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- PDB-31fd: Photosystem II from Arabidopsis thaliana following high light and... -

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Entry
Database: PDB / ID: 31fd
TitlePhotosystem II from Arabidopsis thaliana following high light and high temperature treatment
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 11
  • Expressed protein
  • Oxygen-evolving enhancer protein 1-1, chloroplastic
KeywordsPHOTOSYNTHESIS / Membrane bound / Photosystem II / Arabidopsis / Manganese cluster / oxidoreductase
Function / homology
Function and homology information


photoinhibition / chloroplast stromal thylakoid / chloroplast photosystem II / plastid thylakoid membrane / plastoglobule / thylakoid lumen / chloroplast thylakoid / chloroplast thylakoid lumen / apoplast / photosystem II oxygen evolving complex ...photoinhibition / chloroplast stromal thylakoid / chloroplast photosystem II / plastid thylakoid membrane / plastoglobule / thylakoid lumen / chloroplast thylakoid / chloroplast thylakoid lumen / apoplast / photosystem II oxygen evolving complex / photosystem II assembly / thylakoid / protein phosphatase regulator activity / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / photosystem II / photosynthetic electron transport chain / chlorophyll binding / chloroplast stroma / plastid / poly(U) RNA binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis / chloroplast / electron transfer activity / protein stabilization / iron ion binding / protein domain specific binding / mRNA binding / heme binding / metal ion binding / mitochondrion / cytosol
Similarity search - Function
Photosystem II 5kDa protein, chloroplastic / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL ...Photosystem II 5kDa protein, chloroplastic / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II CP43 reaction centre protein / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II PsbI / Photosystem II CP47 reaction centre protein / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II protein D1 / Photosystem II reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Cytochrome b559 subunits heme-binding site signature. / : / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 ...BETA-CAROTENE / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / CA-MN4-O5 CLUSTER / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Oxygen-evolving enhancer protein 1-1, chloroplastic / Photosystem II D2 protein / Photosystem II CP47 reaction center protein / Photosystem II CP43 reaction center protein / Cytochrome b559 subunit alpha / Photosystem II reaction center protein H / Photosystem II reaction center protein K / Photosystem II reaction center protein L / Photosystem II reaction center protein T / Cytochrome b559 subunit beta / Photosystem II reaction center protein I / Photosystem II reaction center protein M / Photosystem II protein D1 / Photosystem II 5 kDa protein, chloroplastic / Expressed protein
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.74 Å
AuthorsForsman, J.A. / Graca, A.T. / Hall, M. / Messinger, J. / Schroder, W.P.
Funding support Sweden, 6items
OrganizationGrant numberCountry
Sven och Lilly Lawskis fond for naturvetenskaplig forskning Sweden
Swedish Research Council2020-03809 Sweden
Swedish Research Council2024-04804 Sweden
Carl Trygger FoundationCTS 19.324 Sweden
Kempe FoundationJCK-2030 Sweden
Kempe FoundationJCSMK24-599 Sweden
CitationJournal: Photosynth Res / Year: 2026
Title: Effects of high light and elevated temperature on the structure of photosystem II isolated from Arabidopsis thaliana.
Authors: Jack Forsman / André T Graça / Michael Hall / Wolfgang P Schröder / Johannes Messinger /
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 ...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.
History
DepositionJun 1, 2026Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Photosystem II protein D1
B: Photosystem II CP47 reaction center protein
C: Photosystem II CP43 reaction center protein
D: Photosystem II D2 protein
E: Cytochrome b559 subunit alpha
F: Cytochrome b559 subunit beta
H: Photosystem II reaction center protein H
I: Photosystem II reaction center protein I
K: Photosystem II reaction center protein K
L: Photosystem II reaction center protein L
M: Photosystem II reaction center protein M
O: Oxygen-evolving enhancer protein 1-1, chloroplastic
T: Photosystem II reaction center protein T
U: Photosystem II 5 kDa protein, chloroplastic
X: Expressed protein
a: Photosystem II protein D1
b: Photosystem II CP47 reaction center protein
c: Photosystem II CP43 reaction center protein
d: Photosystem II D2 protein
e: Cytochrome b559 subunit alpha
f: Cytochrome b559 subunit beta
h: Photosystem II reaction center protein H
i: Photosystem II reaction center protein I
k: Photosystem II reaction center protein K
l: Photosystem II reaction center protein L
m: Photosystem II reaction center protein M
o: Oxygen-evolving enhancer protein 1-1, chloroplastic
t: Photosystem II reaction center protein T
u: Photosystem II 5 kDa protein, chloroplastic
x: Expressed protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)672,749150
Polymers578,82030
Non-polymers93,929120
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operationidentityx,y,z1
MethodC2 symmetric homodimer

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Components

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Photosystem II ... , 11 types, 22 molecules AaBbCcDdHhIiKkLlMmTtUu

#1: Protein Photosystem II protein D1 / PSII D1 protein / Photosystem II Q(B) protein


Mass: 38961.277 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / References: UniProt: P83755, photosystem II
#2: Protein Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47


Mass: 56091.824 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / References: UniProt: P56777
#3: Protein Photosystem II CP43 reaction center protein / PSII 43 kDa protein / Protein CP-43


Mass: 51915.500 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / References: UniProt: P56778
#4: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 39575.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / References: UniProt: P56761, photosystem II
#7: Protein Photosystem II reaction center protein H / PSII-H / Photosystem II 10 kDa phosphoprotein


Mass: 7706.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / References: UniProt: P56780
#8: Protein/peptide Photosystem II reaction center protein I / PSII-I / PSII 4.8 kDa protein


Mass: 4170.891 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / References: UniProt: P62100
#9: Protein Photosystem II reaction center protein K / PSII-K


Mass: 6977.381 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / References: UniProt: P56782
#10: Protein/peptide Photosystem II reaction center protein L / PSII-L


Mass: 4471.075 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / References: UniProt: P60129
#11: Protein/peptide Photosystem II reaction center protein M / PSII-M


Mass: 3783.538 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / References: UniProt: P62109
#13: Protein/peptide Photosystem II reaction center protein T / PSII-T


Mass: 3825.642 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / References: UniProt: P61839
#14: Protein Photosystem II 5 kDa protein, chloroplastic / PSII-T / Nuclear encoded psbT / PsbTn


Mass: 11042.852 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / References: UniProt: Q39195

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Cytochrome b559 subunit ... , 2 types, 4 molecules EeFf

#5: Protein Cytochrome b559 subunit alpha / PSII reaction center subunit V


Mass: 9393.501 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / References: UniProt: P56779
#6: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 4488.324 Da / Num. of mol.: 2 / Mutation: S26F / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / References: UniProt: P62095

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Protein , 2 types, 4 molecules OoXx

#12: Protein Oxygen-evolving enhancer protein 1-1, chloroplastic / OEE1 / 33 kDa subunit of oxygen evolving system of photosystem II / 33 kDa thylakoid membrane ...OEE1 / 33 kDa subunit of oxygen evolving system of photosystem II / 33 kDa thylakoid membrane protein / Manganese-stabilizing protein 1 / MSP-1 / OEC 33 kDa subunit


Mass: 35180.262 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / References: UniProt: P23321
#15: Protein Expressed protein / PSBX / Photosystem II subunit X / Putative PSII-X protein / Putative uncharacterized protein ...PSBX / Photosystem II subunit X / Putative PSII-X protein / Putative uncharacterized protein At2g06520 / T12H3.7


Mass: 11826.013 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / References: UniProt: Q9SKI3

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Sugars , 1 types, 6 molecules

#24: Sugar
ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 12 types, 166 molecules

#16: Chemical ChemComp-OEX / CA-MN4-O5 CLUSTER


Mass: 339.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CaMn4O5 / Feature type: SUBJECT OF INVESTIGATION
#17: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#18: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 70 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#19: Chemical
ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C55H74N4O5
#20: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C40H56
#21: Chemical ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H78O12S
#22: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#23: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C45H86O10
#25: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#26: Chemical ChemComp-PL9 / 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 / PLASTOQUINONE 9


Mass: 749.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C53H80O2
#27: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#28: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: High-light exposed Photosystem II from Arabidopsis thaliana
Type: COMPLEX
Details: Photosystem II from Arabidopsis thaliana was solubilised and isolated from the thylakoid membranes. The isolated particles were exposed to 30 min of high light (2000 uE) before plunge ...Details: Photosystem II from Arabidopsis thaliana was solubilised and isolated from the thylakoid membranes. The isolated particles were exposed to 30 min of high light (2000 uE) before plunge freezing and data collection
Entity ID: #1-#15 / Source: NATURAL
Molecular weightValue: 0.573 MDa / Experimental value: NO
Source (natural)Organism: Arabidopsis thaliana (thale cress) / Strain: Columbia-0 / Organelle: Thylakoid membranes / Tissue: Leaves
Buffer solutionpH: 6.3
Buffer component
IDConc.NameFormulaBuffer-ID
150 mM2-(N-morpholino)ethanesulfonic acid (MES)C6H13NO4S1
220 mMCalcium ChlorideCaCl21
35 mMMagnesium ChlorideMgCl21
40.6 MBetaineC5H11NO21
50.03 % w/vn-Dodecyl-b-D-maltosideC24H46O111
SpecimenConc.: 9.7 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: Photosystem II particles were solubilised with n-dodecyl-B-matloside and seperated using sucrose gradients. Particles were washed and concentrated, beforebeing exposed to high light (2000 uE) ...Details: Photosystem II particles were solubilised with n-dodecyl-B-matloside and seperated using sucrose gradients. Particles were washed and concentrated, beforebeing exposed to high light (2000 uE) for 30 mins before plunge freezing
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.17 sec. / Electron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 15511
EM imaging opticsEnergyfilter name: TFS Selectris / Energyfilter slit width: 10 eV

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1cryoSPARCparticle selection
2EPU3.4image acquisitionAFIS
4cryoSPARCCTF correction
7UCSF ChimeraXmodel fitting
9PHENIX1.21_5207model refinement
10cryoSPARCinitial Euler assignment
11cryoSPARCfinal Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2002863
3D reconstructionResolution: 2.74 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57560 / Symmetry type: POINT

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