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- EMDB-51101: Semi-active PSII dimer from native Peak4 PSII dimers -

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Basic information

Entry
Database: EMDB / ID: EMD-51101
TitleSemi-active PSII dimer from native Peak4 PSII dimers
Map data
Sample
  • Complex: Semi-active PSII dimer with one PSII lacking extrinsic subunits
    • Protein or peptide: x 20 types
  • Ligand: x 20 types
KeywordsPSII / native intermediate / photodamage / PSII assembly / PHOTOSYNTHESIS
Function / homology
Function and homology information


photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem II / response to herbicide ...photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / photosystem II / response to herbicide / extrinsic component of membrane / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthetic electron transport in photosystem II / phosphate ion binding / photosynthesis, light reaction / : / photosynthesis / respiratory electron transport chain / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
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 PsbX, type 1 subfamily ...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 PsbX, type 1 subfamily / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II PsbI / Photosystem II CP47 reaction centre protein / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Cytochrome b559 subunits heme-binding site signature. / : / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / 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 extrinsic protein V / Photosystem II extrinsic protein O / Photosystem II protein D1 1 / Photosystem II reaction center protein J / Photosystem II D2 protein / 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 ...Photosystem II extrinsic protein V / Photosystem II extrinsic protein O / Photosystem II protein D1 1 / Photosystem II reaction center protein J / Photosystem II D2 protein / 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 reaction center protein K / Photosystem II extrinsic protein U / Photosystem II reaction center protein X
Similarity search - Component
Biological speciesThermosynechococcus vestitus BP-1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsZhao Z / Vercellino I / Nixon PJ / Sazanov LA
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/I00937X/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V002007/1 United Kingdom
CitationJournal: To Be Published
Title: Semi-active PSII dimer from the Peak4 PSII dimers
Authors: Zhao Z / Vercellino I / Nixon PJ / Sazanov LA
History
DepositionJul 18, 2024-
Header (metadata) releaseJul 30, 2025-
Map releaseJul 30, 2025-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51101.png

Downloads & links

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Map

FileDownload / File: emd_51101.map.gz / Format: CCP4 / Size: 103.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
0.5 Å/pix.
x 274 pix.
= 137. Å		0.5 Å/pix.
x 417 pix.
= 208.5 Å		0.5 Å/pix.
x 238 pix.
= 119. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.039
Minimum - Maximum-0.12877771 - 0.38329488
Average (Standard dev.)0.003504643 (±0.025210757)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin213324287
Dimensions417238274
Spacing274417238
CellA: 137.0 Å / B: 208.5 Å / C: 119.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_51101_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51101_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 : Semi-active PSII dimer with one PSII lacking extrinsic subunits

EntireName: Semi-active PSII dimer with one PSII lacking extrinsic subunits
Components
  • Complex: Semi-active PSII dimer with one PSII lacking extrinsic subunits
    • 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 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 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 protein D1 1
  • Ligand: FE (II) ION
  • Ligand: CHLORIDE ION
  • Ligand: CHLOROPHYLL A
  • Ligand: PHEOPHYTIN A
  • Ligand: BETA-CAROTENE
  • 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: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: EICOSANE
  • Ligand: CA-MN4-O5 CLUSTER
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: BICARBONATE ION
  • Ligand: PALMITIC ACID
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: GLYCEROL
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: (3R)-beta,beta-caroten-3-ol
  • Ligand: CALCIUM ION
  • Ligand: water

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Supramolecule #1: Semi-active PSII dimer with one PSII lacking extrinsic subunits

SupramoleculeName: Semi-active PSII dimer with one PSII lacking extrinsic subunits
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#20
Details: This semi-active complex is a PSII dimer with one monomer containing the extrinsic subunits, while the other monomer lacks the extrinsic subunits. This structure was obtained from the Peak4 ...Details: This semi-active complex is a PSII dimer with one monomer containing the extrinsic subunits, while the other monomer lacks the extrinsic subunits. This structure was obtained from the Peak4 PSII, which was eluted as the fourth fraction in the ion exchange chromatography after the nickel affinity pull-down.
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Location in cell: thylakoid membrane

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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 vestitus 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: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus 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: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus 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: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Thermosynechococcus vestitus 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: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus 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: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus 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: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus 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: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria)
Molecular weightTheoretical: 4.438255 KDa
SequenceString:
(FME)ETLKITVYI VVTFFVLLFV FGFLSGDPAR NPKRKDLE

UniProtKB: Photosystem II reaction center protein I

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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 vestitus BP-1 (bacteria)
Molecular weightTheoretical: 4.105908 KDa
SequenceString:
MMSEGGRIPL WIVATVAGMG VIVIVGLFFY GAYAGLGSSL

UniProtKB: Photosystem II reaction center protein J

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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 vestitus 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 #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 vestitus 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 #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 vestitus 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 #13: Photosystem II manganese-stabilizing polypeptide

MacromoleculeName: Photosystem II manganese-stabilizing polypeptide / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria)
Molecular weightTheoretical: 29.637443 KDa
SequenceString: MKYRILMATL LAVCLGIFSL SAPAFAAKQT LTYDDIVGTG LANKCPTLDD TARGAYPIDS SQTYRIARLC LQPTTFLVKE EPKNKRQEA EFVPTKLVTR ETTSLDQIQG ELKVNSDGSL TFVEEDGIDF QPVTVQMAGG ERIPLLFTVK NLVASTQPNV T SITTSTDF ...String:
MKYRILMATL LAVCLGIFSL SAPAFAAKQT LTYDDIVGTG LANKCPTLDD TARGAYPIDS SQTYRIARLC LQPTTFLVKE EPKNKRQEA EFVPTKLVTR ETTSLDQIQG ELKVNSDGSL TFVEEDGIDF QPVTVQMAGG ERIPLLFTVK NLVASTQPNV T SITTSTDF KGEFNVPSYR TANFLDPKGR GLASGYDSAI ALPQAKEEEL ARANVKRFSL TKGQISLNVA KVDGRTGEIA GT FESEQLS DDDMGAHEPH EVKIQGVFYA SIEPA

UniProtKB: Photosystem II extrinsic protein O

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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 vestitus BP-1 (bacteria)
Molecular weightTheoretical: 3.906738 KDa
SequenceString:
(FME)ETITYVFIF ACIIALFFFA IFFREPPRIT KK

UniProtKB: Photosystem II reaction center protein T

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria)
Molecular weightTheoretical: 15.030986 KDa
SequenceString:
MQRLGRWLAL AYFVGVSLLG WINWSAPTLA ATASTEEELV NVVDEKLGTA YGEKIDLNNT NIAAFIQYRG LYPTLAKLIV KNAPYESVE DVLNIPGLTE RQKQILRENL EHFTVTEVET ALVEGGDRYN NGLYK

UniProtKB: Photosystem II extrinsic protein U

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Macromolecule #16: Cytochrome c-550

MacromoleculeName: Cytochrome c-550 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria)
Molecular weightTheoretical: 18.046943 KDa
SequenceString:
MLKKCVWLAV ALCLCLWQFT MGTALAAELT PEVLTVPLNS EGKTITLTEK QYLEGKRLFQ YACASCHVGG ITKTNPSLDL RTETLALAT PPRDNIEGLV DYMKNPTTYD GEQEIAEVHP SLRSADIFPK MRNLTEKDLV AIAGHILVEP KILGDKWGGG K VYY

UniProtKB: Photosystem II extrinsic protein V

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Macromolecule #17: Photosystem II reaction center X protein

MacromoleculeName: Photosystem II reaction center X protein / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus 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 #18: Photosystem II reaction center protein Ycf12

MacromoleculeName: Photosystem II reaction center protein Ycf12 / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus 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 #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 vestitus 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 #20: Photosystem II protein D1 1

MacromoleculeName: Photosystem II protein D1 1 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria)
Molecular weightTheoretical: 39.777301 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 GMEVM(HSK)ERNA HNFPLDLASA ESAPVAMIAP SING

UniProtKB: Photosystem II protein D1 1

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Macromolecule #21: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 21 / Number of copies: 2 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

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Macromolecule #22: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 22 / Number of copies: 3 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #23: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 23 / Number of copies: 70 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #24: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 24 / Number of copies: 4 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

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Macromolecule #25: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 25 / Number of copies: 20 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #26: 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: 26 / 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

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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: 9 / 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

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Macromolecule #28: EICOSANE

MacromoleculeName: EICOSANE / type: ligand / ID: 28 / Number of copies: 30 / Formula: LFA
Molecular weightTheoretical: 282.547 Da
Chemical component information

ChemComp-LFA:
EICOSANE

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Macromolecule #29: CA-MN4-O5 CLUSTER

MacromoleculeName: CA-MN4-O5 CLUSTER / type: ligand / ID: 29 / Number of copies: 1 / Formula: OEX
Molecular weightTheoretical: 339.827 Da
Chemical component information

ChemComp-OEX:
CA-MN4-O5 CLUSTER

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Macromolecule #30: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 30 / Number of copies: 17 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #31: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 31 / Number of copies: 2 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION / pH buffer*YM

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Macromolecule #32: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 32 / Number of copies: 29 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #33: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 33 / 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 #34: GLYCEROL

MacromoleculeName: GLYCEROL / type: ligand / ID: 34 / Number of copies: 1 / Formula: GOL
Molecular weightTheoretical: 92.094 Da
Chemical component information

ChemComp-GOL:
GLYCEROL

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Macromolecule #35: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 35 / Number of copies: 10 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #36: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 36 / Number of copies: 10 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #37: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 37 / Number of copies: 3 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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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

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Macromolecule #39: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 39 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #40: water

MacromoleculeName: water / type: ligand / ID: 40 / Number of copies: 960 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.3 mg/mL
BufferpH: 6.5
Details: 20 mM MES pH 6.5, 2.5 mM MgCl2, 2.5 mM CaCl2, 7 mM MgSO4, 0.03% DDM, 0.05% CHAPS
GridModel: Quantifoil R0.6/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 5 sec.
Details: The grids were glow-discharged for 5 sec at 25 mA before freezing.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 9173 / Average electron dose: 80.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5900000
CTF correctionSoftware - Name: RELION (ver. 4.0.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7nho


Details: also with 3KZI
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 272215
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.0)
Final 3D classificationSoftware - Name: RELION (ver. 4.0.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7nho

chain_id: a, source_name: PDB, initial_model_type: experimental model

7nho

chain_id: b, source_name: PDB, initial_model_type: experimental model

7nho

chain_id: c, source_name: PDB, initial_model_type: experimental model

7nho

chain_id: d, source_name: PDB, initial_model_type: experimental model

7nho

chain_id: e, source_name: PDB, initial_model_type: experimental model

7nho

chain_id: f, source_name: PDB, initial_model_type: experimental model

7nho

chain_id: h, source_name: PDB, initial_model_type: experimental model

7nho

chain_id: i, source_name: PDB, initial_model_type: experimental model

3kzi

chain_id: j, source_name: PDB, initial_model_type: experimental model

7nho

chain_id: k, source_name: PDB, initial_model_type: experimental model

7nho

chain_id: l, source_name: PDB, initial_model_type: experimental model

7nho

chain_id: m, source_name: PDB, initial_model_type: experimental model

7nho

chain_id: t, source_name: PDB, initial_model_type: experimental model

7nho

chain_id: x, source_name: PDB, initial_model_type: experimental model

7nho

chain_id: y, source_name: PDB, initial_model_type: experimental model

7nho

chain_id: z, source_name: PDB, initial_model_type: experimental model

3kzi

chain_id: A, source_name: PDB, initial_model_type: experimental model

3kzi

chain_id: B, source_name: PDB, initial_model_type: experimental model

3kzi

chain_id: C, source_name: PDB, initial_model_type: experimental model

3kzi

chain_id: D, source_name: PDB, initial_model_type: experimental model

3kzi

chain_id: E, source_name: PDB, initial_model_type: experimental model

3kzi

chain_id: F, source_name: PDB, initial_model_type: experimental model

3kzi

chain_id: H, source_name: PDB, initial_model_type: experimental model

3kzi

chain_id: I, source_name: PDB, initial_model_type: experimental model

3kzi

chain_id: J, source_name: PDB, initial_model_type: experimental model

3kzi

chain_id: K, source_name: PDB, initial_model_type: experimental model

3kzi

chain_id: L, source_name: PDB, initial_model_type: experimental model

3kzi

chain_id: M, source_name: PDB, initial_model_type: experimental model

3kzi

chain_id: T, source_name: PDB, initial_model_type: experimental model

3kzi

chain_id: X, source_name: PDB, initial_model_type: experimental model

3kzi

chain_id: Y, source_name: PDB, initial_model_type: experimental model

3kzi

chain_id: Z, source_name: PDB, initial_model_type: experimental model

3kzi

chain_id: O, source_name: PDB, initial_model_type: experimental model

3kzi

chain_id: U, source_name: PDB, initial_model_type: experimental model

3kzi

chain_id: V, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9g6g:
Semi-active PSII dimer from native Peak4 PSII dimers

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