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- PDB-6wj6: Cryo-EM structure of apo-Photosystem II from Synechocystis sp. PC... -

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Basic information

Entry
Database: PDB / ID: 6wj6
TitleCryo-EM structure of apo-Photosystem II from Synechocystis sp. PCC 6803
Components
  • (Cytochrome b559 subunit ...) x 2
  • (Photosystem II ...) x 11
KeywordsPHOTOSYNTHESIS / Photosystem / oxidoreductase / water-splitting / photoactivation
Function / homology
Function and homology information


plasma membrane-derived thylakoid photosystem II / oxygen evolving activity / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem II / response to herbicide / chlorophyll binding / plasma membrane-derived thylakoid membrane ...plasma membrane-derived thylakoid photosystem II / oxygen evolving activity / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem II / response to herbicide / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthetic electron transport in photosystem II / phosphate ion binding / photosynthesis, light reaction / : / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding / identical protein binding
Similarity search - Function
Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosystem II PsbX, type 1 subfamily / 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 ...Photosynthetic Reaction Center, subunit M; domain 1 / Photosystem II protein D1-like / Photosystem II PsbX, type 1 subfamily / 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 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. / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / N-FORMYLMETHIONINE / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHEOPHYTIN A ...BETA-CAROTENE / BICARBONATE ION / CHLOROPHYLL A / DIGALACTOSYL DIACYL GLYCEROL (DGDG) / : / N-FORMYLMETHIONINE / PROTOPORPHYRIN IX CONTAINING FE / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / PHEOPHYTIN A / Chem-PL9 / Chem-SQD / Photosystem II CP47 reaction center protein / Cytochrome b559 subunit alpha / Cytochrome b559 subunit beta / Photosystem II D2 protein / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein H / Photosystem II reaction center protein K / Photosystem II protein D1 2 / Photosystem II reaction center protein X / Photosystem II reaction center protein M / Photosystem II reaction center protein T / Photosystem II reaction center protein I / Photosystem II reaction center protein L
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.58 Å
AuthorsGisriel, C.J.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FG02-05ER15646 United States
CitationJournal: Joule / Year: 2020
Title: Cryo-EM Structure of Monomeric Photosystem II from Synechocystis sp. PCC 6803 Lacking the Water-Oxidation Complex
Authors: Gisriel, C.J. / Zhou, K. / Huang, H. / Debus, R.J. / Xiong, Y. / Brudvig, G.W.
History
DepositionApr 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2020Provider: repository / Type: Initial release
Revision 2.0Mar 6, 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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Structure visualization

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Assembly

Deposited unit
A: Photosystem II protein D1 2
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)286,95986
Polymers232,57513
Non-polymers54,38473
Water3,567198
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosystem II ... , 11 types, 11 molecules ABCDHIKLMTX

#1: Protein Photosystem II protein D1 2 / PSII D1 protein 2 / Photosystem II Q(B) protein 2


Mass: 39744.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P16033, photosystem II
#2: Protein Photosystem II CP47 reaction center protein / PSII 47 kDa protein / Protein CP-47


Mass: 55954.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P05429
#3: Protein Photosystem II CP43 reaction center protein / PSII 43 kDa protein / Protein CP-43


Mass: 50330.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P09193
#4: Protein Photosystem II D2 protein / PSII D2 protein / Photosystem Q(A) protein


Mass: 39519.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P09192, photosystem II
#7: Protein Photosystem II reaction center protein H / PSII-H / 6 kDa phosphoprotein


Mass: 7120.404 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P14835
#8: Protein/peptide Photosystem II reaction center protein I / PSII-I / PSII 4.4 kDa protein


Mass: 4310.109 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: Q54697
#9: Protein/peptide Photosystem II reaction center protein K / PSII-K


Mass: 5114.127 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P15819
#10: Protein/peptide Photosystem II reaction center protein L / PSII-L


Mass: 4476.145 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: Q55354
#11: Protein/peptide Photosystem II reaction center protein M / PSII-M


Mass: 3882.630 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P72701
#12: Protein/peptide Photosystem II reaction center protein T / PSII-T


Mass: 3543.308 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P74787
#13: Protein/peptide Photosystem II reaction center X protein


Mass: 4189.036 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P72575

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

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


Mass: 9454.577 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P09190
#6: Protein/peptide Cytochrome b559 subunit beta / PSII reaction center subunit VI


Mass: 4935.784 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / References: UniProt: P09191

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Sugars , 2 types, 4 molecules

#21: Sugar ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM
#22: Sugar ChemComp-DGD / DIGALACTOSYL DIACYL GLYCEROL (DGDG)


Type: saccharide / Mass: 949.299 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H96O15

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Non-polymers , 13 types, 267 molecules

#14: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#15: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: C55H72MgN4O5 / Feature type: SUBJECT OF INVESTIGATION
#16: Chemical ChemComp-PHO / PHEOPHYTIN A


Mass: 871.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H74N4O5
#17: Chemical
ChemComp-BCR / BETA-CAROTENE


Mass: 536.873 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C40H56
#18: 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.: 7 / Source method: obtained synthetically / Formula: C41H78O12S
#19: 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
#20: Chemical ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C45H86O10
#23: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Cl
#24: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3
#25: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#26: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#27: Chemical ChemComp-FME / N-FORMYLMETHIONINE


Type: L-peptide linking / Mass: 177.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H11NO3S
#28: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: apo-Photosystem II / Type: COMPLEX / Entity ID: #1-#13 / Source: NATURAL
Molecular weightValue: 0.267067 MDa / Experimental value: NO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Buffer solutionpH: 7
Details: 10 mM HEPES pH 7.0 100 mM NaCl 0.03% beta-dodecylmaltoside
SpecimenConc.: 0.025 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Monodisperse single particles
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K

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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: 48.07 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: RELION / Version: 3.1 / Category: 3D reconstruction
CTF correctionType: NONE
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.58 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 212640 / Symmetry type: POINT

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