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- EMDB-28539: Structure of a dimeric photosystem II complex acclimated to far-r... -

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Basic information

Entry
Database: EMDB / ID: EMD-28539
TitleStructure of a dimeric photosystem II complex acclimated to far-red light
Map dataFar-red light-acclimated photosystem II
Sample
  • Complex: Far-red light-acclimated photosystem II
    • Protein or peptide: x 16 types
  • Ligand: x 18 types
Function / homology
Function and homology information


cytochrome c-heme linkage / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / photosynthetic electron transport chain / extrinsic component of membrane / photosystem II ...cytochrome c-heme linkage / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / photosynthetic electron transport chain / extrinsic component of membrane / photosystem II / photosynthesis, light reaction / phosphate ion binding / photosynthetic electron transport in photosystem II / chlorophyll binding / plasma membrane-derived thylakoid membrane / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / 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 PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbX ...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 PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II CP43 reaction centre protein / Photosystem II CP43 reaction centre protein superfamily / Photosystem II PsbK / Photosystem II PsbK superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II CP47 reaction centre protein / Photosystem II PsbI / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II 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 reaction center protein T / Cytochrome c-550 / Cytochrome b559 subunit alpha / Photosystem II reaction center protein L / Photosystem II reaction center X protein / Photosystem II 10 kDa phosphoprotein / Photosystem II CP47 reaction center protein / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II manganese-stabilizing polypeptide ...Photosystem II reaction center protein T / Cytochrome c-550 / Cytochrome b559 subunit alpha / Photosystem II reaction center protein L / Photosystem II reaction center X protein / Photosystem II 10 kDa phosphoprotein / Photosystem II CP47 reaction center protein / Photosystem II CP43 reaction center protein / Photosystem II D2 protein / Photosystem II manganese-stabilizing polypeptide / Cytochrome b559 subunit beta / Photosystem II reaction center protein I / Photosystem II 12 kDa extrinsic protein / Photosystem II reaction center protein K
Similarity search - Component
Biological speciesSynechococcus sp. PCC 7335 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsGisriel CJ / Shen G / Flesher DA / Kurashov V / Golbeck JH / Brudvig GW / Amin M / Bryant DA
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)K99GM140174 United States
National Science Foundation (NSF, United States)MCB-1613022 United States
Department of Energy (DOE, United States)DE-FG02-05ER15646 United States
CitationJournal: J Biol Chem / Year: 2023
Title: Structure of a dimeric photosystem II complex from a cyanobacterium acclimated to far-red light.
Authors: Christopher J Gisriel / Gaozhong Shen / David A Flesher / Vasily Kurashov / John H Golbeck / Gary W Brudvig / Muhamed Amin / Donald A Bryant /
Abstract: Photosystem II (PSII) is the water-splitting enzyme central to oxygenic photosynthesis. To drive water oxidation, light is harvested by accessory pigments, mostly chlorophyll (Chl) a molecules, which ...Photosystem II (PSII) is the water-splitting enzyme central to oxygenic photosynthesis. To drive water oxidation, light is harvested by accessory pigments, mostly chlorophyll (Chl) a molecules, which absorb visible light (400-700 nm). Some cyanobacteria facultatively acclimate to shaded environments by altering their photosynthetic machinery to additionally absorb far-red light (FRL, 700-800 nm), a process termed far-red light photoacclimation or FaRLiP. During far-red light photoacclimation, FRL-PSII is assembled with FRL-specific isoforms of the subunits PsbA, PsbB, PsbC, PsbD, and PsbH, and some Chl-binding sites contain Chls d or f instead of the usual Chl a. The structure of an apo-FRL-PSII monomer lacking the FRL-specific PsbH subunit has previously been determined, but visualization of the dimeric complex has remained elusive. Here, we report the cryo-EM structure of a dimeric FRL-PSII complex. The site assignments for Chls d and f are consistent with those assigned in the previous apo-FRL-PSII monomeric structure. All sites that bind Chl d or Chl f at high occupancy exhibit a FRL-specific interaction of the formyl moiety of the Chl d or Chl f with the protein environment, which in some cases involves a phenylalanine sidechain. The structure retains the FRL-specific PsbH2 subunit, which appears to alter the energetic landscape of FRL-PSII, redirecting energy transfer from the phycobiliprotein complex to a Chl f molecule bound by PsbB2 that acts as a bridge for energy transfer to the electron transfer chain. Collectively, these observations extend our previous understanding of the structure-function relationship that allows PSII to function using lower energy FRL.
History
DepositionOct 8, 2022-
Header (metadata) releaseDec 28, 2022-
Map releaseDec 28, 2022-
UpdateJan 25, 2023-
Current statusJan 25, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28539.png

Downloads & links

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Map

FileDownload / File: emd_28539.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFar-red light-acclimated photosystem II
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 384 pix.
= 319.488 Å		0.83 Å/pix.
x 384 pix.
= 319.488 Å		0.83 Å/pix.
x 384 pix.
= 319.488 Å

Surface

Projections

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0013
Minimum - Maximum-0.016514452 - 0.03239517
Average (Standard dev.)3.493629e-05 (±0.00065255375)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 319.488 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Unsharpened map

Fileemd_28539_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Half map: Half 1

Fileemd_28539_half_map_1.map
AnnotationHalf 1
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: Half 2

Fileemd_28539_half_map_2.map
AnnotationHalf 2
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Sample components

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Entire : Far-red light-acclimated photosystem II

EntireName: Far-red light-acclimated photosystem II
Components
  • Complex: Far-red light-acclimated photosystem II
    • Protein or peptide: Photosystem II CP43 reaction center protein
    • Protein or peptide: Photosystem II protein D1
    • Protein or peptide: Photosystem II CP47 reaction center protein
    • Protein or peptide: Photosystem II D2 protein
    • Protein or peptide: Cytochrome b559 subunit alpha
    • Protein or peptide: Cytochrome b559 subunit beta
    • Protein or peptide: Photosystem II reaction center protein H
    • Protein or peptide: Photosystem II reaction center protein I
    • Protein or peptide: Photosystem II reaction center protein K
    • Protein or peptide: Photosystem II reaction center protein L
    • Protein or peptide: Photosystem II reaction center protein M
    • Protein or peptide: Photosystem II 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
  • Ligand: CA-MN4-O5 CLUSTER
  • Ligand: FE (II) ION
  • Ligand: CHLORIDE ION
  • Ligand: CHLOROPHYLL A
  • 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: BICARBONATE ION
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: Chlorophyll F
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: CHLOROPHYLL D
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: (3R)-beta,beta-caroten-3-ol
  • Ligand: DODECYL-BETA-D-MALTOSIDE
  • Ligand: water

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Supramolecule #1: Far-red light-acclimated photosystem II

SupramoleculeName: Far-red light-acclimated photosystem II / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #3, #1-#2, #4-#16
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria)

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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
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 39.958668 KDa
SequenceString: MTTLIQRPNI SQWERFCQWI TSTENRLYIG WFGVLMLPLL GVSITVFVTA FIAAPPVDID GIREPLSGSL LYGNNIITAA VVPTSNAIG LHFYPIWEAA TLDEWLYNGG PYQMIAFHYI PALLCYLGRE WELSYRLGMR PWICIAYSAP VAATISVFLI Y PIGQGSFS ...String:
MTTLIQRPNI SQWERFCQWI TSTENRLYIG WFGVLMLPLL GVSITVFVTA FIAAPPVDID GIREPLSGSL LYGNNIITAA VVPTSNAIG LHFYPIWEAA TLDEWLYNGG PYQMIAFHYI PALLCYLGRE WELSYRLGMR PWICIAYSAP VAATISVFLI Y PIGQGSFS DGLPMGISGT FNFMFVFQAE HNILMHPFHM LGVAGVLGGS LFCAMHGSLV TSSLVRETSD SQSQNEGYKF GQ EEETYNI LAAHGYFGRL IFQYASFNNS RQLHFFLAAW PVVCIWFVAL GISTMAFNLN GFNFNHSVLD SQGRVLPSWA DVV NRASLG FEVMHERNAH NFPLDLASGE SVQVAMRAPH IGA

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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: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 56.44098 KDa
SequenceString: MGLPWYRVHT SVLNDPGRLI AVHIMHNALC AGFAGSMLLF ELALFDPSDP VLNPMWRQGC FLMPFVSRLG VVNSWQGWSV TGETFTNPG FWTFETVAIA HIIFSGLSFL AACWHWVYWD VATFFDPKTD EPVIDLPKVF GIHLTLAGIL CFGFGAFHLT G LFGPGMWV ...String:
MGLPWYRVHT SVLNDPGRLI AVHIMHNALC AGFAGSMLLF ELALFDPSDP VLNPMWRQGC FLMPFVSRLG VVNSWQGWSV TGETFTNPG FWTFETVAIA HIIFSGLSFL AACWHWVYWD VATFFDPKTD EPVIDLPKVF GIHLTLAGIL CFGFGAFHLT G LFGPGMWV SDPLGLTGHI QGVAPEWGAA GFDPHNPGGV VAHHIALGIV AIIGGLFHIF VRPPEYLYKG LRMGNIEGTL AS GLAVFFS GAFIAAGTMW YGTATTPIEL WGPTRYQWDQ GFFQQAISRQ VKASISDGKS PSEAWSEIPT KLAFYDYIGN SPA KGGLFR VGRMVDGDGL PTGWLGHPVF KDGEGRELTV RRMPNFFENF PVVLFDQDGI VRADIPFRQA ESKYGIEQTG VTVS FYGGE LDGQTFSDPK DVKKYARRAQ LGEPFEFDRS VYDSDGLFRT SNRGFFAFFH VIFGLLWFFG HIWHGLRALF QDVFS GIDP SLSAEQVEWG YFKKVGDPTS QQTPA

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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: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 52.375664 KDa
SequenceString: METPLETIPD LSLSPTAEVG SILAPASPGY DEATSGYAWW AGNARLITPE LTGRFLGAHV AHAGLVALWA GGMLLFEVSH FNLSKPMYE QGCILMPHIA TLGIGVGQSG EITSMFPFFA IGVAHLIGSA VLGIGGMYHA IKGPEKLYGF FQFDWTDRAK V AQILGFHI ...String:
METPLETIPD LSLSPTAEVG SILAPASPGY DEATSGYAWW AGNARLITPE LTGRFLGAHV AHAGLVALWA GGMLLFEVSH FNLSKPMYE QGCILMPHIA TLGIGVGQSG EITSMFPFFA IGVAHLIGSA VLGIGGMYHA IKGPEKLYGF FQFDWTDRAK V AQILGFHI AILGIFALLF AAKAMYWGGL YDPWAPGGGD VRLVTNPTLD PRIIFGYLIK RPTGGEGWIV SVNNLEDIIG GH IWIGCIL IAGGIWHILV PPLRWTYNLF PWTGETYLSQ SLGNVAGQAF IAAAFIWFNN TAYPSVFYGP TVPESSQAQS FVF LMRDQG MGADVASAQG PTGLGKYLQR SPTGEIIFGG ETMRFWDARA PWLEPLRGKN GLDLDKLQHD VQPWQLRRAA EYMT HSPIG SLNSVAGLAT ESNAFNYVSP RTWLASAHFI FGFFFLVGHL WHAGRARAAA AGFETGLDRE DEPVLSMAPI DPSLR SD

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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
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 39.596496 KDa
SequenceString: MTITMGSLGS ARDWIKQLDD WLKRDRFVFI GWSGLLLFPC SFLAIGAWFT GTTFVTSWYT HGLVSSYLEG CNFLTVAVST PAESMGHSL LLLWGPEASG DFVRWCQIGG LWTFTALHGV FGLIGFMLRQ IEIARLVGIR PYNAIAFSAP IAVYCATFLI Y PLGQSSWF ...String:
MTITMGSLGS ARDWIKQLDD WLKRDRFVFI GWSGLLLFPC SFLAIGAWFT GTTFVTSWYT HGLVSSYLEG CNFLTVAVST PAESMGHSL LLLWGPEASG DFVRWCQIGG LWTFTALHGV FGLIGFMLRQ IEIARLVGIR PYNAIAFSAP IAVYCATFLI Y PLGQSSWF FGPGFGVSAI FRFLLFFQGF HNYTLNPFHM MGVTGVLGGA LLCAIHGATV QNTLFRDNQS KNTFKGFSTD QG EETYSMV TANRFWSQIF GIAFSNKRWL HFFMLFVPVT GLWMSAIGMA GLAFNLRAYD FVSQEIRAAE DPEFETFYTK NIL LNEGLR AWLSEMDQPA KKFVFPDEVL PRGFSE

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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: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 9.136276 KDa
SequenceString:
MAGVTGERPF GDIVTSVRYW IIHSITIPAL FIAGWLFVST GLAYDAFGTP RPNEYYPSNQ MELPIVDDRY NPDRTLKYQD

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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: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 5.02396 KDa
SequenceString:
MTNIGREQPI SYPIFTIRWL AIHALAIPSV FFLGSIAAMQ FIQR

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Macromolecule #7: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 7.247715 KDa
SequenceString:
MRQKYVSNKA APLQYPLRKL NSEAGKVVPG WGTAPLMGIM LIALLLFILT ILQLYNGTVI VEGIDV

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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: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 4.229917 KDa
SequenceString:
MVTLKIVVYL TVSFFVGLFI FGFLSGDPAR NPSGRDFD

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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: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 5.069053 KDa
SequenceString:
MDVAFLVAEL PEAYRAFGPL IDVLPILPIF FLLLAFVWQA SVGFR

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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: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 4.566261 KDa
SequenceString:
MADRPTNPNK QPVELNRTSL YLGLLVVFVT GLLFSSYFFN

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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: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 3.980772 KDa
SequenceString:
METNKLGFVA SVLFVFVPTV FLLILYIQTA SKKTGT

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Macromolecule #12: Photosystem II manganese-stabilizing polypeptide

MacromoleculeName: Photosystem II manganese-stabilizing polypeptide / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 29.319096 KDa
SequenceString: MIATVLVLTL GLLTACSGTK IAGDSLTYDD IRGSGLANDC PALTGTNMDA IPLEGSQPYQ IRSLCLQPQT FLVETFPSVN GQLKKQAGR FVEGKLLTRS SFTLDQVSGQ LQKASNGALT FVEQGGFDFQ PVTVQIPNGD RVPLLFTVKG LVAKTAEAID T IRPSTRFS ...String:
MIATVLVLTL GLLTACSGTK IAGDSLTYDD IRGSGLANDC PALTGTNMDA IPLEGSQPYQ IRSLCLQPQT FLVETFPSVN GQLKKQAGR FVEGKLLTRS SFTLDQVSGQ LQKASNGALT FVEQGGFDFQ PVTVQIPNGD RVPLLFTVKG LVAKTAEAID T IRPSTRFS GSFDVPPYRT SSFIDPKGRG LAVGYDAAVG IPIQADREAF SRQNNKSFKV GTGNIVLQVD RVNQSTGEIS GS FESQQPS DTDFGSKPAM TVKILGQFYS RITPEIA

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Macromolecule #13: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 3.606362 KDa
SequenceString:
MEAVAYILIF ACIIGTLFFA IAFREPPKIT KD

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Macromolecule #14: Photosystem II 12 kDa extrinsic protein

MacromoleculeName: Photosystem II 12 kDa extrinsic protein / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 17.325834 KDa
SequenceString:
MKLAIRKALG RWLVFGITLM IVQGFMLSGS SLSAMASPSN SNTAFFANGQ INGITLLANA GGKDLRNTVD DKLATAYGSK IDVNNTNIA AFRKHRGLYP TIAGKVVSNA PYDSIEDILD IPGLREVEKD RLQKNMDIFT ISDPVPALVE GADRFNNGVY K

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Macromolecule #15: Cytochrome c-550

MacromoleculeName: Cytochrome c-550 / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 18.814387 KDa
SequenceString:
MKKVFQKFAW WMATFVFVAI GLFGAGPLVE GAIAAELDAN LRTIPLNEAG DTVTLSLEEF TRGQQKFNNA CAICHLGGIT KTNPNVGLD TESLAGAFPD RNNLEGLVDY LHNPTTYDGL TEISELHPST KSSDIYPKMR NLTEDDLRAI SGHILLMPKI R GDQWGAGK TKSL

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Macromolecule #16: Photosystem II reaction center X protein

MacromoleculeName: Photosystem II reaction center X protein / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechococcus sp. PCC 7335 (bacteria) / Strain: ATCC 29403 / PCC 7335
Molecular weightTheoretical: 4.273182 KDa
SequenceString:
MTPSLTNFML SLLAGLLIVV VPATIALIFI SQRDQIRRG

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Macromolecule #17: CA-MN4-O5 CLUSTER

MacromoleculeName: CA-MN4-O5 CLUSTER / type: ligand / ID: 17 / 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 #18: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 18 / Number of copies: 2 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

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Macromolecule #19: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 19 / Number of copies: 4 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #20: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 20 / Number of copies: 60 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #21: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 21 / Number of copies: 4 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

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Macromolecule #22: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 22 / Number of copies: 14 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #23: 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: 23 / Number of copies: 4 / 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 #24: 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: 24 / 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 #25: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 25 / 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 #26: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 26 / Number of copies: 8 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #27: Chlorophyll F

MacromoleculeName: Chlorophyll F / type: ligand / ID: 27 / 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 #28: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 28 / 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 #29: CHLOROPHYLL D

MacromoleculeName: CHLOROPHYLL D / type: ligand / ID: 29 / Number of copies: 2 / Formula: CL7
Molecular weightTheoretical: 895.462 Da
Chemical component information

ChemComp-CL7:
CHLOROPHYLL D

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

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 30 / Number of copies: 4 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #31: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 31 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #32: (3R)-beta,beta-caroten-3-ol

MacromoleculeName: (3R)-beta,beta-caroten-3-ol / type: ligand / ID: 32 / 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 #33: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 33 / Number of copies: 2 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #34: water

MacromoleculeName: water / type: ligand / ID: 34 / Number of copies: 590 / 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

Concentration0.65 mg/mL
BufferpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 41.1 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: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7sa3

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 90191
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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