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- PDB-9iox: Cryo-EM structure of a TEF30-associated intermediate PSII core di... -

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Basic information

Entry
Database: PDB / ID: 9iox
TitleCryo-EM structure of a TEF30-associated intermediate PSII core dimer complex, type II, from Chlamydomonas reinhardtii
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 12
  • Chloroplast photosystem II subunit X
  • PDZ domain-containing protein
KeywordsPHOTOSYNTHESIS / photosystem II / PSII repair / PSII assembly / PSII intermediate / TEF30
Function / homology
Function and homology information


oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem II ...oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / chlorophyll binding / photosynthetic electron transport in photosystem II / phosphate ion binding / photosynthesis, light reaction / chloroplast thylakoid membrane / : / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) ...Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II CP43 reaction centre protein 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 reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / Photosystem II protein D1 / 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 / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / PDZ domain / PDZ domain profile. / PDZ domain / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHEOPHYTIN A / Chem-PL9 ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / PDZ domain-containing protein / Uncharacterized protein / Photosystem II D2 protein / Photosystem II protein D1 / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein K / Photosystem II reaction center protein H / Photosystem II reaction center protein L / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein T / Cytochrome b559 subunit alpha / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein I / Photosystem II reaction center protein Z / Photosystem II reaction center protein M / Cytochrome b559 subunit beta
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsWang, Y. / Wang, C. / Li, A. / Liu, Z.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To Be Published
Title: TEF30 fulfills versatile functions in the photosystem II repair process
Authors: Wang, Y. / Wang, C. / Li, A. / Liu, Z.
History
DepositionJul 9, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 21, 2025Data content type: Primary map / Data content type: Primary map / 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
G: PDZ domain-containing protein
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
T: Photosystem II reaction center protein T
V: Photosystem II reaction center protein Psb30
X: Chloroplast photosystem II subunit X
Z: Photosystem II reaction center protein Z
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
g: PDZ domain-containing protein
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
t: Photosystem II reaction center protein T
v: Photosystem II reaction center protein Psb30
x: Chloroplast photosystem II subunit X
z: Photosystem II reaction center protein Z
hetero molecules


Theoretical massNumber of molelcules
Total (without water)609,069168
Polymers503,03732
Non-polymers106,032136
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Photosystem II ... , 12 types, 24 molecules AaBbCcDdHhIiKkLlMmTtVvZz

#1: Protein Photosystem II protein D1 / PSII D1 protein / 32 kDa thylakoid membrane protein / Photosystem II Q(B) protein


Mass: 36263.301 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P07753, photosystem II
#2: Protein Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47


Mass: 52938.281 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P37255
#3: Protein Photosystem II CP43 reaction center protein / PSII 43 kDa protein / Protein CP-43 / Protein P6


Mass: 49473.355 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P10898
#4: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 39342.836 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P06007, photosystem II
#8: Protein Photosystem II reaction center protein H / PSII-H / Photosystem II 8 kDa phosphoprotein


Mass: 7751.167 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P22666
#9: Protein/peptide Photosystem II reaction center protein I / PSII-I / PSII 4.8 kDa protein


Mass: 3902.687 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P59763
#10: Protein/peptide Photosystem II reaction center protein K / PSII-K


Mass: 4147.979 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P18263
#11: Protein/peptide Photosystem II reaction center protein L / PSII-L


Mass: 4431.229 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P32974
#12: Protein/peptide Photosystem II reaction center protein M / PSII-M


Mass: 2971.595 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P92277
#13: Protein/peptide Photosystem II reaction center protein T / PSII-T


Mass: 3265.905 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P37256
#14: Protein/peptide Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein Ycf12


Mass: 3087.760 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P50370
#16: Protein Photosystem II reaction center protein Z / PSII-Z


Mass: 6466.732 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P92276

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

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


Mass: 8484.632 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: P48268
#6: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 3535.273 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: Q08363

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Protein / Protein/peptide , 2 types, 4 molecules GgXx

#15: Protein/peptide Chloroplast photosystem II subunit X


Mass: 3056.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Chlamydomonas reinhardtii (plant) / References: UniProt: A8I846
#7: Protein PDZ domain-containing protein


Mass: 22399.248 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlamydomonas reinhardtii (plant) / Gene: CHLRE_01g031100v5 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2K3E6S5

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Sugars , 2 types, 8 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 / Feature type: SUBJECT OF INVESTIGATION
#25: Sugar ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Feature type: SUBJECT OF INVESTIGATION / Comment: detergent*YM

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Non-polymers , 10 types, 128 molecules

#17: 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
#18: Chemical...
ChemComp-CLA / CHLOROPHYLL A


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


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


Mass: 536.873 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#21: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C45H86O10 / Feature type: SUBJECT OF INVESTIGATION
#22: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#23: 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
#26: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#27: 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 / Feature type: SUBJECT OF INVESTIGATION
#28: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY
Has protein modificationN

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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: TEF30-associated PSII core dimer complex, type II / Type: COMPLEX / Entity ID: #1-#16 / Source: NATURAL
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 33509 / Symmetry type: POINT

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