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- EMDB-33561: PSI-LHCs of PBS-PSII-PSI-LHCs from Porphyridium purpureum. -

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Basic information

Entry
Database: EMDB / ID: EMD-33561
TitlePSI-LHCs of PBS-PSII-PSI-LHCs from Porphyridium purpureum.
Map data
Sample
  • Complex: Lateral hexamer of PBS
    • Protein or peptide: x 24 types
  • Ligand: x 12 types
Biological speciesPorphyridium purpureum (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 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 8, 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_33561.png

Downloads & links

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Map

FileDownload / File: emd_33561.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.63 Å/pix.
x 256 pix.
= 417.792 Å		1.63 Å/pix.
x 256 pix.
= 417.792 Å		1.63 Å/pix.
x 256 pix.
= 417.792 Å

Surface

Projections

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Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.632 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-1.11904 - 2.625814
Average (Standard dev.)-0.00022995572 (±0.059641745)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 417.792 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33561_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_33561_half_map_2.map
Projections & Slices
AxesZYX

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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: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein of LHCII type III, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein 1B-21, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein 1B-21, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein 1B-21, chloroplastic
    • Protein or peptide: Fucoxanthin-chlorophyll a-c binding protein, chloroplastic
    • Protein or peptide: RedCAP
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A1
    • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A2
    • Protein or peptide: Photosystem I reaction center subunit II
    • Protein or peptide: Photosystem I reaction center subunit IV
    • Protein or peptide: Photosystem I reaction center subunit III
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: Photosystem I reaction center subunit PsaK
    • Protein or peptide: Photosystem I reaction center subunit XI
    • Protein or peptide: Photosystem I reaction center subunit XII
    • Protein or peptide: Ferredoxin
    • Protein or peptide: Photosystem I subunit O
    • Protein or peptide: PsaR
    • Protein or peptide: LPS1
    • Protein or peptide: Photosystem I iron-sulfur center
    • Protein or peptide: Photosystem I reaction center subunit VIII
    • Protein or peptide: Cytochrome c6
  • Ligand: CHLOROPHYLL A
  • Ligand: beta-D-glucopyranose
  • Ligand: (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol
  • Ligand: PHYLLOQUINONE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: BETA-CAROTENE
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: (2S)-2,3-dihydroxypropyl octadecanoate
  • Ligand: PROLINE
  • Ligand: FE2/S2 (INORGANIC) CLUSTER
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE

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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-#24
Source (natural)Organism: Porphyridium purpureum (eukaryote)

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Macromolecule #1: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 24.109686 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString: MAAAFVSGAG AALGRVNKVA AIQSKSVKAA VPVKAGRIAM MAEMSKSIPF LEKPKNLDGS MAGDVGFDPL GFSDKWDVKF LREAELKHG RICMLAALGF IYPEIMGGKS IPSPEGYFTE LNPLKAVKTI PTAGLLQIVL FVMVLEAISW NKVFMDKTSA P GDFKFDPL ...String:
MAAAFVSGAG AALGRVNKVA AIQSKSVKAA VPVKAGRIAM MAEMSKSIPF LEKPKNLDGS MAGDVGFDPL GFSDKWDVKF LREAELKHG RICMLAALGF IYPEIMGGKS IPSPEGYFTE LNPLKAVKTI PTAGLLQIVL FVMVLEAISW NKVFMDKTSA P GDFKFDPL GLKSPKMELS EVKNGRLAMI AVGGMIHQVL LTKQPILAQL KNGPYLPKES MFPIW

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Macromolecule #2: Chlorophyll a-b binding protein of LHCII type III, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein of LHCII type III, chloroplastic
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 21.795396 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString: MAAFVSGFGL ARASAGRSSV CSKNAHVTMM AKSKAIPFLE APAKLDGTLV GDVGFDPLGL SATLDVKYLR AAELKHGRIA MLAALGFVV QEILAPKQSG PFTEPDPFLA IYKVPVEGWY QIIAAISLVE LVTFKENYDG SAEPGNFGFD PLGLGKDKSV F DKYALSEL ...String:
MAAFVSGFGL ARASAGRSSV CSKNAHVTMM AKSKAIPFLE APAKLDGTLV GDVGFDPLGL SATLDVKYLR AAELKHGRIA MLAALGFVV QEILAPKQSG PFTEPDPFLA IYKVPVEGWY QIIAAISLVE LVTFKENYDG SAEPGNFGFD PLGLGKDKSV F DKYALSEL KNGRLAMIAW TAFAIQQIVT GKGVIKQLME FQPLM

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Macromolecule #3: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 23.179254 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString: MICKMAAAFV SGVGLARASV GRAAVCTKNV QVSMMAKSKS VPFMDAPPAL DGSLAGDVGF DPLNISGFLN IKWLRESELK HGRICMLAA LGMIVQEVYR FPFYQGAPAV ATEAHDYFAK WNGPLGQVLI FASFFEIMTT PAVIQMITGE SDRAPGYFAF D PLGLGKNP ...String:
MICKMAAAFV SGVGLARASV GRAAVCTKNV QVSMMAKSKS VPFMDAPPAL DGSLAGDVGF DPLNISGFLN IKWLRESELK HGRICMLAA LGMIVQEVYR FPFYQGAPAV ATEAHDYFAK WNGPLGQVLI FASFFEIMTT PAVIQMITGE SDRAPGYFAF D PLGLGKNP DARKRFEVSE LKNGRLAMIA VGGMVHQMWL TKMGIIGQLQ AGKFMP

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Macromolecule #4: Chlorophyll a-b binding protein 1B-21, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein 1B-21, chloroplastic / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 23.102139 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString: MSAAFVSGLG LAQARVVRRS VCSSVAAAPM KMVTSKSMPF MEAPPALDGS MVGDVGFDPL GFTRTFDVKW MREAELKHCR ICMLAVLGF VVQEIFRLPM YSGAPKLATD AHDYFVSQGA LKQILLFISF FEVFGTVALW ETMQGTREPG VFGFDPLNLG K NPASYEKY ...String:
MSAAFVSGLG LAQARVVRRS VCSSVAAAPM KMVTSKSMPF MEAPPALDGS MVGDVGFDPL GFTRTFDVKW MREAELKHCR ICMLAVLGF VVQEIFRLPM YSGAPKLATD AHDYFVSQGA LKQILLFISF FEVFGTVALW ETMQGTREPG VFGFDPLNLG K NPASYEKY ALSELKNGRL AMIAVGGFIH QMWVYKQGVL YQLAHFKPMS L

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Macromolecule #5: Chlorophyll a-b binding protein 1B-21, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein 1B-21, chloroplastic / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 22.816656 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString: MAFVSGVGSG LSQSRVAQRS VCKANGAALK MEGKSASVPF LTKPEKLDGS MAGDVGFDPL GFSNYLSLEY LRESEIKHGR VAMLACLGI WIQEIVHLPG KEFSNPLATE AFFQVPAGGI AQIFLACGLA EFIGHRGKMT YMDIAADKER KPGAMGFDPL N MSKGKSAE ...String:
MAFVSGVGSG LSQSRVAQRS VCKANGAALK MEGKSASVPF LTKPEKLDGS MAGDVGFDPL GFSNYLSLEY LRESEIKHGR VAMLACLGI WIQEIVHLPG KEFSNPLATE AFFQVPAGGI AQIFLACGLA EFIGHRGKMT YMDIAADKER KPGAMGFDPL N MSKGKSAE AMKKLELNEV KNGRLAMIGV GGLIHAMFIS HQPTLFQLAH FKPL

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Macromolecule #6: Chlorophyll a-b binding protein 1B-21, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein 1B-21, chloroplastic / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 23.60559 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString: MDGKVNKMAA FVSSLGLARA SVGRGAVCTK PGSAQLSMMA KSKSVPFMEA PAALDGSMVG DVGFDPLGFS NYIDLKFLRE AELKHCRIC MLAALGIIVQ EVYQFPFYSG APRLATDAHD YFVKFGSLNQ ILLFASFIEL VAGTPGIIQT MRGETDRAPG Y FAFDPLGL ...String:
MDGKVNKMAA FVSSLGLARA SVGRGAVCTK PGSAQLSMMA KSKSVPFMEA PAALDGSMVG DVGFDPLGFS NYIDLKFLRE AELKHCRIC MLAALGIIVQ EVYQFPFYSG APRLATDAHD YFVKFGSLNQ ILLFASFIEL VAGTPGIIQT MRGETDRAPG Y FAFDPLGL GKDKAKFERY QLSELKNGRL AMIAVGGFIH QAWMAKVPVL EQLSTGKLLP

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Macromolecule #7: Fucoxanthin-chlorophyll a-c binding protein, chloroplastic

MacromoleculeName: Fucoxanthin-chlorophyll a-c binding protein, chloroplastic
type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 22.20876 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString: MAAFVSGFSG LAVRAHTSRA SCAAVRMAAS PMSKSVPFLK KPTQLDGWAG SAEFDPIGIS EYVDIRYLRE SELKHGRICM LAAVGLIVQ ELVTFGGKYF PKMLPVQAHD FYLGGMSQLL LFIAAFESLS YFAIRETLEG KREPGDFGFD PLNLGKEPAA F AKFRESEL ...String:
MAAFVSGFSG LAVRAHTSRA SCAAVRMAAS PMSKSVPFLK KPTQLDGWAG SAEFDPIGIS EYVDIRYLRE SELKHGRICM LAAVGLIVQ ELVTFGGKYF PKMLPVQAHD FYLGGMSQLL LFIAAFESLS YFAIRETLEG KREPGDFGFD PLNLGKEPAA F AKFRESEL KNGRLAMIAV GGMIHQQWVS GQGTLEQLFH FKPL

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Macromolecule #8: RedCAP

MacromoleculeName: RedCAP / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 36.156082 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString: MYGFVSTAGG VSGAGVRPVG AASKLAARAV SVPAKRASLR MGVFEKAMSD FKSDFPQFAK KGWGVTVKSE RWNGRHAMAG WLIIWITAY MKGHGMLPSG ILEPSVWGPL AQLGGYEPIP RERAVVLIAN VHLLLVSVAA TIAPFSFQDK LLLDEGESDE A PAGLIPSF ...String:
MYGFVSTAGG VSGAGVRPVG AASKLAARAV SVPAKRASLR MGVFEKAMSD FKSDFPQFAK KGWGVTVKSE RWNGRHAMAG WLIIWITAY MKGHGMLPSG ILEPSVWGPL AQLGGYEPIP RERAVVLIAN VHLLLVSVAA TIAPFSFQDK LLLDEGESDE A PAGLIPSF KLGLTKEAEL WNGRLAMLGL IVIVFASVSS GTSILDLTNQ MFGNASQIGS ARLVADVWKS APLLPQPQKS SR RPVFCEN PLWRRAQEGE KTPTEATKWQ TRSPWTGLGT VICASSFPKP FDTCITVAKW RCVIAFVLRH HFGEQMIFAQ TMR LRTGFI PMPCAQ

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Macromolecule #9: Photosystem I P700 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 83.31168 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString: MTTSSKEQEA KKVRITVDKD PVETSFEKWA KPGHFSRTLA KGPKTTTWIW NLHADAHDFD GHTSSLEDVS RKIFSAHFGQ LSVIFLWLS GMYFHGARFS NYVAWLSNPT AIKPSAQVVW PIVGQDILNG DVGGGFQGVQ ITSGFFQLWR ASGITNEKQL Y ATAIGGLV ...String:
MTTSSKEQEA KKVRITVDKD PVETSFEKWA KPGHFSRTLA KGPKTTTWIW NLHADAHDFD GHTSSLEDVS RKIFSAHFGQ LSVIFLWLS GMYFHGARFS NYVAWLSNPT AIKPSAQVVW PIVGQDILNG DVGGGFQGVQ ITSGFFQLWR ASGITNEKQL Y ATAIGGLV MSALMLFAGW FHYHKAAPKL EWFQNVESMM NHHLAGLLGL GCLSWAGHQI HVSLPINKLL DAGVAPSEIP LP HEFIVNR ELMAQLYPSF SKGLTPFFTL DWNAYSDFLT FKGGLNPITG GLWLSDTAHH HLALAVLFIV AGHMYRTNWG IGH SMKEIL EAHKGPFTGE GHKGLYEILT TSWHAQLAIN LAMIGSLSII VAHHMYAMPP YPYIATDYPT QLSLFTHHMW IGGF CVTGA AAHGAIFMVR DYSPAQNYNN LLDRMIRHRD AIISHLNWVC IFLGFHSFGL YIHNDTMRAL GRSQDMFSDT AIQLQ PIFA QWIQSIHTLA PGNTAPNALA ATSYAFGGDI VAVNGKIAMM PIALGTADFM VHHIHAFTIH VTVLILLKGV LFARNS RLI PDKANLGFRF PCDGPGRGGT CQVSAWDHVF LGLFWMYNSL SIVIFHFSWK MQSDVWGSVT PNGAVSHITG GNFAQSA IT INGWLRDFLW AQASQVIQSY GSALSAYGLI FLGAHFVWAF SLMFLFSGRG YWQELIESIV WAHNKLKLGP AIQPRALS I TQGRAVGLAH YLVGGIGTTW AFFLARIIAV G

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Macromolecule #10: Photosystem I P700 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 82.257852 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString: MATKFPKFSQ ALAQDPSTRR IWFGIATSHD FESHDGMTEE NLYQKIFASH FGHLAIIFLW TSGNLFHVAW QGNFEQWVLN PLKTKPIAH AIWDPHFGQP AIKAFTKGGV TYPVDIAYSG VYHWWYTIGM RTNNDLYSGA LFLLVLSAVF LFAGWLHLQP R FKPSLSWF ...String:
MATKFPKFSQ ALAQDPSTRR IWFGIATSHD FESHDGMTEE NLYQKIFASH FGHLAIIFLW TSGNLFHVAW QGNFEQWVLN PLKTKPIAH AIWDPHFGQP AIKAFTKGGV TYPVDIAYSG VYHWWYTIGM RTNNDLYSGA LFLLVLSAVF LFAGWLHLQP R FKPSLSWF KNNESRLNHH LSGLFGVSSL AWTGHMIHVA IPESRGQHIG WDNFTTVRPH PAGLEPFFSG NWSVYAQNPD TP NHIFGTS EGAGTAILTF LGGFHPQTQS LWLTDMAHHH LAIAVVFIVA GHMYRTNWGI GHSLKEILEA HEPPSGRLGK GHK GLFETI TNSLHMQLGL ALASLGVITS LVAQHMYALP PYAFMAKDFT TQAALYTHHQ YIAGFLMVGA FAHGAIFFVR DYDA EQNEG NVLARMLEHK EAIISHLSWV SLFLGFHTLG LYIHNDVVVA FGTPEKQILV EPVFAQWIQA ASGKALYGFD VLLSS SNSV ATQAGGNIWL PGWLEAINSG KNSLFLTIGP GDFLVHHAIA LGLHTTALIL IKGALDARGS KLMPDKKDFG YSFPCD GPG RGGTCDISAW DAFYLSVFWM LNTIGWVTFY WHWKHVTIWQ GNVAQFNESS TYLMGWLRDY LWLNSSPLIN GYNPYGM NS LSVWAWMFLF GHLIWATGFM FLISWRGYWQ ELIETLAWAH ERTPLANLVR WKDKPVALSI VQARLVGLAH FSVGYILT Y AAFVIASTTG KFG

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Macromolecule #11: Photosystem I reaction center subunit II

MacromoleculeName: Photosystem I reaction center subunit II / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 15.851997 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MSETINLQMP SPTFGGSTGG WLRAAETEEK YAITWTGKKE EIFEIPTGGA AIMREGDNLL YLARKEQCLA LGTQLRNSFK ISDYKIYRI FPTGEVQYLH PKDGVFPEKV NEGRVGINNV SRNIGKNPNP ISVKFTGKST FEV

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Macromolecule #12: Photosystem I reaction center subunit IV

MacromoleculeName: Photosystem I reaction center subunit IV / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 7.008944 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MIKRGSKVRV LRKESYWYQE IGTVATVDTS GIRYPVVVRF EKVNYSGVNT NNFAESELIE A

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Macromolecule #13: Photosystem I reaction center subunit III

MacromoleculeName: Photosystem I reaction center subunit III / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 20.753357 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MKRSLLIIFL VISLVMFDSQ QAKADVAGLV PCKDSKEFSR RLDLSVKKLE QRLKKYEPGT PPYLAIQKSI ETTKIRFDRY AKGGLLCGK DGLPHLITDG RLSHATEFII PGLLFLYING WIGWVGRAYL IAIRSSDKPA EKEIILDIPL ALGFMSSGFL W PLSAWKEF TSGELLVDAN EVTVSPR

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Macromolecule #14: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 4.832742 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MENNFLKYLS VMPVAGTIFM IFTAGLVIEV NRFYPDALFF PL

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Macromolecule #15: Photosystem I reaction center subunit PsaK

MacromoleculeName: Photosystem I reaction center subunit PsaK / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 6.992322 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MVNSSKAGIM LIANVLSIMI GRYAIQVRGL GPSIPLGVEG FGLPELIATT SLGHIIGAGA ILGLSSIGSI

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Macromolecule #16: Photosystem I reaction center subunit XI

MacromoleculeName: Photosystem I reaction center subunit XI / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 15.344557 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MTDFISPYNE DPFVGNLSTP INTSSFTKGL LSNLPAYRRG LSPLLRGLEI GMAHGYFLIG PFYKLGPLRS TDVALLSGFL STVGLILIL TTCLSIYGSV SFDKEDTKDS LQTSEGWGQF TAGFLVGAVG GSGFAYLLLA NLPIA

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Macromolecule #17: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 3.187857 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MVNDTQILIA LLIALISGVL AIRLGTSLYT

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Macromolecule #18: Ferredoxin

MacromoleculeName: Ferredoxin / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 10.590564 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MATYKVRLLS EAEGIDVTID CADDVYILDA AEEQGVDLPY SCRAGACSTC AGKVSEGTID QSDQSFLDDD QTGAGFVLTC VAYPTSDCT ILTHQEESLY

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Macromolecule #19: Photosystem I subunit O

MacromoleculeName: Photosystem I subunit O / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 14.977179 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MAAFVNAAAG SLTASRVSAR RVVGAHQRSV HAPRSQRAVL KMQDGYEISE GSSFDANPLV IGLALIGWVV PSSVPSNIPL LDGKGLTPA FVASISDNLS RWPQGPQLAD PFWLLMGMWH VGLFATLIFG TVGYNLRKGN Y

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Macromolecule #20: PsaR

MacromoleculeName: PsaR / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 12.45658 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MAFINGAALG GGAKVAFSGK AVASRRVVAA STANKRSVVV KMADNYPSSE VLGLGKNIPS ALYVLISIAC FAIGVTSVAK SNLITPLTP ESINPQYVVG SLLLPISWGA HTAAFIQKVN KK

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Macromolecule #21: LPS1

MacromoleculeName: LPS1 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 5.634938 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

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Macromolecule #22: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 8.807258 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MAHSVKVYDT CIGCTQCVRA CPCDVLEMVP WDGCKAKQIA SAPRTEDCIG CKRCETACPT DFLSVRVYLG GETTRSLGLA Y

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Macromolecule #23: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 3.519346 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MTAAYLPPIL VPLVGLIFPA ISMALLFIYI EQ

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Macromolecule #24: Cytochrome c6

MacromoleculeName: Cytochrome c6 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Porphyridium purpureum (eukaryote)
Molecular weightTheoretical: 11.033479 KDa
Recombinant expressionOrganism: Porphyridium purpureum (eukaryote)
SequenceString:
MIAIAMITSF CLFTTNVFAA DIEHGEQIFT ANCSACHAGG NNVIMPEKTL KKDALEANGM NSVSAITNQV TNGKNAMPAF GGRLADNDI EDVANYVLAQ SVKGW

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Macromolecule #25: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 25 / Number of copies: 187 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #26: beta-D-glucopyranose

MacromoleculeName: beta-D-glucopyranose / type: ligand / ID: 26 / Number of copies: 1 / Formula: BGC
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-BGC:
beta-D-glucopyranose

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Macromolecule #27: (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,...

MacromoleculeName: (1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol
type: ligand / ID: 27 / Number of copies: 2 / Formula: ZEX
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-ZEX:
(1R,2S)-4-{(1E,3E,5E,7E,9E,11E,13E,15E,17E)-18-[(4S)-4-hydroxy-2,6,6-trimethylcyclohex-1-en-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaen-1-yl}-2,5,5-trimethylcyclohex-3-en-1-ol

+
Macromolecule #28: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 28 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

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Macromolecule #29: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 29 / Number of copies: 2 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #30: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 30 / Number of copies: 21 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #31: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 31 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER

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Macromolecule #32: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 32 / Number of copies: 1 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #33: (2S)-2,3-dihydroxypropyl octadecanoate

MacromoleculeName: (2S)-2,3-dihydroxypropyl octadecanoate / type: ligand / ID: 33 / Number of copies: 1 / Formula: 3XQ
Molecular weightTheoretical: 358.556 Da
Chemical component information

ChemComp-3XQ:
(2S)-2,3-dihydroxypropyl octadecanoate

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Macromolecule #34: PROLINE

MacromoleculeName: PROLINE / type: ligand / ID: 34 / Number of copies: 1 / Formula: PRO
Molecular weightTheoretical: 115.13 Da
Chemical component information

ChemComp-PRO:
PROLINE

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Macromolecule #35: FE2/S2 (INORGANIC) CLUSTER

MacromoleculeName: FE2/S2 (INORGANIC) CLUSTER / type: ligand / ID: 35 / Number of copies: 1 / Formula: FES
Molecular weightTheoretical: 175.82 Da
Chemical component information

ChemComp-FES:
FE2/S2 (INORGANIC) CLUSTER

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Macromolecule #36: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 36 / Number of copies: 1 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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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: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 112000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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