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- EMDB-30547: Cryo-EM Structure of PSII at 1.95 angstrom resolution -

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Basic information

Entry
Database: EMDB / ID: EMD-30547
TitleCryo-EM Structure of PSII at 1.95 angstrom resolution
Map data
Sample
  • Complex: PSII dimer
    • Protein or peptide: x 20 types
  • Ligand: x 19 types
Function / homology
Function and homology information


photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / photosystem II / photosystem II reaction center / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II ...photosystem II assembly / photosystem II stabilization / oxygen evolving activity / photosystem II oxygen evolving complex / photosystem II / photosystem II reaction center / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II / extrinsic component of membrane / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / phosphate ion binding / photosynthesis / respiratory electron transport chain / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II protein Y (PsbY) / Photosystem II PsbY / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily ...Photosystem II protein Y (PsbY) / Photosystem II PsbY / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / 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 CP43 reaction centre protein superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / 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 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 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 / 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. / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
Photosystem II CP47 reaction center protein / Photosystem II extrinsic protein O / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein X / Photosystem II reaction center protein Z / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II extrinsic protein V / Photosystem II reaction center protein Y / Cytochrome b559 subunit alpha ...Photosystem II CP47 reaction center protein / Photosystem II extrinsic protein O / Photosystem II reaction center protein Psb30 / Photosystem II reaction center protein X / Photosystem II reaction center protein Z / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II extrinsic protein V / Photosystem II reaction center protein Y / Cytochrome b559 subunit alpha / Cytochrome b559 subunit beta / Photosystem II reaction center protein I / Photosystem II reaction center protein L / Photosystem II reaction center protein M / Photosystem II reaction center protein T / Photosystem II reaction center protein H / Photosystem II reaction center protein K / Photosystem II protein D1 / Photosystem II extrinsic protein U / Photosystem II reaction center protein J
Similarity search - Component
Biological speciesThermosynechococcus vulcanus (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.95 Å
AuthorsKato K / Miyazaki N / Hamaguchi T / Nakajima Y / Akita F / Yonekura K / Shen JR
CitationJournal: Commun Biol / Year: 2021
Title: High-resolution cryo-EM structure of photosystem II reveals damage from high-dose electron beams.
Authors: Koji Kato / Naoyuki Miyazaki / Tasuku Hamaguchi / Yoshiki Nakajima / Fusamichi Akita / Koji Yonekura / Jian-Ren Shen /
Abstract: Photosystem II (PSII) plays a key role in water-splitting and oxygen evolution. X-ray crystallography has revealed its atomic structure and some intermediate structures. However, these structures are ...Photosystem II (PSII) plays a key role in water-splitting and oxygen evolution. X-ray crystallography has revealed its atomic structure and some intermediate structures. However, these structures are in the crystalline state and its final state structure has not been solved. Here we analyzed the structure of PSII in solution at 1.95 Å resolution by single-particle cryo-electron microscopy (cryo-EM). The structure obtained is similar to the crystal structure, but a PsbY subunit was visible in the cryo-EM structure, indicating that it represents its physiological state more closely. Electron beam damage was observed at a high-dose in the regions that were easily affected by redox states, and reducing the beam dosage by reducing frames from 50 to 2 yielded a similar resolution but reduced the damage remarkably. This study will serve as a good indicator for determining damage-free cryo-EM structures of not only PSII but also all biological samples, especially redox-active metalloproteins.
History
DepositionSep 15, 2020-
Header (metadata) releaseMar 31, 2021-
Map releaseMar 31, 2021-
UpdateApr 7, 2021-
Current statusApr 7, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7d1t
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7d1t
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30547.png

Downloads & links

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Map

FileDownload / File: emd_30547.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.822 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.097950734 - 0.24216053
Average (Standard dev.)0.00016159083 (±0.0045615123)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 328.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8220.8220.822
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z328.800328.800328.800
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0980.2420.000

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Supplemental data

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Half map: #1

Fileemd_30547_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_30547_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : PSII dimer

EntireName: PSII dimer
Components
  • Complex: PSII dimer
    • Protein or peptide: Photosystem II protein D1
    • Protein or peptide: Photosystem II CP47 reaction center protein
    • Protein or peptide: Photosystem II CP43 reaction center protein
    • Protein or peptide: Photosystem II D2 protein
    • Protein or peptide: Cytochrome b559 subunit alpha
    • Protein or peptide: Cytochrome b559 subunit beta
    • Protein or peptide: Photosystem II reaction center protein H
    • Protein or peptide: Photosystem II reaction center protein I
    • Protein or peptide: Photosystem II reaction center protein J
    • Protein or peptide: Photosystem II reaction center protein K
    • Protein or peptide: Photosystem II reaction center protein L
    • Protein or peptide: Photosystem II reaction center protein M
    • Protein or peptide: Photosystem II manganese-stabilizing polypeptide
    • Protein or peptide: Photosystem II reaction center protein T
    • Protein or peptide: Photosystem II 12 kDa extrinsic protein
    • Protein or peptide: Cytochrome c-550
    • Protein or peptide: Photosystem II reaction center protein Ycf12
    • Protein or peptide: Photosystem II reaction center protein X
    • Protein or peptide: Photosystem II reaction center protein Z
    • Protein or peptide: Photosystem II protein Y
  • Ligand: CA-MN4-O5 CLUSTER
  • Ligand: FE (II) ION
  • Ligand: CHLORIDE IONChloride
  • Ligand: CHLOROPHYLL A
  • Ligand: PHEOPHYTIN APheophytin
  • Ligand: BETA-CAROTENEΒ-Carotene
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: 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
  • Ligand: UNKNOWN LIGAND
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: BICARBONATE IONBicarbonate
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: MAGNESIUM ION
  • Ligand: HEME C
  • Ligand: (3R)-beta,beta-caroten-3-ol
  • Ligand: water

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Supramolecule #1: PSII dimer

SupramoleculeName: PSII dimer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#20
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 725 KDa

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Macromolecule #1: Photosystem II protein D1

MacromoleculeName: Photosystem II protein D1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 37.029234 KDa
SequenceString: ANLWERFCNW VTSTDNRLYV GWFGVIMIPT LLAATICFVI AFIAAPPVDI DGIREPVSGS LLYGNNIITG AVVPSSNAIG LHFYPIWEA ASLDEWLYNG GPYQLIIFHF LLGASCYMGR QWELSYRLGM RPWICVAYSA PLASAFAVFL IYPIGQGSFS D GMPLGISG ...String:
ANLWERFCNW VTSTDNRLYV GWFGVIMIPT LLAATICFVI AFIAAPPVDI DGIREPVSGS LLYGNNIITG AVVPSSNAIG LHFYPIWEA ASLDEWLYNG GPYQLIIFHF LLGASCYMGR QWELSYRLGM RPWICVAYSA PLASAFAVFL IYPIGQGSFS D GMPLGISG TFNFMIVFQA EHNILMHPFH QLGVAGVFGG ALFCAMHGSL VTSSLIRETT ETESANYGYK FGQEEETYNI VA AHGYFGR LIFQYASFNN SRSLHFFLAA WPVVGVWFAA LGISTMAFNL NGFNFNHSVI DAKGNVINTW ADIINRANLG MEV MHERNA HNFPLDLA

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Macromolecule #2: Photosystem II CP47 reaction center protein

MacromoleculeName: Photosystem II CP47 reaction center protein / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 56.068742 KDa
SequenceString: GLPWYRVHTV LINDPGRLIA AHLMHTALVA GWAGSMALYE LATFDPSDPV LNPMWRQGMF VLPFMARLGV TGSWSGWSIT GETGIDPGF WSFEGVALAH IVLSGLLFLA ACWHWVYWDL ELFRDPRTGE PALDLPKMFG IHLFLAGLLC FGFGAFHLTG L FGPGMWVS ...String:
GLPWYRVHTV LINDPGRLIA AHLMHTALVA GWAGSMALYE LATFDPSDPV LNPMWRQGMF VLPFMARLGV TGSWSGWSIT GETGIDPGF WSFEGVALAH IVLSGLLFLA ACWHWVYWDL ELFRDPRTGE PALDLPKMFG IHLFLAGLLC FGFGAFHLTG L FGPGMWVS DPYGLTGSVQ PVAPEWGPDG FNPYNPGGVV AHHIAAGIVG IIAGLFHILV RPPQRLYKAL RMGNIETVLS SS IAAVFFA AFVVAGTMWY GSATTPIELF GPTRYQWDSS YFQQEINRRV QASLASGATL EEAWSAIPEK LAFYDYIGNN PAK GGLFRT GPMNKGDGIA QAWKGHAVFR NKEGEELFVR RMPAFFESFP VILTDKNGVV KADIPFRRAE SKYSFEQQGV TVSF YGGEL NGQTFTDPPT VKSYARKAIF GEIFEFDTET LNSDGIFRTS PRGWFTFAHA VFALLFFFGH IWHGARTLFR DVFSG IDPE LSPEQVEWGF YQKVGDVTTR K

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Macromolecule #3: Photosystem II CP43 reaction center protein

MacromoleculeName: Photosystem II CP43 reaction center protein / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 49.20725 KDa
SequenceString: ATNRDQESSG FAWWAGNARL INLSGKLLGA HVAHAGLIVF WAGAMTLFEL AHFIPEKPMY EQGLILIPHI ATLGWGVGPG GEVVDTFPF FVVGVVHLIS SAVLGFGGVY HAIRGPETLE EYSSFFGYDW KDKNKMTTIL GFHLIVLGIG ALLLVAKAMF F GGLYDTWA ...String:
ATNRDQESSG FAWWAGNARL INLSGKLLGA HVAHAGLIVF WAGAMTLFEL AHFIPEKPMY EQGLILIPHI ATLGWGVGPG GEVVDTFPF FVVGVVHLIS SAVLGFGGVY HAIRGPETLE EYSSFFGYDW KDKNKMTTIL GFHLIVLGIG ALLLVAKAMF F GGLYDTWA PGGGDVRVIT NPTLDPRVIF GYLLKSPFGG EGWIVSVNNL EDVVGGHIWI GLICIAGGIW HILTTPFGWA RR AFIWSGE AYLSYSLGAL SMMGFIATCF VWFNNTVYPS EFYGPTGPEA SQAQAMTFLI RDQKLGANVG SAQGPTGLGK YLM RSPTGE IIFGGETMRF WDFRGPWLEP LRGPNGLDLN KIKNDIQPWQ ERRAAEYMTH APLGSLNSVG GVATEINSVN FVSP RSWLA TSHFVLAFFF LVGHLWHAGR ARAAAAGFEK GIDRESEPVL SMPSLD

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Macromolecule #4: Photosystem II D2 protein

MacromoleculeName: Photosystem II D2 protein / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 38.419941 KDa
SequenceString: ERGWFDILDD WLKRDRFVFV GWSGILLFPC AYLALGGWLT GTTFVTSWYT HGLASSYLEG CNFLTVAVST PANSMGHSLL LLWGPEAQG DFTRWCQLGG LWTFIALHGA FGLIGFMLRQ FEIARLVGVR PYNAIAFSAP IAVFVSVFLI YPLGQSSWFF A PSFGVAAI ...String:
ERGWFDILDD WLKRDRFVFV GWSGILLFPC AYLALGGWLT GTTFVTSWYT HGLASSYLEG CNFLTVAVST PANSMGHSLL LLWGPEAQG DFTRWCQLGG LWTFIALHGA FGLIGFMLRQ FEIARLVGVR PYNAIAFSAP IAVFVSVFLI YPLGQSSWFF A PSFGVAAI FRFLLFFQGF HNWTLNPFHM MGVAGVLGGA LLCAIHGATV ENTLFQDGEG ASTFRAFNPT QAEETYSMVT AN RFWSQIF GIAFSNKRWL HFFMLFVPVT GLWMSAIGVV GLALNLRSYD FISQEIRAAE DPEFETFYTK NLLLNEGIRA WMA PQDQP(HSK) ENFVFPEEVL PRGNAL

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Macromolecule #5: Cytochrome b559 subunit alpha

MacromoleculeName: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 9.321515 KDa
SequenceString:
TTGERPFSDI ITSVRYWVIH SITIPALFIA GWLFVSTGLA YDVFGTPRPD SYYAQEQRSI PLVTDRFEAK QQVETFLEQL K

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Macromolecule #6: Cytochrome b559 subunit beta

MacromoleculeName: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 3.868611 KDa
SequenceString:
SYPIFTVRWV AVHTLAVPTI FFLGAIAAMQ FIQR

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Macromolecule #7: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 7.057349 KDa
SequenceString:
ARRTWLGDIL RPLNSEYGKV APGWGTTPLM AVFMGLFLVF LLIILEIYNS TLILDGVNVS WKA

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Macromolecule #8: Photosystem II reaction center protein I

MacromoleculeName: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 4.195983 KDa
SequenceString:
(FME)ETLKITVYI VVTFFVLLFV FGFLSGDPAR NPKRKD

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Macromolecule #9: Photosystem II reaction center protein J

MacromoleculeName: Photosystem II reaction center protein J / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 3.756439 KDa
SequenceString:
EGGRIPLWIV ATVAGMGVIV IVGLFFYGAY AGLGSSL

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Macromolecule #10: Photosystem II reaction center protein K

MacromoleculeName: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 4.101911 KDa
SequenceString:
KLPEAYAIFD PLVDVLPVIP VLFLALAFVW QAAVGFR

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Macromolecule #11: Photosystem II reaction center protein L

MacromoleculeName: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 4.299044 KDa
SequenceString:
MEPNPNRQPV ELNRTSLYLG LLLILVLALL FSSYFFN

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Macromolecule #12: Photosystem II reaction center protein M

MacromoleculeName: Photosystem II reaction center protein M / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 3.835527 KDa
SequenceString:
(FME)EVNQLGLIA TALFVLVPSV FLIILYVQTE SQQK

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Macromolecule #13: Photosystem II manganese-stabilizing polypeptide

MacromoleculeName: Photosystem II manganese-stabilizing polypeptide / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 26.651707 KDa
SequenceString: QTLTYDDIVG TGLANKCPTL DDTARGAYPI DSSQTYRIAR LCLQPTTFLV KEEPKNKRQE AEFVPTKLVT RETTSLDQIQ GELKVNSDG SLTFVEEDGI DFQPVTVQMA GGERIPLLFT VKNLVASTQP NVTSITTSTD FKGEFNVPSY RTANFLDPKG R GLASGYDS ...String:
QTLTYDDIVG TGLANKCPTL DDTARGAYPI DSSQTYRIAR LCLQPTTFLV KEEPKNKRQE AEFVPTKLVT RETTSLDQIQ GELKVNSDG SLTFVEEDGI DFQPVTVQMA GGERIPLLFT VKNLVASTQP NVTSITTSTD FKGEFNVPSY RTANFLDPKG R GLASGYDS AIALPQAKEE ELARANVKRF SLTKGQISLN VAKVDGRTGE IAGTFESEQL SDDDMGAHEP HEVKIQGVFY AS IEPA

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Macromolecule #14: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 3.777559 KDa
SequenceString:
(FME)ETITYVFIF ACIIALFFFA IFFREPPRIT K

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Macromolecule #15: Photosystem II 12 kDa extrinsic protein

MacromoleculeName: Photosystem II 12 kDa extrinsic protein / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 10.966317 KDa
SequenceString:
ELVNVVDEKL GTAYGEKIDL NNTNIAAFIQ YRGLYPTLAK LIVKNAPYES VEDVLNIPGL TERQKQILRE NLEHFTVTEV ETALVEGGD RYNNGLYK

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Macromolecule #16: Cytochrome c-550

MacromoleculeName: Cytochrome c-550 / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 15.148255 KDa
SequenceString:
AELTPEVLTV PLNSEGKTIT LTEKQYLEGK RLFQYACASC HVGGITKTNP SLDLRTETLA LATPPRDNIE GLVDYMKNPT TYDGEQEIA EVHPSLRSAD IFPKMRNLTE KDLVAIAGHI LVEPKILGDK WGGGKVYY

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Macromolecule #17: Photosystem II reaction center protein Ycf12

MacromoleculeName: Photosystem II reaction center protein Ycf12 / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 3.228035 KDa
SequenceString:
EVIAQLTMIA MIGIAGPMII FLLAVRRGNL

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Macromolecule #18: Photosystem II reaction center protein X

MacromoleculeName: Photosystem II reaction center protein X / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 4.19103 KDa
SequenceString:
TITPSLKGFF IGLLSGAVVL GLTFAVLIAI SQIDKVQRSL

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Macromolecule #19: Photosystem II reaction center protein Z

MacromoleculeName: Photosystem II reaction center protein Z / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 6.766187 KDa
SequenceString:
MTILFQLALA ALVILSFVMV IGVPVAYASP QDWDRSKQLI FLGSGLWIAL VLVVGVLNFF VV

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Macromolecule #20: Photosystem II protein Y

MacromoleculeName: Photosystem II protein Y / type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vulcanus (bacteria)
Molecular weightTheoretical: 3.859732 KDa
SequenceString:
DWRVLVVLLP VLLAAGWAVR NILPYAVKQV QKLL

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Macromolecule #21: CA-MN4-O5 CLUSTER

MacromoleculeName: CA-MN4-O5 CLUSTER / type: ligand / ID: 21 / Number of copies: 2 / Formula: OEX
Molecular weightTheoretical: 339.827 Da
Chemical component information

ChemComp-OEX:
CA-MN4-O5 CLUSTER

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Macromolecule #22: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 22 / Number of copies: 2 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

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Macromolecule #23: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 23 / Number of copies: 4 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #24: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 24 / Number of copies: 70 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

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Macromolecule #25: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 25 / Number of copies: 4 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A / Pheophytin

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Macromolecule #26: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 26 / Number of copies: 20 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE / Β-Carotene

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Macromolecule #27: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

MacromoleculeName: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
type: ligand / ID: 27 / Number of copies: 8 / Formula: SQD
Molecular weightTheoretical: 795.116 Da
Chemical component information

ChemComp-SQD:
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

+
Macromolecule #28: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,...

MacromoleculeName: 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
type: ligand / ID: 28 / Number of copies: 4 / Formula: PL9
Molecular weightTheoretical: 749.201 Da
Chemical component information

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

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Macromolecule #29: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 29 / Number of copies: 36 / Formula: UNL
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

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Macromolecule #30: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 30 / Number of copies: 10 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

ChemComp-LMG:
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

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Macromolecule #31: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 31 / Number of copies: 8 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #32: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 32 / Number of copies: 8 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

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Macromolecule #33: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 33 / Number of copies: 2 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION / pH buffer*YM / Bicarbonate

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Macromolecule #34: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 34 / Number of copies: 10 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

ChemComp-LHG:
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / phospholipid*YM / Phosphatidylglycerol

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Macromolecule #35: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 35 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

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Macromolecule #36: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 36 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

+
Macromolecule #37: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 37 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C / Heme C

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Macromolecule #38: (3R)-beta,beta-caroten-3-ol

MacromoleculeName: (3R)-beta,beta-caroten-3-ol / type: ligand / ID: 38 / Number of copies: 2 / Formula: RRX
Molecular weightTheoretical: 552.872 Da
Chemical component information

ChemComp-RRX:
(3R)-beta,beta-caroten-3-ol / Β-Cryptoxanthin

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Macromolecule #39: water

MacromoleculeName: water / type: ligand / ID: 39 / Number of copies: 2432 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2.0 mg/mL
BufferpH: 6 / Component:
ConcentrationFormula
20.0 mMMES-NaOH
0.04 %DDM
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 83.0 e/Å2

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Image processing

CTF correctionSoftware - Name: CTFFIND (ver. 4.1)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3wu2

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 1.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 174099
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3wu2

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7d1t:
Cryo-EM Structure of PSII at 1.95 angstrom resolution

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