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- EMDB-24407: High-resolution structure of photosystem II from the mesophilic c... -

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Basic information

Entry
Database: EMDB / ID: EMD-24407
TitleHigh-resolution structure of photosystem II from the mesophilic cyanobacterium, Synechocystis sp. PCC 6803
Map dataPhotosystem II from Synechocystis sp. PCC 6803 at low dose sharpened
Sample
  • Complex: Photosystem II
    • Protein or peptide: x 21 types
  • Ligand: x 17 types
KeywordsPhotosystem II / Cyanobacteria / Synechocystis 6803 / Mesophile / CyanoQ / PHOTOSYNTHESIS
Function / homology
Function and homology information


plasma membrane-derived thylakoid photosystem II / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide ...plasma membrane-derived thylakoid photosystem II / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / photosynthetic electron transport chain / response to herbicide / photosystem II / extrinsic component of membrane / chlorophyll binding / plasma membrane-derived thylakoid membrane / photosynthetic electron transport in photosystem II / phosphate ion binding / photosynthesis, light reaction / : / photosynthesis / respiratory electron transport chain / manganese ion binding / electron transfer activity / protein stabilization / iron ion binding / heme binding / calcium ion binding / metal ion binding / identical protein binding
Similarity search - Function
Photosystem II PsbQ, cyanobacteria / Oxygen-evolving enhancer protein 3 / Oxygen evolving enhancer protein 3 / PsbQ-like domain superfamily / 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 ...Photosystem II PsbQ, cyanobacteria / Oxygen-evolving enhancer protein 3 / Oxygen evolving enhancer protein 3 / PsbQ-like domain superfamily / 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 PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II PsbI / Photosystem II CP47 reaction centre protein / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / Photosystem II protein D1 / Photosystem II D2 protein / Photosystem II cytochrome b559, conserved site / Photosystem II cytochrome b559, alpha subunit / Photosystem II cytochrome b559, beta subunit / Photosystem II cytochrome b559, N-terminal / Photosystem II cytochrome b559, alpha subunit, lumenal region / Photosystem II cytochrome b559, alpha subunit superfamily / Cytochrome b559, alpha (gene psbE) and beta (gene psbF)subunits / Lumenal portion of Cytochrome b559, alpha (gene psbE) subunit / Cytochrome b559 subunits heme-binding site signature. / : / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
Photosystem II CP47 reaction center protein / Cytochrome b559 subunit alpha / Cytochrome b559 subunit beta / Photosystem II D2 protein / Photosystem II CP43 reaction center protein / Photosystem II extrinsic protein O / Photosystem II reaction center protein H / Photosystem II reaction center protein K / Photosystem II protein D1 2 / Photosystem II reaction center protein X ...Photosystem II CP47 reaction center protein / Cytochrome b559 subunit alpha / Cytochrome b559 subunit beta / Photosystem II D2 protein / Photosystem II CP43 reaction center protein / Photosystem II extrinsic protein O / Photosystem II reaction center protein H / Photosystem II reaction center protein K / Photosystem II protein D1 2 / Photosystem II reaction center protein X / Photosystem II reaction center protein M / CyanoQ / Photosystem II reaction center protein J / Photosystem II reaction center protein Z / Photosystem II reaction center protein Y / Photosystem II reaction center protein T / Photosystem II reaction center protein I / Photosystem II extrinsic protein V / Photosystem II extrinsic protein U / Photosystem II reaction center protein L / Photosystem II reaction center protein Psb30
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria) / Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.01 Å
AuthorsGisriel CJ / Brudvig GW
Funding support United States, 1 items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)DE-FG02-05ER15646 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: High-resolution cryo-electron microscopy structure of photosystem II from the mesophilic cyanobacterium, sp. PCC 6803.
Authors: Christopher J Gisriel / Jimin Wang / Jinchan Liu / David A Flesher / Krystle M Reiss / Hao-Li Huang / Ke R Yang / William H Armstrong / M R Gunner / Victor S Batista / Richard J Debus / Gary W Brudvig /
Abstract: Photosystem II (PSII) enables global-scale, light-driven water oxidation. Genetic manipulation of PSII from the mesophilic cyanobacterium sp. PCC 6803 has provided insights into the mechanism of ...Photosystem II (PSII) enables global-scale, light-driven water oxidation. Genetic manipulation of PSII from the mesophilic cyanobacterium sp. PCC 6803 has provided insights into the mechanism of water oxidation; however, the lack of a high-resolution structure of oxygen-evolving PSII from this organism has limited the interpretation of biophysical data to models based on structures of thermophilic cyanobacterial PSII. Here, we report the cryo-electron microscopy structure of PSII from sp. PCC 6803 at 1.93-Å resolution. A number of differences are observed relative to thermophilic PSII structures, including the following: the extrinsic subunit PsbQ is maintained, the C terminus of the D1 subunit is flexible, some waters near the active site are partially occupied, and differences in the PsbV subunit block the Large (O1) water channel. These features strongly influence the structural picture of PSII, especially as it pertains to the mechanism of water oxidation.
History
DepositionJul 8, 2021-
Header (metadata) releaseDec 29, 2021-
Map releaseDec 29, 2021-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0035
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0035
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7rcv
  • Surface level: 0.0035
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24407.png

Downloads & links

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Map

FileDownload / File: emd_24407.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPhotosystem II from Synechocystis sp. PCC 6803 at low dose sharpened
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

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.832 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0035 / Movie #1: 0.0035
Minimum - Maximum-0.036043998 - 0.10133186
Average (Standard dev.)0.00007573805 (±0.0015736797)
SymmetrySpace group: 1
Details

EMDB XML:

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

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8320.8320.832
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z319.488319.488319.488
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0360.1010.000

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Supplemental data

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Additional map: Photosystem II from Synechocystis sp. PCC 6803 at...

Fileemd_24407_additional_1.map
AnnotationPhotosystem II from Synechocystis sp. PCC 6803 at low dose unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Photosystem II

EntireName: Photosystem II
Components
  • Complex: Photosystem II
    • Protein or peptide: Photosystem II protein D1 2
    • Protein or peptide: Photosystem II CP47 reaction center protein
    • Protein or peptide: Photosystem II CP43 reaction center protein
    • Protein or peptide: Photosystem II D2 protein
    • Protein or peptide: Cytochrome b559 subunit alpha
    • Protein or peptide: Cytochrome b559 subunit beta
    • Protein or peptide: Photosystem II reaction center protein H
    • Protein or peptide: Photosystem II reaction center protein I
    • Protein or peptide: Photosystem II reaction center protein J
    • Protein or peptide: Photosystem II reaction center protein K
    • Protein or peptide: Photosystem II reaction center protein L
    • Protein or peptide: Photosystem II reaction center protein M
    • Protein or peptide: Photosystem II manganese-stabilizing polypeptide
    • Protein or peptide: Sll1638 protein
    • Protein or peptide: Photosystem II protein Y
    • Protein or peptide: Photosystem II reaction center protein T
    • Protein or peptide: Photosystem II 12 kDa extrinsic protein
    • Protein or peptide: Cytochrome c-550
    • Protein or peptide: Photosystem II reaction center X protein
    • Protein or peptide: Photosystem II reaction center protein Ycf12
    • Protein or peptide: Photosystem II reaction center protein Z
  • 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: 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: DODECYL-BETA-D-MALTOSIDE
  • Ligand: BICARBONATE ION
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: CALCIUM ION
  • Ligand: (3R)-beta,beta-caroten-3-ol
  • Ligand: water

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Supramolecule #1: Photosystem II

SupramoleculeName: Photosystem II / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#21
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)

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Macromolecule #1: Photosystem II protein D1 2

MacromoleculeName: Photosystem II protein D1 2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 39.744117 KDa
SequenceString: MTTTLQQRES ASLWEQFCQW VTSTNNRIYV GWFGTLMIPT LLTATTCFII AFIAAPPVDI DGIREPVAGS LLYGNNIISG AVVPSSNAI GLHFYPIWEA ASLDEWLYNG GPYQLVVFHF LIGIFCYMGR QWELSYRLGM RPWICVAYSA PVSAATAVFL I YPIGQGSF ...String:
MTTTLQQRES ASLWEQFCQW VTSTNNRIYV GWFGTLMIPT LLTATTCFII AFIAAPPVDI DGIREPVAGS LLYGNNIISG AVVPSSNAI GLHFYPIWEA ASLDEWLYNG GPYQLVVFHF LIGIFCYMGR QWELSYRLGM RPWICVAYSA PVSAATAVFL I YPIGQGSF SDGMPLGISG TFNFMIVFQA EHNILMHPFH MLGVAGVFGG SLFSAMHGSL VTSSLVRETT EVESQNYGYK FG QEEETYN IVAAHGYFGR LIFQYASFNN SRSLHFFLGA WPVIGIWFTA MGVSTMAFNL NGFNFNQSIL DSQGRVIGTW ADV LNRANI GFEVMHERNA HNFPLDLASG EQAPVALTAP AVNG

UniProtKB: Photosystem II protein D1 2

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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: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 55.954355 KDa
SequenceString: MGLPWYRVHT VVLNDPGRLI SVHLMHTALV AGWAGSMALY ELAIFDSSDA VLNPMWRQGM FVLPFMARLG VTSSWNGWSV TGETGLDPG FWSFEGVAAA HIVLSGLLFL AAVWHWVFWD LELFVDPRTG ESALDLPKMF GIHLFLSGLL CFGFGAFHLT G VWGPGMWV ...String:
MGLPWYRVHT VVLNDPGRLI SVHLMHTALV AGWAGSMALY ELAIFDSSDA VLNPMWRQGM FVLPFMARLG VTSSWNGWSV TGETGLDPG FWSFEGVAAA HIVLSGLLFL AAVWHWVFWD LELFVDPRTG ESALDLPKMF GIHLFLSGLL CFGFGAFHLT G VWGPGMWV SDPYGLTGHV QPVAPEWGPA GFNPFNPGGV VAHHIAAGIV GIIAGLFHLT VRPPERLYKA LRMGNIETVL SS SIAAVFF AAFVVAGTMW YGNATTPIEL FGPTRYQWDK GYFQEEIQRR VDSQLAEGAS LSEAWSTIPE KLAFYDYVGN SPA KGGLFR TGAMNSGDGI AQEWIGHPIF KDKEGRELEV RRMPNFFETF PVIMTDADGV VRADIPFRRS ESKFSVEQTG VTVS FYGGA LDGQTFSNPS DVKKFARKAQ LGEGFDFDTE TFNSDGVFRT SPRGWFTFGH AVFALLFFFG HIWHGSRTLF RDVFA GVDP GLEEQVEFGV FAKVGDLSTR KEA

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: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 50.344723 KDa
SequenceString: MVTLSNTSMV GGRDLPSTGF AWWSGNARLI NLSGKLLGAH VAHAGLIVFW AGAMTLFEVA HFIPEKPMYE QGLILLPHIA TLGWGVGPA GEVTDIFPFF VVGVLHLISS AVLGLGGIYH ALRGPEVLEE YSSFFGYDWK DKNQMTNIIG YHLILLGCGA L LLVFKAMF ...String:
MVTLSNTSMV GGRDLPSTGF AWWSGNARLI NLSGKLLGAH VAHAGLIVFW AGAMTLFEVA HFIPEKPMYE QGLILLPHIA TLGWGVGPA GEVTDIFPFF VVGVLHLISS AVLGLGGIYH ALRGPEVLEE YSSFFGYDWK DKNQMTNIIG YHLILLGCGA L LLVFKAMF FGGVYDTWAP GGGDVRVITN PTLNPAIIFG YLLKAPFGGE GWIISVNNME DIIGGHIWIG LICISGGIWH IL TKPFGWA RRALIWSGEA YLSYSLGALS LMGFIASVFV WFNNTAYPSE FYGPTGMEAS QSQAFTFLVR DQRLGANIAS AQG PTGLGK YLMRSPSGEI IFGGETMRFW DFRGPWLEPL RGPNGLDLDK LRNDIQPWQV RRAAEYMTHA PLGSLNSVGG VITD VNSFN YVSPRAWLAT SHFVLGFFFL VGHLWHAGRA RAAAAGFEKG IDRETEPTLF MPDLD

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: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 39.519238 KDa
SequenceString: MTIAVGRAPV ERGWFDVLDD WLKRDRFVFI GWSGLLLFPC AFMALGGWLT GTTFVTSWYT HGLASSYLEG ANFLTVAVSS PADAFGHSL LFLWGPEAQG NLTRWFQIGG LWPFVALHGA FGLIGFMLRQ FEISRLVGIR PYNAIAFSGP IAVFVSVFLM Y PLGQSSWF ...String:
MTIAVGRAPV ERGWFDVLDD WLKRDRFVFI GWSGLLLFPC AFMALGGWLT GTTFVTSWYT HGLASSYLEG ANFLTVAVSS PADAFGHSL LFLWGPEAQG NLTRWFQIGG LWPFVALHGA FGLIGFMLRQ FEISRLVGIR PYNAIAFSGP IAVFVSVFLM Y PLGQSSWF FAPSFGVAGI FRFILFLQGF HNWTLNPFHM MGVAGILGGA LLCAIHGATV ENTLFEDGED SNTFRAFEPT QA EETYSMV TANRFWSQIF GIAFSNKRWL HFFMLFVPVT GLWMSSVGIV GLALNLRAYD FVSQELRAAE DPEFETFYTK NIL LNEGMR AWMAPQDQPH ENFIFPEEVL 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: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 9.454577 KDa
SequenceString:
MSGTTGERPF SDIVTSIRYW VIHSITIPML FIAGWLFVST GLAYDAFGTP RPDEYFTQTR QELPILQERY DINQEIQEFN Q

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: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 4.935784 KDa
SequenceString:
MATQNPNQPV TYPIFTVRWL AVHTLAVPSV FFVGAIAAMQ FIQR

UniProtKB: Cytochrome b559 subunit beta

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Macromolecule #7: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 7.120404 KDa
SequenceString:
MAQRTRLGDI LRPLNSEYGK VVPGWGTTPV MGVFMALFLV FLLIILQIYN SSLILEGFSV DWAG

UniProtKB: Photosystem II reaction center protein H

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Macromolecule #8: Photosystem II reaction center protein I

MacromoleculeName: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 4.338119 KDa
SequenceString:
(FME)LTLKIAVYI VVGLFISLFI FGFLSSDPTR NPGRKDFE

UniProtKB: Photosystem II reaction center protein I

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Macromolecule #9: Photosystem II reaction center protein J

MacromoleculeName: Photosystem II reaction center protein J / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 3.976687 KDa
SequenceString:
(FME)FAEGRIPLW VVGVVAGIGA IGVLGLFFYG AYAGLGSSM

UniProtKB: Photosystem II reaction center protein J

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Macromolecule #10: Photosystem II reaction center protein K

MacromoleculeName: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 5.114127 KDa
SequenceString:
METIYLLAKL PEAYQIFDPL VDVLPVIPLF FLALAFVWQA AVGFK

UniProtKB: Photosystem II reaction center protein K

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Macromolecule #11: Photosystem II reaction center protein L

MacromoleculeName: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 4.476145 KDa
SequenceString:
MDRNSNPNRQ PVELNRTSLY LGLLLVAVLG ILFSSYFFN

UniProtKB: Photosystem II reaction center protein L

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Macromolecule #12: Photosystem II reaction center protein M

MacromoleculeName: Photosystem II reaction center protein M / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 3.910639 KDa
SequenceString:
(FME)QVNNLGFIA SILFVLVPTV FLLILFIQTG KQSES

UniProtKB: Photosystem II reaction center protein M

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Macromolecule #13: Photosystem II manganese-stabilizing polypeptide

MacromoleculeName: Photosystem II manganese-stabilizing polypeptide / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 26.959 KDa
SequenceString: AVDKSQLTYD DIVNTGLANV CPEISSFTRG TIEVEPNTKY FVSDFCMEPQ EYFVKEEPVN KRQKAEYVKG KVLTRQTTSL EQIRGSIAV GADGTLTFKE KDGIDFQPIT VLLPGGEEVP FFFTVKNFTG TTEPGFTSIN SSTDFVGDFN VPSYRGAGFL D PKARGLYT ...String:
AVDKSQLTYD DIVNTGLANV CPEISSFTRG TIEVEPNTKY FVSDFCMEPQ EYFVKEEPVN KRQKAEYVKG KVLTRQTTSL EQIRGSIAV GADGTLTFKE KDGIDFQPIT VLLPGGEEVP FFFTVKNFTG TTEPGFTSIN SSTDFVGDFN VPSYRGAGFL D PKARGLYT GYDNAVALPS AADKFRTNKK ETPLGKGTLS LQVTQVDGST GEIAGIFESE QPSDTDLGAK EPLDVKVRGI FY GRVDTDV

UniProtKB: Photosystem II extrinsic protein O

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Macromolecule #14: Sll1638 protein

MacromoleculeName: Sll1638 protein / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 16.494934 KDa
SequenceString:
MSRLRSLLSL ILVLVTTVLV SCSSPQVEIP TTYSPEKIAQ LQVYVNPIAV ARDGMEKRLQ GLIADQNWVD TQTYIHGPLG QLRRDMLGL ASSLLPKDQD KAKTLAKEVF GHLERLDAAA KDRNGSQAKI QYQEALADFD SFLNLLPQAS

UniProtKB: CyanoQ

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Macromolecule #15: Photosystem II protein Y

MacromoleculeName: Photosystem II protein Y / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 4.204958 KDa
SequenceString:
MDWRVIVVVS PLLIAATWAA INIGAAAIRQ LQDVLGREA

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: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 3.571318 KDa
SequenceString:
(FME)ESVAYILVL TMALAVLFFA IAFREPPRIE K

UniProtKB: Photosystem II reaction center protein T

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Macromolecule #17: Photosystem II 12 kDa extrinsic protein

MacromoleculeName: Photosystem II 12 kDa extrinsic protein / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 14.256163 KDa
SequenceString:
MKFISRLLVA CSLLIGLMGF LGADLAQALT PNPILAELNA VDAKLTTDFG QKIDLNNSDI RDFRGLRGFY PNLASEIIKN APYDTVEEV LDIPGLSETQ KSRLEANLGS FTVTEPSIEL TSGDDRINPG VY

UniProtKB: Photosystem II extrinsic protein U

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Macromolecule #18: Cytochrome c-550

MacromoleculeName: Cytochrome c-550 / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 17.901045 KDa
SequenceString:
MKRFFLVAIA SVLFFFNTMV GSANAVELTE STRTIPLDEA GGTTTLTARQ FTNGQKIFVD TCTQCHLQGK TKTNNNVSLG LADLAGAEP RRDNVLALVE FLKNPKSYDG EDDYSELHPN ISRPDIYPEM RNYTEDDIFD VAGYTLIAPK LDERWGGTIY F

UniProtKB: Photosystem II extrinsic protein V

+
Macromolecule #19: Photosystem II reaction center X protein

MacromoleculeName: Photosystem II reaction center X protein / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 4.189036 KDa
SequenceString:
MTPSLANFLW SLVLGAAIVL IPATVGLIFI SQKDKITRS

UniProtKB: Photosystem II reaction center protein X

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Macromolecule #20: Photosystem II reaction center protein Ycf12

MacromoleculeName: Photosystem II reaction center protein Ycf12 / type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 4.143993 KDa
SequenceString:
MELLAALNLE PIFQLTFLGL IVLAGPAVVF VLAFRGGDL

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: Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa
Molecular weightTheoretical: 6.736161 KDa
SequenceString:
MSIVFQIALA ALVLFSFVMV VGVPVAYASP QNWDRSKPLL YLGSGIWAIL VIVVALLNFL VV

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: 70 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #26: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 26 / Number of copies: 4 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

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Macromolecule #27: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 27 / Number of copies: 18 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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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: 14 / 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: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 29 / Number of copies: 12 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

+
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: DODECYL-BETA-D-MALTOSIDE

MacromoleculeName: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 31 / Number of copies: 62 / Formula: LMT
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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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 / pH buffer*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: 14 / 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: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 34 / 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 #35: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 35 / 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 #36: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 36 / Number of copies: 6 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #37: (3R)-beta,beta-caroten-3-ol

MacromoleculeName: (3R)-beta,beta-caroten-3-ol / type: ligand / ID: 37 / 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 #38: water

MacromoleculeName: water / type: ligand / ID: 38 / Number of copies: 1236 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.8
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: 40.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.01 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 202844
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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