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- EMDB-63639: cryo-EM structure of PSII D1-V185T from Thermosynechococcus vesti... -

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Basic information

Entry
Database: EMDB / ID: EMD-63639
Titlecryo-EM structure of PSII D1-V185T from Thermosynechococcus vestitus BP-1
Map dataprimary map
Sample
  • Complex: cryo-EM structure of psbA3 PSII D1-V185T from Thermosynechococcus vestitus BP-1
    • Protein or peptide: x 19 types
  • Ligand: x 20 types
KeywordsPSII mutation / 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 / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to herbicide / photosystem II ...photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / 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 / plasma membrane-derived thylakoid membrane / photosynthetic electron transport in photosystem II / chlorophyll binding / photosynthesis, light reaction / phosphate ion binding / 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 PsbX, type 1 subfamily / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ ...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 PsbX, type 1 subfamily / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / 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 CP43 reaction centre protein / 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 PsbK 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 protein D1 / Photosystem II reaction centre protein H / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II reaction centre protein H superfamily / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Photosystem II 10 kDa phosphoprotein / Cytochrome b559 subunits heme-binding site signature. / : / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / 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 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 extrinsic protein V / Photosystem II extrinsic protein O / 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 protein D1 3 / 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 (bacteria) / Thermosynechococcus vestitus BP-1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.88 Å
AuthorsJiang HW / Nakajima Y / Akita F / Li HJ / Kato K / Sugiura M / Shen JR
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2026
Title: Cryo-EM structure of photosystem II D1-V185T mutant from Thermosynechococcus vestitus.
Authors: Haowei Jiang / Yoshiki Nakajima / Fusamichi Akita / Hongjie Li / Koji Kato / Miwa Sugiura / Jian-Ren Shen /
Abstract: Photosystem II (PSII) catalyzes water oxidation into electrons, protons and dioxygen at its catalytic center, a MnCaO cluster, utilizing light energy. An amino acid residue D1-V185 in the D1 protein ...Photosystem II (PSII) catalyzes water oxidation into electrons, protons and dioxygen at its catalytic center, a MnCaO cluster, utilizing light energy. An amino acid residue D1-V185 in the D1 protein is located close to the MnCaO cluster, and plays a critical role in its catalytic function. In this research we purified PSII dimers from a D1-V185T mutant of Thermosynechococcus vestitus and analyzed its structure using low-damage cryo-electron microscopy (cryo-EM) at a resolution of 1.88 Å. The results revealed the presence of multi-conformations at the mutation site. Unlike the wild-type valine, which does not allow water molecules to be able to form hydrogen-bonds with it, both conformations of the mutant formed hydrogen bonds with nearby water molecules, which leads to rearrangement of the hydrogen bond networks in the O1 and Cl-1 channels. In conformation-A, the mutated Thr residue forms a hydrogen bond with a water molecule W6, which creates a new channel that bypasses the original O1 channel. Due to the hydrophilic OH group of Thr, the side-chain of D1-Glu189 was attracted and shifted toward the mutant Thr residue. In conformation-B, it forms a hydrogen bond with a water molecule W9 in the Cl-1 channel, bringing W9 closer and thereby disrupting the hydrogen bond network of the Cl-1 channel. In addition, multi-conformations of D2-K317, which is a ligand of Cl-1, were found in the mutant. These changes alter the environment surrounding the Cl-1 ion and MnCaO, thereby affecting the PSII water-oxidation activity.
History
DepositionMar 5, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateAug 12, 2026-
Current statusAug 12, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63639.png

Downloads & links

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Map

FileDownload / File: emd_63639.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.45 Å/pix.
x 640 pix.
= 290.56 Å		0.45 Å/pix.
x 640 pix.
= 290.56 Å		0.45 Å/pix.
x 640 pix.
= 290.56 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.454 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.023045622 - 0.060289513
Average (Standard dev.)0.000013469525 (±0.0011831333)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 290.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63639_msk_1.map
Projections & Slices
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Half map: #2

Fileemd_63639_half_map_1.map
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Half map: #1

Fileemd_63639_half_map_2.map
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Sample components

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Entire : cryo-EM structure of psbA3 PSII D1-V185T from Thermosynechococcus...

EntireName: cryo-EM structure of psbA3 PSII D1-V185T from Thermosynechococcus vestitus BP-1
Components
  • Complex: cryo-EM structure of psbA3 PSII D1-V185T from Thermosynechococcus vestitus BP-1
    • Protein or peptide: Photosystem II protein D1 3
    • 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 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 reaction center protein T
    • Protein or peptide: Photosystem II extrinsic protein U
    • Protein or peptide: Photosystem II extrinsic protein V
    • Protein or peptide: Photosystem II reaction center protein X
    • Protein or peptide: Photosystem II reaction center protein Psb30
    • Protein or peptide: Cytochrome b559 subunit alpha
    • Protein or peptide: Photosystem II extrinsic protein O
    • Protein or peptide: Photosystem II reaction center protein Z
  • Ligand: CA-MN4-O5 CLUSTER
  • Ligand: FE (II) ION
  • Ligand: CHLORIDE ION
  • Ligand: CHLOROPHYLL A
  • Ligand: PHEOPHYTIN A
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • 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: UNKNOWN LIGAND
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: BICARBONATE ION
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: (3R)-beta,beta-caroten-3-ol
  • Ligand: MAGNESIUM ION
  • Ligand: HEME C
  • Ligand: CALCIUM ION
  • Ligand: water

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Supramolecule #1: cryo-EM structure of psbA3 PSII D1-V185T from Thermosynechococcus...

SupramoleculeName: cryo-EM structure of psbA3 PSII D1-V185T from Thermosynechococcus vestitus BP-1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#19
Source (natural)Organism: Thermosynechococcus vestitus (bacteria)

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Macromolecule #1: Photosystem II protein D1 3

MacromoleculeName: Photosystem II protein D1 3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: NIES-2133 / IAM M-273 / BP-1
Molecular weightTheoretical: 39.782312 KDa
SequenceString: MTTVLQRREQ LNLWEQFCSW VTSTNNRLYV GWFGVLMIPT LLAATICFVI AFIAAPPVDI DGIREPVSGS LLYGNNIITG AVVPSSNAI GLHFYPIWEA ASLDEWLYNG GPYQLIIFHF LIGVFCYMGR EWELSYRLGM RPWICVAYSA PVAAATAVFL I YPIGQGSF ...String:
MTTVLQRREQ LNLWEQFCSW VTSTNNRLYV GWFGVLMIPT LLAATICFVI AFIAAPPVDI DGIREPVSGS LLYGNNIITG AVVPSSNAI GLHFYPIWEA ASLDEWLYNG GPYQLIIFHF LIGVFCYMGR EWELSYRLGM RPWICVAYSA PVAAATAVFL I YPIGQGSF SDGMPLGISG TFNFMLTFQA EHNILMHPFH QLGVAGVFGG ALFSAMHGSL VTSSLIRETT ETESANYGYK FG QEEETYN IVAAHGYFGR LIFQYASFNN SRALHFFLAA WPVIGIWFTA LGISTMAFNL NGFNFNHSVV DAQGNVINTW ADI INRANL GMEVMHERNA HNFPLDLASA ESAPVAMIAP SING

UniProtKB: Photosystem II protein D1 3

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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) / Strain: NIES-2133 / IAM M-273 / BP-1
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) / Strain: NIES-2133 / IAM M-273 / BP-1
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) / Strain: NIES-2133 / IAM M-273 / BP-1
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 beta

MacromoleculeName: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: NIES-2133 / IAM M-273 / BP-1
Molecular weightTheoretical: 5.0679 KDa
SequenceString:
MTSNTPNQEP VSYPIFTVRW VAVHTLAVPT IFFLGAIAAM QFIQR

UniProtKB: Cytochrome b559 subunit beta

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Macromolecule #6: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: NIES-2133 / IAM M-273 / BP-1
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 #7: Photosystem II reaction center protein I

MacromoleculeName: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: NIES-2133 / IAM M-273 / BP-1
Molecular weightTheoretical: 4.438255 KDa
SequenceString:
(FME)ETLKITVYI VVTFFVLLFV FGFLSGDPAR NPKRKDLE

UniProtKB: Photosystem II reaction center protein I

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Macromolecule #8: Photosystem II reaction center protein J

MacromoleculeName: Photosystem II reaction center protein J / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: NIES-2133 / IAM M-273 / BP-1
Molecular weightTheoretical: 4.105908 KDa
SequenceString:
MMSEGGRIPL WIVATVAGMG VIVIVGLFFY GAYAGLGSSL

UniProtKB: Photosystem II reaction center protein J

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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: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: NIES-2133 / IAM M-273 / BP-1
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: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: NIES-2133 / IAM M-273 / BP-1
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: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: NIES-2133 / IAM M-273 / BP-1
Molecular weightTheoretical: 4.009682 KDa
SequenceString:
(FME)EVNQLGLIA 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: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: NIES-2133 / IAM M-273 / BP-1
Molecular weightTheoretical: 3.906738 KDa
SequenceString:
(FME)ETITYVFIF ACIIALFFFA IFFREPPRIT KK

UniProtKB: Photosystem II reaction center protein T

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Macromolecule #13: Photosystem II extrinsic protein U

MacromoleculeName: Photosystem II extrinsic protein U / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: NIES-2133 / IAM M-273 / BP-1
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 #14: Photosystem II extrinsic protein V

MacromoleculeName: Photosystem II extrinsic protein V / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: NIES-2133 / IAM M-273 / BP-1
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 #15: Photosystem II reaction center protein X

MacromoleculeName: Photosystem II reaction center protein X / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: NIES-2133 / IAM M-273 / BP-1
Molecular weightTheoretical: 4.322226 KDa
SequenceString:
MTITPSLKGF FIGLLSGAVV LGLTFAVLIA ISQIDKVQRS L

UniProtKB: Photosystem II reaction center protein X

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Macromolecule #16: Photosystem II reaction center protein Psb30

MacromoleculeName: Photosystem II reaction center protein Psb30 / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: NIES-2133 / IAM M-273 / BP-1
Molecular weightTheoretical: 5.039143 KDa
SequenceString:
MGIFNGIIEF LSNINFEVIA QLTMIAMIGI AGPMIIFLLA VRRGNL

UniProtKB: Photosystem II reaction center protein Psb30

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Macromolecule #17: Cytochrome b559 subunit alpha

MacromoleculeName: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: NIES-2133 / IAM M-273 / BP-1
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 #18: Photosystem II extrinsic protein O

MacromoleculeName: Photosystem II extrinsic protein O / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus vestitus BP-1 (bacteria) / Strain: NIES-2133 / IAM M-273 / BP-1
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 #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) / Strain: NIES-2133 / IAM M-273 / BP-1
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: CA-MN4-O5 CLUSTER

MacromoleculeName: CA-MN4-O5 CLUSTER / type: ligand / ID: 20 / 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 #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: 4 / 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: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 26 / 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 #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: 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 #28: 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: 28 / 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

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Macromolecule #29: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 29 / Number of copies: 22 / Formula: UNL
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

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Macromolecule #30: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 30 / Number of copies: 10 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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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: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 32 / Number of copies: 2 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION

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Macromolecule #33: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 33 / 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 #34: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 34 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #35: (3R)-beta,beta-caroten-3-ol

MacromoleculeName: (3R)-beta,beta-caroten-3-ol / type: ligand / ID: 35 / 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 #36: MAGNESIUM ION

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

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Macromolecule #37: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 37 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 620.519 Da
Chemical component information

ChemComp-HEC:
HEME C

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Macromolecule #38: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 38 / Number of copies: 2 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #39: water

MacromoleculeName: water / type: ligand / ID: 39 / Number of copies: 2565 / 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

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Sample preparation

Concentration2.5 mg/mL
BufferpH: 6.5
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7yq7

Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 171514
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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