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- EMDB-12336: Structure of PSII-I (PSII with Psb27, Psb28, and Psb34) -

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Basic information

Entry
Database: EMDB / ID: EMD-12336
TitleStructure of PSII-I (PSII with Psb27, Psb28, and Psb34)
Map dataCryoEM Map of PSII-I (PSII-Psb28-Psb34-Psb27)
Sample
  • Complex: PsII-I
    • Protein or peptide: x 18 types
  • Ligand: x 10 types
KeywordsMembrane Protein Biogenesis Assembly Factors Photosystem II / PHOTOSYNTHESIS
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 / 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 / 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 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 / 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
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 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.72 Å
AuthorsZabret J / Bohn S
Funding support Germany, 3 items
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, 2021-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.007
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.007
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7nhp
  • Surface level: 0.007
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_12336.png

Downloads & links

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Map

FileDownload / File: emd_12336.map.gz / Format: CCP4 / Size: 67 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM Map of PSII-I (PSII-Psb28-Psb34-Psb27)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 260 pix.
= 283.4 Å		1.09 Å/pix.
x 260 pix.
= 283.4 Å		1.09 Å/pix.
x 260 pix.
= 283.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007 / Movie #1: 0.007
Minimum - Maximum-0.034819007 - 0.061757557
Average (Standard dev.)0.000003107878 (±0.001998797)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions260260260
Spacing260260260
CellA=B=C: 283.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z260260260
origin x/y/z0.0000.0000.000
length x/y/z283.400283.400283.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS260260260
D min/max/mean-0.0350.0620.000

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Supplemental data

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Sample components

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Entire : PsII-I

EntireName: PsII-I
Components
  • Complex: PsII-I
    • Protein or peptide: Photosystem II protein D1 1
    • 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 K
    • Protein or peptide: Photosystem II reaction center protein L
    • Protein or peptide: Photosystem II reaction center protein M
    • Protein or peptide: Photosystem II reaction center protein T
    • Protein or peptide: Photosystem II reaction center X protein
    • Protein or peptide: Photosystem II reaction center protein Ycf12
    • Protein or peptide: Photosystem II reaction center protein Z
    • Protein or peptide: Photosystem II lipoprotein Psb27
    • Protein or peptide: Photosystem II reaction center Psb28 protein
    • Protein or peptide: Tsl0063 protein
  • Ligand: MANGANESE (II) ION
  • Ligand: CHLORIDE ION
  • Ligand: PHEOPHYTIN A
  • Ligand: CHLOROPHYLL A
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: FE (III) ION
  • 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: PROTOPORPHYRIN IX CONTAINING FE

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Supramolecule #1: PsII-I

SupramoleculeName: PsII-I / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#18
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)

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Macromolecule #1: Photosystem II protein D1 1

MacromoleculeName: Photosystem II protein D1 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)
Molecular weightTheoretical: 39.762309 KDa
SequenceString: MTTTLQRRES ANLWERFCNW VTSTDNRLYV GWFGVIMIPT LLAATICFVI AFIAAPPVDI DGIREPVSGS LLYGNNIITG AVVPSSNAI GLHFYPIWEA ASLDEWLYNG GPYQLIIFHF LLGASCYMGR QWELSYRLGM RPWICVAYSA PLASAFAVFL I YPIGQGSF ...String:
MTTTLQRRES ANLWERFCNW VTSTDNRLYV GWFGVIMIPT LLAATICFVI AFIAAPPVDI DGIREPVSGS LLYGNNIITG AVVPSSNAI GLHFYPIWEA ASLDEWLYNG GPYQLIIFHF LLGASCYMGR QWELSYRLGM RPWICVAYSA PLASAFAVFL I YPIGQGSF SDGMPLGISG TFNFMIVFQA EHNILMHPFH QLGVAGVFGG ALFCAMHGSL VTSSLIRETT ETESANYGYK FG QEEETYN IVAAHGYFGR LIFQYASFNN SRSLHFFLAA WPVVGVWFTA LGISTMAFNL NGFNFNHSVI DAKGNVINTW ADI INRANL GMEVMHERNA HNFPLDLASA ESAPVAMIAP SING

UniProtKB: Photosystem II protein D1 1

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)
Molecular weightTheoretical: 56.656457 KDa
SequenceString: MGLPWYRVHT VLINDPGRLI AAHLMHTALV AGWAGSMALY ELATFDPSDP VLNPMWRQGM FVLPFMARLG VTGSWSGWSI TGETGIDPG FWSFEGVALA HIVLSGLLFL AACWHWVYWD LELFRDPRTG EPALDLPKMF GIHLFLAGLL CFGFGAFHLT G LFGPGMWV ...String:
MGLPWYRVHT VLINDPGRLI AAHLMHTALV AGWAGSMALY ELATFDPSDP VLNPMWRQGM FVLPFMARLG VTGSWSGWSI TGETGIDPG FWSFEGVALA HIVLSGLLFL AACWHWVYWD LELFRDPRTG EPALDLPKMF GIHLFLAGLL CFGFGAFHLT G LFGPGMWV SDPYGLTGSV QPVAPEWGPD GFNPYNPGGV VAHHIAAGIV GIIAGLFHIL VRPPQRLYKA LRMGNIETVL SS SIAAVFF AAFVVAGTMW YGSATTPIEL FGPTRYQWDS SYFQQEINRR VQASLASGAT LEEAWSAIPE KLAFYDYIGN NPA KGGLFR TGPMNKGDGI AQAWKGHAVF RNKEGEELFV RRMPAFFESF PVILTDKNGV VKADIPFRRA ESKYSFEQQG VTVS FYGGE LNGQTFTDPP TVKSYARKAI FGEIFEFDTE TLNSDGIFRT SPRGWFTFAH AVFALLFFFG HIWHGARTLF RDVFS GIDP ELSPEQVEWG FYQKVGDVTT RRKEAV

UniProtKB: Photosystem II CP47 reaction center protein

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)
Molecular weightTheoretical: 50.2875 KDa
SequenceString: MVTLSSNSIF ATNRDQESSG FAWWAGNARL INLSGKLLGA HVAHAGLIVF WAGAMTLFEL AHFIPEKPMY EQGLILIPHI ATLGWGVGP GGEVVDTFPF FVVGVVHLIS SAVLGFGGVY HAIRGPETLE EYSSFFGYDW KDKNKMTTIL GFHLIVLGIG A LLLVAKAM ...String:
MVTLSSNSIF ATNRDQESSG FAWWAGNARL INLSGKLLGA HVAHAGLIVF WAGAMTLFEL AHFIPEKPMY EQGLILIPHI ATLGWGVGP GGEVVDTFPF FVVGVVHLIS SAVLGFGGVY HAIRGPETLE EYSSFFGYDW KDKNKMTTIL GFHLIVLGIG A LLLVAKAM FFGGLYDTWA PGGGDVRVIT NPTLDPRVIF GYLLKSPFGG EGWIVSVNNL EDVVGGHIWI GLICIAGGIW HI LTTPFGW ARRAFIWSGE AYLSYSLGAL SMMGFIATCF VWFNNTVYPS EFYGPTGPEA SQAQAMTFLI RDQKLGANVG SAQ GPTGLG KYLMRSPTGE IIFGGETMRF WDFRGPWLEP LRGPNGLDLN KIKNDIQPWQ ERRAAEYMTH APLGSLNSVG GVAT EINSV NFVSPRSWLA TSHFVLAFFF LVGHLWHAGR ARAAAAGFEK GIDRESEPVL SMPSLD

UniProtKB: Photosystem II CP43 reaction center protein

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Macromolecule #4: Photosystem II D2 protein

MacromoleculeName: Photosystem II D2 protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)
Molecular weightTheoretical: 39.388156 KDa
SequenceString: MTIAIGRAPA ERGWFDILDD WLKRDRFVFV GWSGILLFPC AYLALGGWLT GTTFVTSWYT HGLASSYLEG CNFLTVAVST PANSMGHSL LLLWGPEAQG DFTRWCQLGG LWTFIALHGA FGLIGFMLRQ FEIARLVGVR PYNAIAFSAP IAVFVSVFLI Y PLGQSSWF ...String:
MTIAIGRAPA ERGWFDILDD WLKRDRFVFV GWSGILLFPC AYLALGGWLT GTTFVTSWYT HGLASSYLEG CNFLTVAVST PANSMGHSL LLLWGPEAQG DFTRWCQLGG LWTFIALHGA FGLIGFMLRQ FEIARLVGVR PYNAIAFSAP IAVFVSVFLI Y PLGQSSWF FAPSFGVAAI FRFLLFFQGF HNWTLNPFHM MGVAGVLGGA LLCAIHGATV ENTLFQDGEG ASTFRAFNPT QA EETYSMV TANRFWSQIF GIAFSNKRWL HFFMLFVPVT GLWMSAIGVV GLALNLRSYD FISQEIRAAE DPEFETFYTK NLL LNEGIR AWMAPQDQPH ENFVFPEEVL PRGNAL

UniProtKB: Photosystem II D2 protein

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Macromolecule #5: Cytochrome b559 subunit alpha

MacromoleculeName: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)
Molecular weightTheoretical: 9.58084 KDa
SequenceString:
MAGTTGERPF SDIITSVRYW VIHSITIPAL FIAGWLFVST GLAYDVFGTP RPDSYYAQEQ RSIPLVTDRF EAKQQVETFL EQLK

UniProtKB: Cytochrome b559 subunit alpha

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Macromolecule #6: Cytochrome b559 subunit beta

MacromoleculeName: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)
Molecular weightTheoretical: 5.0679 KDa
SequenceString:
MTSNTPNQEP VSYPIFTVRW VAVHTLAVPT IFFLGAIAAM QFIQR

UniProtKB: Cytochrome b559 subunit beta

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)
Molecular weightTheoretical: 7.358754 KDa
SequenceString:
MARRTWLGDI LRPLNSEYGK VAPGWGTTPL MAVFMGLFLV FLLIILEIYN STLILDGVNV SWKALG

UniProtKB: Photosystem II reaction center protein H

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)
Molecular weightTheoretical: 4.410245 KDa
SequenceString:
METLKITVYI VVTFFVLLFV FGFLSGDPAR NPKRKDLE

UniProtKB: Photosystem II reaction center protein I

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Macromolecule #9: Photosystem II reaction center protein K

MacromoleculeName: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)
Molecular weightTheoretical: 5.028083 KDa
SequenceString:
MIDALVLVAK LPEAYAIFDP LVDVLPVIPV LFLALAFVWQ AAVGFR

UniProtKB: Photosystem II reaction center protein K

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Macromolecule #10: Photosystem II reaction center protein L

MacromoleculeName: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)
Molecular weightTheoretical: 4.299044 KDa
SequenceString:
MEPNPNRQPV ELNRTSLYLG LLLILVLALL FSSYFFN

UniProtKB: Photosystem II reaction center protein L

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Macromolecule #11: Photosystem II reaction center protein M

MacromoleculeName: Photosystem II reaction center protein M / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)
Molecular weightTheoretical: 3.981673 KDa
SequenceString:
MEVNQLGLIA TALFVLVPSV FLIILYVQTE SQQKSS

UniProtKB: Photosystem II reaction center protein M

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Macromolecule #12: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)
Molecular weightTheoretical: 3.878728 KDa
SequenceString:
METITYVFIF ACIIALFFFA IFFREPPRIT KK

UniProtKB: Photosystem II reaction center protein T

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Macromolecule #13: Photosystem II reaction center X protein

MacromoleculeName: Photosystem II reaction center X protein / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)
Molecular weightTheoretical: 4.322226 KDa
SequenceString:
MTITPSLKGF FIGLLSGAVV LGLTFAVLIA ISQIDKVQRS L

UniProtKB: Photosystem II reaction center protein X

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Macromolecule #14: Photosystem II reaction center protein Ycf12

MacromoleculeName: Photosystem II reaction center protein Ycf12 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)
Molecular weightTheoretical: 5.039143 KDa
SequenceString:
MGIFNGIIEF LSNINFEVIA QLTMIAMIGI AGPMIIFLLA VRRGNL

UniProtKB: Photosystem II reaction center protein Psb30

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Macromolecule #15: Photosystem II reaction center protein Z

MacromoleculeName: Photosystem II reaction center protein Z / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)
Molecular weightTheoretical: 6.766187 KDa
SequenceString:
MTILFQLALA ALVILSFVMV IGVPVAYASP QDWDRSKQLI FLGSGLWIAL VLVVGVLNFF VV

UniProtKB: Photosystem II reaction center protein Z

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Macromolecule #16: Photosystem II lipoprotein Psb27

MacromoleculeName: Photosystem II lipoprotein Psb27 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)
Molecular weightTheoretical: 15.120396 KDa
SequenceString:
MKRFWAMVCA LFLSVSLLLT SCANVPTGLT GNFREDTLAL ISSLREAIAL PENDPNKKAA QAEARKKLND FFALYRRDDS LRSLSSFMT MQTALNSLAG HYSSYPNRPL PEKLKARLEQ EFKQVELALD REAKS

UniProtKB: Photosystem II assembly factor lipoprotein Psb27

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Macromolecule #17: Photosystem II reaction center Psb28 protein

MacromoleculeName: Photosystem II reaction center Psb28 protein / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)
Molecular weightTheoretical: 13.188769 KDa
SequenceString:
MGAMAEIQFI RGINEEVVPD VRLTRARDGS SGQAMFYFDN PKIVQEGNLE VTGMYMVDEE GEIVTRDVNA KFINGQPVAI EATYTMRSP QEWDRFIRFM DRYAASHGLG FQKSENS

UniProtKB: Photosystem II assembly factor Psb28 protein

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Macromolecule #18: Tsl0063 protein

MacromoleculeName: Tsl0063 protein / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria)
Molecular weightTheoretical: 5.943893 KDa
SequenceString:
MRYTTDEGGR LNNFAIEPKV YQAQPWTPQQ KVRAALLVGG GLLLVAGLVA IAVGVS

UniProtKB: Photosystem II assembly protein Psb34

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Macromolecule #19: MANGANESE (II) ION

MacromoleculeName: MANGANESE (II) ION / type: ligand / ID: 19 / Number of copies: 1 / Formula: MN
Molecular weightTheoretical: 54.938 Da

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Macromolecule #20: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 20 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #21: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 21 / Number of copies: 2 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

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Macromolecule #22: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 22 / Number of copies: 35 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #23: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 23 / Number of copies: 10 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #24: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 24 / Number of copies: 1 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #25: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 25 / Number of copies: 7 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #26: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 26 / Number of copies: 1 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #27: 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: 27 / Number of copies: 1 / 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

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Macromolecule #28: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 28 / Number of copies: 1 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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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

BufferpH: 6.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.72 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 57268
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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