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- EMDB-33597: PSII-d1-d2 of PBS-PSII-PSI-LHCs megacomplex from Porphyridium pur... -

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Basic information

Entry
Database: EMDB / ID: EMD-33597
TitlePSII-d1-d2 of PBS-PSII-PSI-LHCs megacomplex from Porphyridium purpureum.
Map data
Sample
  • Complex: Lateral hexamer of PBS
    • Protein or peptide: x 3 types
  • Protein or peptide: x 26 types
  • Ligand: x 14 types
Function / homology
Function and homology information


monooxygenase activity / 2 iron, 2 sulfur cluster binding / metal ion binding / membrane
Similarity search - Function
Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily
Similarity search - Domain/homology
Methanesulfonate monooxygenase ferredoxin subunit / Uncharacterized protein / Uncharacterized protein
Similarity search - Component
Biological speciesPorphyridium purpureum (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsYou X / Zhang X / Cheng J / Xiao YN / Sun S / Sui SF
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structure of lateral hexamer of PBS-PSII-PSI-LHCs megacomplex at 6.3 Angstroms resolution.
Authors: You X / Zhang X / Cheng J / Xiao YN / Sun S / Sui SF
History
DepositionJun 12, 2022-
Header (metadata) releaseJan 18, 2023-
Map releaseJan 18, 2023-
UpdateJan 18, 2023-
Current statusJan 18, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33597.png

Downloads & links

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Map

FileDownload / File: emd_33597.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 384 pix.
= 417.792 Å		1.09 Å/pix.
x 384 pix.
= 417.792 Å		1.09 Å/pix.
x 384 pix.
= 417.792 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.088 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.74992794 - 1.0320665
Average (Standard dev.)0.0005404581 (±0.041370396)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 417.79202 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33597_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_33597_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Lateral hexamer of PBS

EntireName: Lateral hexamer of PBS
Components
  • Complex: Lateral hexamer of PBS
    • Protein or peptide: CNT
    • Protein or peptide: CNT
    • Protein or peptide: CNT
  • 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: Cytochrome b559 subunit beta
  • Protein or peptide: PSII_Pbs31 domain-containing protein
  • Protein or peptide: Photosystem II reaction center protein K
  • Protein or peptide: LPP1
  • Protein or peptide: Cytochrome c550
  • Protein or peptide: Psb34
  • Protein or peptide: Psb34
  • Protein or peptide: Oxygen-evolving enhancer protein
  • Protein or peptide: Photosystem II reaction center protein T
  • Protein or peptide: PS II complex 12 kDa extrinsic protein
  • Protein or peptide: Photosystem II D2 protein
  • 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 L
  • Protein or peptide: PsbM
  • Protein or peptide: Photosystem II reaction center protein Ycf12
  • Protein or peptide: Photosystem II reaction center X protein
  • Protein or peptide: Photosystem II reaction center protein Z
  • Protein or peptide: Photosystem II protein Y
  • Protein or peptide: PsbQ'
  • Protein or peptide: Cytochrome b559 subunit alpha
  • Protein or peptide: Photosystem II reaction center Psb28 protein
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: BETA-CAROTENE
  • Ligand: CHLORIDE ION
  • Ligand: CHLOROPHYLL A
  • Ligand: CA-MN4-O5 CLUSTER
  • Ligand: FE (III) ION
  • Ligand: PHEOPHYTIN A
  • 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: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: BICARBONATE ION
  • Ligand: GLYCEROL
  • Ligand: water

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Supramolecule #1: Lateral hexamer of PBS

SupramoleculeName: Lateral hexamer of PBS / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Porphyridium purpureum (eukaryote)

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Macromolecule #1: CNT

MacromoleculeName: CNT / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 2.292505 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AA

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Macromolecule #2: CNT

MacromoleculeName: CNT / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 1.652805 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
AAAAAAAAAA AAAAAAAAAA AAA

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Macromolecule #3: CNT

MacromoleculeName: CNT / type: protein_or_peptide / ID: 3 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 5.135611 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AA

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Macromolecule #4: Photosystem II protein D1

MacromoleculeName: Photosystem II protein D1 / type: protein_or_peptide / ID: 4 / Number of copies: 4 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 38.341629 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString: ASLWERFCSW VTSTENRLYI GWFGVLMIPT LLTATSVFII AFVAAPPVDI DGIREPVAGS LLYGNNIISG AVIPSSAAIG IHFYPIWEA ASLDEWLYNG GCYPLIVLHF LLGVACYMGR EWELSYRLGM RPWIAVAFSA PVAAATAVFL IYPIGQGSFS D GMPLGISG ...String:
ASLWERFCSW VTSTENRLYI GWFGVLMIPT LLTATSVFII AFVAAPPVDI DGIREPVAGS LLYGNNIISG AVIPSSAAIG IHFYPIWEA ASLDEWLYNG GCYPLIVLHF LLGVACYMGR EWELSYRLGM RPWIAVAFSA PVAAATAVFL IYPIGQGSFS D GMPLGISG TFNFMIVFQA EHNILMHPFH QLGVAGVFGG SLFSAMHGSL VTSSLIRETT ENESANYGYK FGQEEETYNI VA AHGYFGR LIFQYASFNN SRSLHFFLGL WPVVGIWLTS ISVSTMAFNL NGFNFNQSVV DSQGRVINTW ADIINRANLG MEV MHERNA HNFPLDLASG ESLPVALTAP AVNG

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Macromolecule #5: Photosystem II CP47 reaction center protein

MacromoleculeName: Photosystem II CP47 reaction center protein / type: protein_or_peptide / ID: 5 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 56.412215 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString: MGLPWYRVHT VVLNDPGRLI AVHLMHTALV AGWAGSMALY ELAVFDPSDP VLNPMWRQGM FVMPFMTRLG VTDSWGGWSI TGESVSNPG IWSFEGVALT HIVLSGLLFL AAIWHWIYWD LELFRDPRTG EPALDLPKIF GIHLLLASIL CFGFGAFHVT G LFGPGIWV ...String:
MGLPWYRVHT VVLNDPGRLI AVHLMHTALV AGWAGSMALY ELAVFDPSDP VLNPMWRQGM FVMPFMTRLG VTDSWGGWSI TGESVSNPG IWSFEGVALT HIVLSGLLFL AAIWHWIYWD LELFRDPRTG EPALDLPKIF GIHLLLASIL CFGFGAFHVT G LFGPGIWV SDAYGITGKV QPVAPAWGPE GFNPFNPGGV ASHHIAAGTV GILAGVFHLS IRPPQRLYRA LRMGNIETVL SS SIAAVFF AAFITSGTMW YGCATTPIEL FGPTRYQWDS GYFQQEIERQ VENSLSEGLS LSDAWSRIPD KLAFYDYIGN NPA KGGLFR SGPMDKGDGI AEAWLGHPVF KDKEGRELTV RRMPAFFETF PVILVDQDGI IRADIPFRRA ESKYSIEQVG VTID FYGGK LNGQSFTDAP TVKKYARKAQ LGEVFEFDRT TLESDGVFRS SPRGWYTFGH ANFALLFFFG HLWHGSRTLF RDVFA GIGA EVTEQVEFGA FAKLGDRTTK KQGIV

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Macromolecule #6: Photosystem II CP43 reaction center protein

MacromoleculeName: Photosystem II CP43 reaction center protein / type: protein_or_peptide / ID: 6 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 52.294605 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString: NVMKTLYSQR RFCHVETPFN NNVSAAGRDI ESTGFAWWSG NARLINVSGK LLGAHVAHAG IMVFWCGAMT LFEVAHFIPE KPLYEQGFI LLPHLATLGW GVGPGGEIVD TYPYFVVGVL HLISSAVLGF GGIYHSIIGP DTLEESFPFF GYDWRDKNKM T TILGIHLI ...String:
NVMKTLYSQR RFCHVETPFN NNVSAAGRDI ESTGFAWWSG NARLINVSGK LLGAHVAHAG IMVFWCGAMT LFEVAHFIPE KPLYEQGFI LLPHLATLGW GVGPGGEIVD TYPYFVVGVL HLISSAVLGF GGIYHSIIGP DTLEESFPFF GYDWRDKNKM T TILGIHLI LLGLGSFLLV AKAMFFGGIY DTWAPGGGDV RYVTNPTLNP AVIFGYVLKS PFGGDGWVVS INNQEDLVGG HV WVGVICI AGGIWHILTK PFAWARRAFV WSGEAYLSYS LAALALMGFT ASCYAWYNNT AYPSEFYGPT GPEASQAQAF TFL VRDQRL GANVASAQGP TGLGKYLMRS PSGEIIFGGE TMRFWDLRAP WLEPLRGPNG LDLNKIKNDI QPWQERRAAE YMTH APLGS LNSVGGVATE INSVNYVSPR SWLTSSHFFL PFFLFIGHLW HAGRARAAAA GFEKGINREN EPVLFMRPLD

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Macromolecule #7: Cytochrome b559 subunit beta

MacromoleculeName: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 7 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 5.032883 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MTRGNPNQSV TYPIFTFRWL AIHGIAVPTV FFLGAITSMQ FIQR

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Macromolecule #8: PSII_Pbs31 domain-containing protein

MacromoleculeName: PSII_Pbs31 domain-containing protein / type: protein_or_peptide / ID: 8 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 22.527773 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString: MAFVNGVVPV AASASVHRRA VCVRMSEQDA ALSRRAVLGL AGSAAAALAL AAAPISPALA DGAVSSATKY RARNLYGSRI FDAAPMIEK LVAAVNAKNW DTVESIVGKK GPLEDLKNSF TLFATGAYPT DKLVQTDLIG NTAVIYEMAG ILRKAADQQD Q KKALKAVN ...String:
MAFVNGVVPV AASASVHRRA VCVRMSEQDA ALSRRAVLGL AGSAAAALAL AAAPISPALA DGAVSSATKY RARNLYGSRI FDAAPMIEK LVAAVNAKNW DTVESIVGKK GPLEDLKNSF TLFATGAYPT DKLVQTDLIG NTAVIYEMAG ILRKAADQQD Q KKALKAVN ELVKSYKEYL AAGELKENPF ADAPGQAWSG DFSPLRKTGK SPYIE

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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: 4 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 5.178225 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MHNHFFLAAL PEAYSIFKPL VDILPVIPVF FLLLAFVWQA AIGFR

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Macromolecule #10: LPP1

MacromoleculeName: LPP1 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 8.476257 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA

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Macromolecule #11: Cytochrome c550

MacromoleculeName: Cytochrome c550 / type: protein_or_peptide / ID: 11 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 17.764377 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MLKKVFWQPV IIGLIVLLSS EYVLAIELDD ITRTIPLEAS GTTITLTPEQ VKRGKRLFNS SCAICHNGGI TKTNPNVGLD PESLSLATP PRDNVNSLID YMKDPTSYDG SESIAEIHPS IKSADIFPKM RSLSDDDLFA IAGHILIQPK VASEKWGGGK I YY

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Macromolecule #12: Psb34

MacromoleculeName: Psb34 / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 1.937116 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
AAAAAAAAAA AAAAAAAAAA AAAAAAA

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Macromolecule #13: Psb34

MacromoleculeName: Psb34 / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 2.079272 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
AAAAAAAAAA AAAAAAAAAA AAAAAAAAA

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Macromolecule #14: Oxygen-evolving enhancer protein

MacromoleculeName: Oxygen-evolving enhancer protein / type: protein_or_peptide / ID: 14 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 30.890066 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString: MEVVGKDSKA KSALAALAVS AAVMGTQMTP VQAFTEEDFR QLSYEQVKGT GLANRCPEVD GTKGSIKIEK GKKYKIVDMC IEPKSFQVE DEVGKGKQAR KEFVDTKLMT RATYTLTGIE GPLTVNANGD LEFQEKDGID YAATTVQLPG GERVPFLFTV K ELVATAKG ...String:
MEVVGKDSKA KSALAALAVS AAVMGTQMTP VQAFTEEDFR QLSYEQVKGT GLANRCPEVD GTKGSIKIEK GKKYKIVDMC IEPKSFQVE DEVGKGKQAR KEFVDTKLMT RATYTLTGIE GPLTVNANGD LEFQEKDGID YAATTVQLPG GERVPFLFTV K ELVATAKG DSIGSGTEFG GEFTVPSYRT GLFLDPKGRG GVTGYDMAVA LPGMMADGAE GQDELFKETN KVFQVTKGEI EM GVQKVDP STNEIAGVFV SEQLTDTDMG AKAPKNILLK GVFYARIVEE

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Macromolecule #15: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 15 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 3.579424 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MEALVYVFLL VGTLMVIFFA VFFRDPPKIA K

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Macromolecule #16: PS II complex 12 kDa extrinsic protein

MacromoleculeName: PS II complex 12 kDa extrinsic protein / type: protein_or_peptide / ID: 16 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 16.382673 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MAFVGASVMG AQTRRSQSTC GVRMSMNADD AQVSRRQMLS VAAAAVAAFG VARGANAEME YEGVMYLGGS DKIDVNNANI RAYTKYPGM YPNIAREIVK NGPFESVDDV LKIETLTATQ KSVVEKYKNN LIALPSRPEY VIDKLNNGLY R

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Macromolecule #17: Photosystem II D2 protein

MacromoleculeName: Photosystem II D2 protein / type: protein_or_peptide / ID: 17 / Number of copies: 4 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 39.253891 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString: MTIAIGQEKG RGWFDLIDDW LKRDRFVFIG WSGLLLLPCS YLALGGWLTG TTFVTSWYTH GLASSYLEGC NFLTAAVSTP ANSMGHSLL FLWGPEAQGD FTRWCQIGGL WTFIALHGAF GLIGFCLRQF EIARLVGLRP YNAIAFSGPI SVFVSVFLMY P LGQASWFF ...String:
MTIAIGQEKG RGWFDLIDDW LKRDRFVFIG WSGLLLLPCS YLALGGWLTG TTFVTSWYTH GLASSYLEGC NFLTAAVSTP ANSMGHSLL FLWGPEAQGD FTRWCQIGGL WTFIALHGAF GLIGFCLRQF EIARLVGLRP YNAIAFSGPI SVFVSVFLMY P LGQASWFF APSFGVAAIF RFLLFLQGFH NWTLNPFHMM GVAGILGGAL LCAIHGATVE NTLFEDGDAA DTFRAFTPTQ SE ETYSMVT ANRFWSQIFG VAFSNKRWLH FFMLFVPVTG LWTSSIGIVG LALNLRAYDF VSQELRAAED PEFETFYTKN ILL NEGIRA WMAAQDQPHE NFIFPEEVLP RGNAL

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Macromolecule #18: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 18 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 7.576939 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MALRTRLGEI LRPLNSEYGK VAPGWGTTPI MGVFMLLFFL FLLIILQIYN SSLIIENVDV DWTSLGN

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Macromolecule #19: Photosystem II reaction center protein I

MacromoleculeName: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 19 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 4.522269 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MFTLKIFVYT TVIFFISLFV FGFLSNDPSR NPNRKDLE

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Macromolecule #20: Photosystem II reaction center protein J

MacromoleculeName: Photosystem II reaction center protein J / type: protein_or_peptide / ID: 20 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 3.944665 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MATTGRVPIW LVAFVGGIAV IGLLGLFIYG SYSGVGSSL

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Macromolecule #21: Photosystem II reaction center protein L

MacromoleculeName: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 21 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 4.420138 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MSNPNPNKQP VELNRTSLFW GLLLIFVLAV LFSSYFFN

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Macromolecule #22: PsbM

MacromoleculeName: PsbM / type: protein_or_peptide / ID: 22 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 10.463042 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MYGFVSGSPI SARVNQNNRL AVASKRAAVA VPAGSRKVAM NFDLGATSNN MVLLAEGGGM SVSFPAYLAV LLGTFVPVAF LVILYIQSE ARKAGASSKS DE

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Macromolecule #23: Photosystem II reaction center protein Ycf12

MacromoleculeName: Photosystem II reaction center protein Ycf12 / type: protein_or_peptide / ID: 23 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 3.681562 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MINWQVIGQL VSLAIIVLVG PAVIFLLAFK KGNL

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Macromolecule #24: Photosystem II reaction center X protein

MacromoleculeName: Photosystem II reaction center X protein / type: protein_or_peptide / ID: 24 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 4.147984 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MTPSLSSFIN SLILGLVIVV IPISGALLFV SQKDKVTRS

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Macromolecule #25: Photosystem II reaction center protein Z

MacromoleculeName: Photosystem II reaction center protein Z / type: protein_or_peptide / ID: 25 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 6.500705 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MVTALQILVF ALTILSTILV VSIPVILASP GQWEQSKNLV FTGAGVWSGL VIVTGLLNSF AT

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Macromolecule #26: Photosystem II protein Y

MacromoleculeName: Photosystem II protein Y / type: protein_or_peptide / ID: 26 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 3.72749 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
DTRLLIVLLP VLAAASWALY NIGRVALQQF KRL

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Macromolecule #27: PsbQ'

MacromoleculeName: PsbQ' / type: protein_or_peptide / ID: 27 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 22.397451 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString: MAFVSGFAGA QIASGSSAQV CRAPAAVRMS AAGEEMSRRD LMAGVATAAA GLLVIPGAAM AGDAPKQSFF GGSSASSPFV YNMKQTGEI LYKPLNDEDL QFHKNVLEKS RGELDRTSEQ IARKSWDDMR GVIRNQMYNM RHSQLRLIES VESAEKQKAA K KNYNDLKK ...String:
MAFVSGFAGA QIASGSSAQV CRAPAAVRMS AAGEEMSRRD LMAGVATAAA GLLVIPGAAM AGDAPKQSFF GGSSASSPFV YNMKQTGEI LYKPLNDEDL QFHKNVLEKS RGELDRTSEQ IARKSWDDMR GVIRNQMYNM RHSQLRLIES VESAEKQKAA K KNYNDLKK SLEEMDLAAR NKKQEDARKF RASALKAFDS FTTSVGI

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Macromolecule #28: Cytochrome b559 subunit alpha

MacromoleculeName: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 28 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 9.47764 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MSGGSTGERP FSDIITSIRY WVIHSITIPS LFVAGWLFVS TGLAYDVFGT PRPNEYFTQD RQQVPLVNDR FSAKQELEDL TKGL

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Macromolecule #29: Photosystem II reaction center Psb28 protein

MacromoleculeName: Photosystem II reaction center Psb28 protein / type: protein_or_peptide / ID: 29 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 12.850428 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MAVIQFIPGL NETVIPEVKL TRSRDGNTGT ATFRFTNPNV LDISTSKEGD ITGMYLDDEE GQLITRDVNA KFVNGRPQAI EAVYVIRSP EDWDRFMRFM ERYANANGLT FTKAA

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Macromolecule #30: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 30 / Number of copies: 30 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #31: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 31 / Number of copies: 40 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #32: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 32 / Number of copies: 4 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #33: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 33 / Number of copies: 140 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #34: CA-MN4-O5 CLUSTER

MacromoleculeName: CA-MN4-O5 CLUSTER / type: ligand / ID: 34 / Number of copies: 4 / Formula: OEX
Molecular weightTheoretical: 339.827 Da
Chemical component information

ChemComp-OEX:
CA-MN4-O5 CLUSTER

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Macromolecule #35: FE (III) ION

MacromoleculeName: FE (III) ION / type: ligand / ID: 35 / Number of copies: 4 / Formula: FE
Molecular weightTheoretical: 55.845 Da

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Macromolecule #36: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 36 / Number of copies: 8 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

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Macromolecule #37: 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: 37 / Number of copies: 8 / 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 #38: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 38 / Number of copies: 36 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #39: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 39 / Number of copies: 40 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #40: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 40 / Number of copies: 8 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #41: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 41 / Number of copies: 4 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION

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Macromolecule #42: GLYCEROL

MacromoleculeName: GLYCEROL / type: ligand / ID: 42 / Number of copies: 4 / Formula: GOL
Molecular weightTheoretical: 92.094 Da
Chemical component information

ChemComp-GOL:
GLYCEROL

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Macromolecule #43: water

MacromoleculeName: water / type: ligand / ID: 43 / Number of copies: 4 / 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 statecell

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Sample preparation

BufferpH: 7
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: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 6.0 µm / Nominal defocus min: 1.0 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:

6kgx

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 321000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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