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- EMDB-55593: Chlorophyll f-containing dimeric far-red Photosystem II from Chro... -

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Basic information

Entry
Database: EMDB / ID: EMD-55593
TitleChlorophyll f-containing dimeric far-red Photosystem II from Chroococcidiopsis thermalis PCC 7203
Map data
Sample
  • Complex: Dimeric far-red Photosystem II
    • Protein or peptide: x 21 types
  • Ligand: x 18 types
KeywordsChlorophyll f / photosystem II / ELECTRON TRANSPORT / FaRLiP
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 / 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 / photosynthetic electron transport chain / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosystem II / response to herbicide / 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 / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II protein Y (PsbY) / Photosystem II PsbY / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbJ ...Photosystem II protein Y (PsbY) / Photosystem II PsbY / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II 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 / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Photosystem II reaction center protein I / Photosystem II reaction center protein K / Photosystem II extrinsic protein V / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein Psb30 / Photosystem II protein D1 / Photosystem II phosphoprotein PsbH / Photosystem II CP47 reaction center protein / Photosystem II extrinsic protein O / Photosystem II D2 protein ...Photosystem II reaction center protein I / Photosystem II reaction center protein K / Photosystem II extrinsic protein V / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein Psb30 / Photosystem II protein D1 / Photosystem II phosphoprotein PsbH / Photosystem II CP47 reaction center protein / Photosystem II extrinsic protein O / Photosystem II D2 protein / Uncharacterized protein / Photosystem II reaction center protein L / Cytochrome b559 subunit beta / Photosystem II reaction center protein J / Cytochrome b559 subunit alpha / Photosystem II extrinsic protein U / Photosystem II reaction center protein Y / Photosystem II reaction center protein Z / Photosystem II reaction center protein X / Photosystem II reaction center protein M / Photosystem II reaction center protein T
Similarity search - Component
Biological speciesChroococcidiopsis thermalis PCC 7203 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.17 Å
AuthorsLeong HF / Consoli G / Murray JW / Fantuzzi A / Rutherford AW
Funding support United Kingdom, European Union, 11 items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M011178/1 United Kingdom
Royal SocietyRSRP/S2/242010 United Kingdom
H2020 Marie Curie Actions of the European Commission955520European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R001383/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/V002015/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/R00921X United Kingdom
Leverhulme TrustRPG-2022-203 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/Z516740/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)UKRI2820 United Kingdom
Imperial College LondonPresidents PhD Scholarship United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/X019284/1 United Kingdom
CitationJournal: Nat Commun / Year: 2026
Title: Mapping the absorption landscape of far-red Photosystem II.
Authors: Ho Fong Leong / Giovanni Consoli / Geoffry A Davis / Ben Hancox-Lachman / Kenta Renard / Fiazall Tufail / Lauren E Lee / Lucas Gautier / James W Murray / Andrea Fantuzzi / A William Rutherford /
Abstract: Far-red light photoacclimation enables some cyanobacteria to survive in white-light-depleted environments by extending the red limit of photosynthesis. In far-red Photosystem II, paralogous subunits ...Far-red light photoacclimation enables some cyanobacteria to survive in white-light-depleted environments by extending the red limit of photosynthesis. In far-red Photosystem II, paralogous subunits replace their canonical counterparts, allowing the incorporation of some chlorophyll f molecules and one chlorophyll d that are red-shifted and spectrally distinct from the chlorophyll a manifold, and from each other. Here, we present a comparative study of far-red Photosystem II from Chroococcidiopsis thermalis PCC 7203 and Calothrix sp. NIES-3974. In C. thermalis, the cryo-electron microscopy structure reveals the far-red-exclusive subunit, PsbH2', which forms part of a chlorophyll f binding site. We also assign four chlorophyll f sites using sequence comparisons and electrostatic potential analyses. In Calothrix, psbH2' is absent, and the same analyses show that only two of these chlorophyll f sites are present. Comparative phylogenetic, structural, and spectroscopic analyses allow the assignment of specific wavelengths to all the red-shifted chlorophylls. This provides the framework needed to model excitation energy transfer in far-red Photosystem II, and to understand the conserved features that allow survival under far-red light.
History
DepositionNov 5, 2025-
Header (metadata) releaseJun 10, 2026-
Map releaseJun 10, 2026-
UpdateJun 17, 2026-
Current statusJun 17, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55593.png

Downloads & links

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Map

FileDownload / File: emd_55593.map.gz / Format: CCP4 / Size: 1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 650 pix.
= 469.95 Å		0.72 Å/pix.
x 650 pix.
= 469.95 Å		0.72 Å/pix.
x 650 pix.
= 469.95 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.723 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.14707743 - 0.3566915
Average (Standard dev.)0.00012177045 (±0.008015131)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions650650650
Spacing650650650
CellA=B=C: 469.94998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55593_msk_1.map
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Half map: #2

Fileemd_55593_half_map_1.map
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Half map: #1

Fileemd_55593_half_map_2.map
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Sample components

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Entire : Dimeric far-red Photosystem II

EntireName: Dimeric far-red Photosystem II
Components
  • Complex: Dimeric far-red Photosystem II
    • Protein or peptide: Photosystem II protein D1
    • Protein or peptide: Photosystem II CP47 reaction center protein
    • Protein or peptide: Photosystem II CP43 reaction center protein
    • Protein or peptide: Photosystem II D2 protein
    • Protein or peptide: Cytochrome b559 subunit alpha
    • Protein or peptide: Cytochrome b559 subunit beta
    • Protein or peptide: PsbH2'
    • Protein or peptide: Photosystem II phosphoprotein PsbH
    • 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 extrinsic protein O
    • Protein or peptide: Photosystem II reaction center protein Y
    • 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: Photosystem II reaction center protein Z
  • Ligand: CA-MN4-O5 CLUSTER
  • Ligand: FE (II) ION
  • Ligand: CHLORIDE ION
  • Ligand: CHLOROPHYLL A
  • Ligand: CHLOROPHYLL D
  • Ligand: PHEOPHYTIN A
  • Ligand: BETA-CAROTENE
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: 2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: Chlorophyll F
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: BICARBONATE ION
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: HEME C
  • Ligand: water

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Supramolecule #1: Dimeric far-red Photosystem II

SupramoleculeName: Dimeric far-red Photosystem II / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#21
Details: Chlorophyll f-containing dimeric far-red Photosystem II from Chroococcidiopsis thermalis PCC 7203
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 690 KDa

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Macromolecule #1: Photosystem II protein D1

MacromoleculeName: Photosystem II protein D1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 40.732535 KDa
SequenceString: MTTVLQRQLN RVPAWERFCN WVTSTENRLY IGWFGVLMIP LLGVSICVFT IAFIAAPPVD IDGIREPVSG SLLYGNNIIT GAVVPMSNA IGLHFYPIWE AASMDEWLYN GGPYQMIGFH YIPALCCYAG REWELSYRLG MRPWIAVAYT APVAATSSVF L VYPIGQGS ...String:
MTTVLQRQLN RVPAWERFCN WVTSTENRLY IGWFGVLMIP LLGVSICVFT IAFIAAPPVD IDGIREPVSG SLLYGNNIIT GAVVPMSNA IGLHFYPIWE AASMDEWLYN GGPYQMIGFH YIPALCCYAG REWELSYRLG MRPWIAVAYT APVAATSSVF L VYPIGQGS FSDGLPMGIS GTFNFMFVFQ AEHNILMHPF HMLGVAGVLG GSLFCAMHGS LVTSSLIRET SDNESQNYGY KF GQESETY NIVAAHGYFG RLIFQYASFN NSRSLHFFLA AWPVICIWAT ALGISTMAFN LNGFNFNNSV LDSQGRVLPT WAD VLNRAN LGFEVMHERN AHNFPLDLAC SDAVPVAFKA PAIAEVPPQA IAS

UniProtKB: Photosystem II protein D1

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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: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 57.614652 KDa
SequenceString: MGLPWYRVHT SVINDPGRLI AVHLMHNALC AGFAGSMLLF ELALYDSSDP VLNPMWRQGC FLMPFVARLG VTNSWQGWSI TGESVADPG FWTFETVAIA HIIFSGLEFL AACWHWVYWD LATFFDPKTN EPVLDLPRIF GIHLLLAGLL CFGFGAFHLT G IFGPGMWV ...String:
MGLPWYRVHT SVINDPGRLI AVHLMHNALC AGFAGSMLLF ELALYDSSDP VLNPMWRQGC FLMPFVARLG VTNSWQGWSI TGESVADPG FWTFETVAIA HIIFSGLEFL AACWHWVYWD LATFFDPKTN EPVLDLPRIF GIHLLLAGLL CFGFGAFHLT G IFGPGMWV SDPYGLTGHV QGVAPVWGAE GFNPYNPGGV VAHHIAAGIV GIIGGLFHIV TRPPEVLYKA LRMGNIEGAL AS GLAVFFF AGFVACGSMW YGTATTPIEL WGPTRFQWDQ NYFKKEIDRR VQSNLAEGKS LSEAWSAIPE KLAFYDYVGN SPA KGGLFR VGRMVDGDGV AKAWLGHAIF KDGEGRELNV RRMPNFFETF PVVLTDKDDV VRADIPFRRA EAKYSFEQKG VTVS FVGGT LDGQAYTEPS TVKKFARQAQ LGEVFDFDRE TYNSDGVFRT SNRGFFAFFH CCFALVWFFG HIWHGSRAIF RDVFA GIDP GLDEQVEFGV FQKVGDLTTR KKIPVAAMAG TREPAA

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: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 50.827785 KDa
SequenceString: METPFDRSIT TTTNVDTPRE GRDEASTGYA WWAGNARFIN LSGRFLGAHV AHAGLVAFWA GAMLMFEVAH YVPEKPMYEQ GLILMPHIA TLGFGVGQGG QVVDIFPFFA IAAIHLIGSA VLGFGGVYHS IKGPERLAGF YDFDWTDKDK VTSILGYHLI A LGLGALLL ...String:
METPFDRSIT TTTNVDTPRE GRDEASTGYA WWAGNARFIN LSGRFLGAHV AHAGLVAFWA GAMLMFEVAH YVPEKPMYEQ GLILMPHIA TLGFGVGQGG QVVDIFPFFA IAAIHLIGSA VLGFGGVYHS IKGPERLAGF YDFDWTDKDK VTSILGYHLI A LGLGALLL VARAMYLGGL YDTWAPGGGD VRVVTNPTLD PRIIFGYLFK GFTGGAGNIA SVNNLEDIVG GHIWMGSILI AG GIWHVLT KPFKWAERVF IWSGEAYLSQ SLGNVAGQAL IAACFIWFNN TAYPSEFYGP TAPEASQAQA LNFLVRDQQL GAN VVSAQG PTGLGKYLMR SPTGEIIFGG ETMRFWDFKG PWLEPLRGPN GLDLEKIRYD IQPWQIRRAS EYMTHAPLGS LNSV GGVAT EINSFNYVSP RAWLASAHFV FAFLFLVGHL WHAGRARAAA AGFERGIDRE DEPVLSMPPL D

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: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 39.825586 KDa
SequenceString: MTIAIRSTPI GWGWFGVLDD WLKRDRFVFI GWSGLLLFPC SYMAIGGWFT GTTFVTSWYT HGVVSSYLEG CNFLTTAVST PADSMGHSL LFLWGPEANW DFTRWCQIGG LWSFVTLHGV FGLIGFCLRQ MEIARVVGIR PYNALAFTAP ISVFVSVFLI Y PLGQSSWF ...String:
MTIAIRSTPI GWGWFGVLDD WLKRDRFVFI GWSGLLLFPC SYMAIGGWFT GTTFVTSWYT HGVVSSYLEG CNFLTTAVST PADSMGHSL LFLWGPEANW DFTRWCQIGG LWSFVTLHGV FGLIGFCLRQ MEIARVVGIR PYNALAFTAP ISVFVSVFLI Y PLGQSSWF FAPSYGVAGI FRFLLFFQAF HNYTLNPFHM MGVAGVLGGA LLCAIHGATV ENTLFRDTKG FNTFRGFSTT QA EETYSFV TANRYWSQIF GIAFSNKRWL HFFMLFVPVT GLWMSSIGMV GLAFNVRAYD FVSQELRAAE DPEFETFYTK NIL LNEGAR AWLAPQDQPH EKFQFPEEVL 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: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 9.465691 KDa
SequenceString:
MSGTTGERPF SDIITSVRYW VIHSITIPAL FIAGWLFVST GLAYDVFGTP RPNEYYPQER QELPIVSDRF ESRKQIEEFI GK

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: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 5.06593 KDa
SequenceString:
MNTNQVNQPI QYPIFTVRWL AVHTLAVPTV FFLGAIASMQ FIQR

UniProtKB: Cytochrome b559 subunit beta

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Macromolecule #7: PsbH2'

MacromoleculeName: PsbH2' / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 5.323152 KDa
SequenceString:
MHHIYYFAYG EGQFASTATG VLFGLLAAFL LCVLLIVYAS STYPADRR

UniProtKB: Uncharacterized protein

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Macromolecule #8: Photosystem II phosphoprotein PsbH

MacromoleculeName: Photosystem II phosphoprotein PsbH / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 7.834357 KDa
SequenceString:
MQQPKYQPKK TAPVQYFFRN FNSEAGKVAP GWGTTPLMVG LMLLFFLFLL IILELANASL MVRGIHVGW

UniProtKB: Photosystem II phosphoprotein PsbH

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Macromolecule #9: Photosystem II reaction center protein I

MacromoleculeName: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 4.377158 KDa
SequenceString:
(FME)LTLKIVVYI VVGFFLTLFV FGFLSNDPAR NPGRRDLD

UniProtKB: Photosystem II reaction center protein I

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Macromolecule #10: Photosystem II reaction center protein J

MacromoleculeName: Photosystem II reaction center protein J / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 4.015678 KDa
SequenceString:
MSGSGRIPLW VVATIAGLGV IVVVGTFFYG SYTHLGSSL

UniProtKB: Photosystem II reaction center protein J

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Macromolecule #11: Photosystem II reaction center protein K

MacromoleculeName: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 6.690924 KDa
SequenceString:
MHVNSESCVE KENLSMEAAL LLAKLPEAYS ILDPLVDVLP LIPLFFLLLA FVWQAAVGFR

UniProtKB: Photosystem II reaction center protein K

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Macromolecule #12: Photosystem II reaction center protein L

MacromoleculeName: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 4.762552 KDa
SequenceString:
MPLERSKNPN NQPVELNRTS LYLGLLLIFV LGILFSSYFF N

UniProtKB: Photosystem II reaction center protein L

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Macromolecule #13: Photosystem II reaction center protein M

MacromoleculeName: Photosystem II reaction center protein M / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 4.156904 KDa
SequenceString:
(FME)QVNDLGFVA SILFVLVPSV FLIILYIQTA SREGKKD

UniProtKB: Photosystem II reaction center protein M

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Macromolecule #14: Photosystem II extrinsic protein O

MacromoleculeName: Photosystem II extrinsic protein O / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 29.794619 KDa
SequenceString: MKYRALIVAF LALCLGFLTA CSEPSQVASR ELLTYEQIRG TGLANKCPQL SETSRGSIAI DPNQSYRMVE LCLEPTSFFI KEEPVNKRQ EAEYIAGKLL TRYTSTIDQV QGDLKVNPDK SLTFVEKDGL DFQAITVQLP GGERVPFLFT IKNLVAQTQP G LTSINTST ...String:
MKYRALIVAF LALCLGFLTA CSEPSQVASR ELLTYEQIRG TGLANKCPQL SETSRGSIAI DPNQSYRMVE LCLEPTSFFI KEEPVNKRQ EAEYIAGKLL TRYTSTIDQV QGDLKVNPDK SLTFVEKDGL DFQAITVQLP GGERVPFLFT IKNLVAQTQP G LTSINTST DFEGKFNVPS YRTANFLDPK GRGVTTGYDN AVALPASADK QGYANVKSAG IENGSISLQV AKVDNATGEV AG TFESIQP SDTDMGAKEA LDVKVRGLFY ARIEPQA

UniProtKB: Photosystem II extrinsic protein O

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Macromolecule #15: Photosystem II reaction center protein Y

MacromoleculeName: Photosystem II reaction center protein Y / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 4.505308 KDa
SequenceString:
MDIDLRVAFV LLPVIAAASW ALFNIAPAAI RQIQGFFNKE A

UniProtKB: Photosystem II reaction center protein Y

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Macromolecule #16: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 3.654408 KDa
SequenceString:
(FME)ESVAYILIL ALAIGTLFFA IAFREPPRIE KK

UniProtKB: Photosystem II reaction center protein T

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Macromolecule #17: Photosystem II extrinsic protein U

MacromoleculeName: Photosystem II extrinsic protein U / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 16.995383 KDa
SequenceString:
MQRGRETVKK LIRLLTILSV LVGCLGWLGI SQPAIATNLS DFSLRTVPIL AVESPARSSN RADAKLATDF GKKIDLNNTN VAAFRRYPG LYPTLARKIV QNAPYENVED VMELPGLSER QKQTLEANIG NFTVTDVEAA YTMGDDRYNN GIYR

UniProtKB: Photosystem II extrinsic protein U

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Macromolecule #18: Photosystem II extrinsic protein V

MacromoleculeName: Photosystem II extrinsic protein V / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 17.602111 KDa
SequenceString:
MFKRLIGLVM ATVMLAFGLV VGSAAAVEMS EAIRTVPLND SGDTTVLSLK QVQEGKRLFN YACAQCHVGG VTKTNQNVGL DPESLAGAS PSRNNIEGLV DYMKNPTTYD GEEEIAEIHP SIKSADIYPA MRNLRDEDLT AIAGHVLLQP KILGDKWGGG K IYY

UniProtKB: Photosystem II extrinsic protein V

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Macromolecule #19: Photosystem II reaction center protein X

MacromoleculeName: Photosystem II reaction center protein X / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 4.326171 KDa
SequenceString:
(FME)TPSLMNFFF SLLAGLAIVV IPVTVGLIFI SQQDKIQRS

UniProtKB: Photosystem II reaction center protein X

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Macromolecule #20: Photosystem II reaction center protein Psb30

MacromoleculeName: Photosystem II reaction center protein Psb30 / type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 4.660479 KDa
SequenceString:
MSGIFDAIGS FQWETLFQLV SVALIMLAGP AVIFVLAFRN GDL

UniProtKB: Photosystem II reaction center protein Psb30

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Macromolecule #21: Photosystem II reaction center protein Z

MacromoleculeName: Photosystem II reaction center protein Z / type: protein_or_peptide / ID: 21 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chroococcidiopsis thermalis PCC 7203 (bacteria)
Molecular weightTheoretical: 6.890349 KDa
SequenceString:
MLSALFQLAL VALVFLSFAL VIGVPVAYAT PQNWVESKRL LWIGSIAWFG LVIVIGVLNF LVV

UniProtKB: Photosystem II reaction center protein Z

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Macromolecule #22: CA-MN4-O5 CLUSTER

MacromoleculeName: CA-MN4-O5 CLUSTER / type: ligand / ID: 22 / 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 #23: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 23 / Number of copies: 2 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

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Macromolecule #24: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 24 / Number of copies: 4 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #25: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 25 / Number of copies: 60 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #26: CHLOROPHYLL D

MacromoleculeName: CHLOROPHYLL D / type: ligand / ID: 26 / Number of copies: 2 / Formula: CL7
Molecular weightTheoretical: 895.462 Da
Chemical component information

ChemComp-CL7:
CHLOROPHYLL D

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Macromolecule #27: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 27 / Number of copies: 4 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

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Macromolecule #28: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 28 / Number of copies: 20 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #29: 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: 29 / Number of copies: 12 / 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 #30: 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: 30 / 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 #31: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 31 / Number of copies: 14 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #32: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 32 / Number of copies: 20 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 33 / Number of copies: 20 / 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: Chlorophyll F

MacromoleculeName: Chlorophyll F / type: ligand / ID: 34 / Number of copies: 8 / Formula: F6C
Molecular weightTheoretical: 905.457 Da
Chemical component information


ChemComp, No image

ChemComp-F6C:
Chlorophyll F

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Macromolecule #35: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 35 / Number of copies: 6 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #36: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 36 / 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 #37: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 37 / 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 #38: HEME C

MacromoleculeName: HEME C / type: ligand / ID: 38 / Number of copies: 2 / Formula: HEC
Molecular weightTheoretical: 618.503 Da
Chemical component information

ChemComp-HEC:
HEME C

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Macromolecule #39: water

MacromoleculeName: water / type: ligand / ID: 39 / Number of copies: 660 / 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

BufferpH: 6.5
Details: 50 mM MES, 1 M betaine monohydrate, 20 mM CaCl2, 5 mM MgCl2 and 10% (v/v) glycerol, pH 6.8 adjusted with NaOH
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 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: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.17 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 49763
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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