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- PDB-7nhp: Structure of PSII-I (PSII with Psb27, Psb28, and Psb34) -

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Basic information

Entry
Database: PDB / ID: 7nhp
TitleStructure of PSII-I (PSII with Psb27, Psb28, and Psb34)
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 15
  • Tsl0063 protein
KeywordsPHOTOSYNTHESIS / Membrane Protein Biogenesis Assembly Factors Photosystem II
Function / homology
Function and homology information


photosystem II repair / thylakoid lumen / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / thylakoid / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor ...photosystem II repair / thylakoid lumen / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / thylakoid / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / photosynthesis, light reaction / phosphate ion binding / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II Psb27, cyanobacteria / : / Photosystem II Psb28, class 1 / Photosystem II Pbs27 / Photosystem II Pbs27 superfamily / Photosystem II Psb28, class 1 superfamily / Psb28 protein / Photosystem II Pbs27 / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 ...Photosystem II Psb27, cyanobacteria / : / Photosystem II Psb28, class 1 / Photosystem II Pbs27 / Photosystem II Pbs27 superfamily / Photosystem II Psb28, class 1 superfamily / Psb28 protein / Photosystem II Pbs27 / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II PsbX, type 1 subfamily / 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 CP43 reaction centre protein / Photosystem II CP43 reaction centre protein superfamily / Photosystem II PsbK / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II CP47 reaction centre protein / Photosystem II PsbI / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / 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 reaction centre protein H superfamily / 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 / Photosystem II 10 kDa phosphoprotein / Cytochrome b559 subunits heme-binding site signature. / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Photosystem II protein D1 / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
BETA-CAROTENE / CHLOROPHYLL A / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / : / PHEOPHYTIN A / Chem-PL9 / Photosystem II protein D1 1 ...BETA-CAROTENE / CHLOROPHYLL A / : / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / : / PHEOPHYTIN A / Chem-PL9 / Photosystem II protein D1 1 / Photosystem II D2 protein / Photosystem II assembly factor lipoprotein Psb27 / Photosystem II reaction center protein M / Photosystem II reaction center protein Z / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein L / Cytochrome b559 subunit beta / Cytochrome b559 subunit alpha / Photosystem II reaction center protein T / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein H / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein I / Photosystem II assembly factor Psb28 protein / Photosystem II assembly protein Psb34 / Photosystem II reaction center protein K / Photosystem II reaction center protein X
Similarity search - Component
Biological speciesThermosynechococcus elongatus BP-1 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsZabret, J. / Bohn, S. / Schuller, S.K. / Arnolds, O. / Chan, A. / Tajkhorshid, E. / Stoll, R. / Engel, B.D. / Rudack, T. / Schuller, J.M. / Nowaczyk, M.M.
Funding support Germany, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)NO 836/4-1 Germany
German Research Foundation (DFG)836/3-2 Germany
German Research Foundation (DFG)SCHU 3364/1-1 Germany
CitationJournal: Nat Plants / Year: 2021
Title: Structural insights into photosystem II assembly.
Authors: Jure Zabret / Stefan Bohn / Sandra K Schuller / Oliver Arnolds / Madeline Möller / Jakob Meier-Credo / Pasqual Liauw / Aaron Chan / Emad Tajkhorshid / Julian D Langer / Raphael Stoll / Anja ...Authors: Jure Zabret / Stefan Bohn / Sandra K Schuller / Oliver Arnolds / Madeline Möller / Jakob Meier-Credo / Pasqual Liauw / Aaron Chan / Emad Tajkhorshid / Julian D Langer / Raphael Stoll / Anja Krieger-Liszkay / Benjamin D Engel / Till Rudack / Jan M Schuller / Marc M Nowaczyk /
Abstract: Biogenesis of photosystem II (PSII), nature's water-splitting catalyst, is assisted by auxiliary proteins that form transient complexes with PSII components to facilitate stepwise assembly events. ...Biogenesis of photosystem II (PSII), nature's water-splitting catalyst, is assisted by auxiliary proteins that form transient complexes with PSII components to facilitate stepwise assembly events. Using cryo-electron microscopy, we solved the structure of such a PSII assembly intermediate from Thermosynechococcus elongatus at 2.94 Å resolution. It contains three assembly factors (Psb27, Psb28 and Psb34) and provides detailed insights into their molecular function. Binding of Psb28 induces large conformational changes at the PSII acceptor side, which distort the binding pocket of the mobile quinone (Q) and replace the bicarbonate ligand of non-haem iron with glutamate, a structural motif found in reaction centres of non-oxygenic photosynthetic bacteria. These results reveal mechanisms that protect PSII from damage during biogenesis until water splitting is activated. Our structure further demonstrates how the PSII active site is prepared for the incorporation of the MnCaO cluster, which performs the unique water-splitting reaction.
History
DepositionFeb 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 2.0May 1, 2024Group: Data collection / Database references / Non-polymer description
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_chiral
Item: _chem_comp.formula / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: Photosystem II protein D1 1
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
T: Photosystem II reaction center protein T
X: Photosystem II reaction center X protein
y: Photosystem II reaction center protein Ycf12
Z: Photosystem II reaction center protein Z
1: Photosystem II lipoprotein Psb27
2: Photosystem II reaction center Psb28 protein
3: Tsl0063 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)326,20978
Polymers280,08018
Non-polymers46,12860
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area144690 Å2
ΔGint-1162 kcal/mol
Surface area89100 Å2

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Components

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Photosystem II ... , 15 types, 15 molecules ABCDHIKLMTXyZ12

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


Mass: 39762.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: P0A444, photosystem II
#2: Protein Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47


Mass: 56656.457 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: Q8DIQ1
#3: Protein Photosystem II CP43 reaction center protein / PSII 43 kDa protein / Protein CP-43


Mass: 50287.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: Q8DIF8
#4: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem II Q(A) protein


Mass: 39388.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: Q8CM25, photosystem II
#7: Protein Photosystem II reaction center protein H / PSII-H


Mass: 7358.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: Q8DJ43
#8: Protein/peptide Photosystem II reaction center protein I / PSII-I / PSII 4.4 kDa protein


Mass: 4410.245 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: Q8DJZ6
#9: Protein/peptide Photosystem II reaction center protein K / PSII-K


Mass: 5028.083 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: Q9F1K9
#10: Protein/peptide Photosystem II reaction center protein L / PSII-L


Mass: 4299.044 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: Q8DIN8
#11: Protein/peptide Photosystem II reaction center protein M / PSII-M


Mass: 3981.673 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: Q8DHA7
#12: Protein/peptide Photosystem II reaction center protein T / PSII-Tc


Mass: 3878.728 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: Q8DIQ0
#13: Protein/peptide Photosystem II reaction center X protein


Mass: 4322.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: Q9F1R6
#14: Protein/peptide Photosystem II reaction center protein Ycf12


Mass: 5039.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: Q8DJI1
#15: Protein Photosystem II reaction center protein Z / PSII-Z


Mass: 6766.187 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: Q8DHJ2
#16: Protein Photosystem II lipoprotein Psb27 / Photosystem II 11 kDa protein


Mass: 15120.396 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: Q8DG60
#17: Protein Photosystem II reaction center Psb28 protein / Photosystem II 13 kDa protein / Photosystem II reaction center W protein


Mass: 13188.769 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: Q8DLJ8

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Cytochrome b559 subunit ... , 2 types, 2 molecules EF

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


Mass: 9580.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: Q8DIP0
#6: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 5067.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: Q8DIN9

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Protein , 1 types, 1 molecules 3

#18: Protein Tsl0063 protein


Mass: 5943.893 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Thermosynechococcus elongatus BP-1 (bacteria)
References: UniProt: Q8DMP8

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Non-polymers , 10 types, 60 molecules

#19: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#20: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#21: Chemical ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74N4O5
#22: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#23: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C40H56
#24: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


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


Mass: 787.158 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C45H86O10
#26: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#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.: 1 / Source method: obtained synthetically / Formula: C53H80O2
#28: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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Details

Has ligand of interestN

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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: PsII-I / Type: COMPLEX / Entity ID: #1-#18 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 57268 / Symmetry type: POINT

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