
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



Download:Ideal Coordinates CCD File
GC [auth D]
JB [auth C]
ND [auth b]
QE [auth d]
RA [auth B]
GC [auth D],
JB [auth C],
ND [auth b],
QE [auth d],
RA [auth B],
SD [auth c]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
PL9

Query on PL9



Download:Ideal Coordinates CCD File
FC [auth D],
ME [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



Download:Ideal Coordinates CCD File
CC [auth D]
HC [auth D]
KE [auth d]
LC [auth L]
NA [auth A]
CC [auth D],
HC [auth D],
KE [auth d],
LC [auth L],
NA [auth A],
NE [auth d],
TE [auth l],
VC [auth a]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
HEM

Query on HEM



Download:Ideal Coordinates CCD File
IC [auth F],
RE [auth f]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
BCR

Query on BCR



Download:Ideal Coordinates CCD File
AB [auth B]
BC [auth D]
FD [auth b]
KC [auth H]
LA [auth A]
AB [auth B],
BC [auth D],
FD [auth b],
KC [auth H],
LA [auth A],
LD [auth b],
MC [auth a],
OE [auth d],
SE [auth h],
XA [auth B],
XC [auth b],
ZA [auth B]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
OEX
(Subject of Investigation/LOI)

Query on OEX



Download:Ideal Coordinates CCD File
EA [auth A],
NC [auth a]
CA-MN4-O5 CLUSTER
Ca Mn4 O5
SEXWDHMBWJEXOJ-UHFFFAOYSA-N
FE2
(Subject of Investigation/LOI)

Query on FE2



Download:Ideal Coordinates CCD File
JE [auth d],
ZB [auth D]
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
FA [auth A],
IB [auth C],
RD [auth c],
TC [auth a]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.74 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21_5207
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sven och Lilly Lawskis fond for naturvetenskaplig forskningSweden--
Swedish Research CouncilSweden2020-03809
Swedish Research CouncilSweden2024-04804
Carl Trygger FoundationSwedenCTS 19.324
Kempe FoundationSwedenJCK-2030
Kempe FoundationSwedenJCSMK24-599

Revision History  (Full details and data files)

  • Version 1.0: 2026-10-21
    Type: Initial release