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- EMDB-9956: Cryo-EM structure of the C2S2M2L2-type PSII-LHCII supercomplex fr... -

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Basic information

Entry
Database: EMDB / ID: EMD-9956
TitleCryo-EM structure of the C2S2M2L2-type PSII-LHCII supercomplex from Chlamydomonas reihardtii
Map data
Sample
  • Complex: The C2S2M2L2-type PSII-LHCII supercomplex
    • Protein or peptide: x 23 types
  • Ligand: x 17 types
KeywordsPhotosystemII / supercomplex / PHOTOSYNTHESIS
Function / homology
Function and homology information


thylakoid light-harvesting complex / photosystem II antenna complex / nonphotochemical quenching / PSII associated light-harvesting complex II / photosynthesis, light harvesting / photosynthesis, light harvesting in photosystem I / photosystem II oxygen evolving complex / photosystem II assembly / oxygen evolving activity / photosystem II stabilization ...thylakoid light-harvesting complex / photosystem II antenna complex / nonphotochemical quenching / PSII associated light-harvesting complex II / photosynthesis, light harvesting / photosynthesis, light harvesting in photosystem I / 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 / photosystem I / photosynthetic electron transport chain / response to herbicide / photosystem II / photosynthesis, light reaction / chloroplast thylakoid membrane / phosphate ion binding / photosynthetic electron transport in photosystem II / chlorophyll binding / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / response to light stimulus / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / protein domain specific binding / mRNA binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM ...Photosystem II PsbW, class 2 / Photosystem II reaction centre W protein (PsbW) / Photosystem II PsbJ / Photosystem II PsbJ superfamily / PsbJ / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / 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 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) / Chlorophyll A-B binding protein, plant and chromista / 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. / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / Photosystem II protein D1 / 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.
Similarity search - Domain/homology
Uncharacterized protein / Photosystem II reaction center protein J / Photosystem II D2 protein / Photosystem II protein D1 / Photosystem II CP43 reaction center protein / Oxygen-evolving enhancer protein 1, chloroplastic / Photosystem II reaction center protein K / Photosystem II reaction center protein H / Photosystem II reaction center protein L / Photosystem II CP47 reaction center protein ...Uncharacterized protein / Photosystem II reaction center protein J / Photosystem II D2 protein / Photosystem II protein D1 / Photosystem II CP43 reaction center protein / Oxygen-evolving enhancer protein 1, chloroplastic / Photosystem II reaction center protein K / Photosystem II reaction center protein H / Photosystem II reaction center protein L / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein T / Cytochrome b559 subunit alpha / Photosystem II reaction center protein I / Photosystem II reaction center protein Z / Photosystem II reaction center protein M / Cytochrome b559 subunit beta / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein CP29 / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Photosystem II reaction center W protein, chloroplastic
Similarity search - Component
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsSheng X / Watanabe A
Funding support China, Japan, 4 items
OrganizationGrant numberCountry
Ministry of Science and Technology (China)2017YFA0503702 China
Chinese Academy of SciencesXDB27020106 China
Chinese Academy of SciencesXDB08020302 China
Japan Society for the Promotion of Science16H06553 Japan
CitationJournal: Nat Plants / Year: 2019
Title: Structural insight into light harvesting for photosystem II in green algae.
Authors: Xin Sheng / Akimasa Watanabe / Anjie Li / Eunchul Kim / Chihong Song / Kazuyoshi Murata / Danfeng Song / Jun Minagawa / Zhenfeng Liu /
Abstract: Green algae and plants rely on light-harvesting complex II (LHCII) to collect photon energy for oxygenic photosynthesis. In Chlamydomonas reinhardtii, LHCII molecules associate with photosystem II ...Green algae and plants rely on light-harvesting complex II (LHCII) to collect photon energy for oxygenic photosynthesis. In Chlamydomonas reinhardtii, LHCII molecules associate with photosystem II (PSII) to form various supercomplexes, including the CSML type, which is the largest PSII-LHCII supercomplex in algae and plants that is presently known. Here, we report high-resolution cryo-electron microscopy (cryo-EM) maps and structural models of the CSML and CS supercomplexes from C. reinhardtii. The CS supercomplex contains an LhcbM1-LhcbM2/7-LhcbM3 heterotrimer in the strongly associated LHCII, and the LhcbM1 subunit assembles with CP43 through two interfacial galactolipid molecules. The loosely and moderately associated LHCII trimers interact closely with the minor antenna complex CP29 to form an intricate subcomplex bound to CP47 in the CSML supercomplex. A notable direct pathway is established for energy transfer from the loosely associated LHCII to the PSII reaction centre, as well as several indirect routes. Structure-based computational analysis on the excitation energy transfer within the two supercomplexes provides detailed mechanistic insights into the light-harvesting process in green algae.
History
DepositionJun 21, 2019-
Header (metadata) releaseOct 23, 2019-
Map releaseOct 23, 2019-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6kad
  • Surface level: 0.012
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9956.png

Downloads & links

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Map

FileDownload / File: emd_9956.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.)
1.32 Å/pix.
x 384 pix.
= 506.88 Å		1.32 Å/pix.
x 384 pix.
= 506.88 Å		1.32 Å/pix.
x 384 pix.
= 506.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.012
Minimum - Maximum-0.03503261 - 0.082211025
Average (Standard dev.)0.000029917996 (±0.0028341173)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 506.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z506.880506.880506.880
α/β/γ90.00090.00090.000
start NX/NY/NZ-51-35-11
NX/NY/NZ11110799
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0350.0820.000

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Supplemental data

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Sample components

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Entire : The C2S2M2L2-type PSII-LHCII supercomplex

EntireName: The C2S2M2L2-type PSII-LHCII supercomplex
Components
  • Complex: The C2S2M2L2-type PSII-LHCII supercomplex
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Photosystem II protein D1
    • Protein or peptide: Photosystem II CP47 reaction center protein
    • Protein or peptide: Photosystem II CP43 reaction center protein
    • Protein or peptide: Photosystem II D2 protein
    • Protein or peptide: Cytochrome b559 subunit alpha
    • Protein or peptide: Cytochrome b559 subunit beta
    • Protein or peptide: 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: Oxygen-evolving enhancer protein 1, chloroplastic
    • Protein or peptide: Chlorophyll a-b binding protein CP29
    • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
    • Protein or peptide: Photosystem II reaction center protein T
    • Protein or peptide: Photosystem II reaction center protein Ycf12
    • Protein or peptide: Photosystem II reaction center W protein, chloroplastic
    • Protein or peptide: 4.1 kDa photosystem II subunit
    • Protein or peptide: Photosystem II reaction center protein Z
  • Ligand: CHLOROPHYLL B
  • Ligand: CHLOROPHYLL A
  • Ligand: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
  • Ligand: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: CA-MN4-O5 CLUSTER
  • Ligand: FE (II) ION
  • Ligand: CHLORIDE ION
  • 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: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: BICARBONATE ION
  • 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: PROTOPORPHYRIN IX CONTAINING FE

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Supramolecule #1: The C2S2M2L2-type PSII-LHCII supercomplex

SupramoleculeName: The C2S2M2L2-type PSII-LHCII supercomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#23
Source (natural)Organism: Chlamydomonas reinhardtii (plant)

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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: 6 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 27.591336 KDa
SequenceString: MAFALAKSSA RAAVSRRSTV KVEARRTVKP ASKASTPDSF WYGPERPLFL GAFTGEPPSY LTGEFPGDYG WDTAGLSADP ETFKRYREL ELIHARWAML GALGCIFPEL LGSYGVPFGE AVWFKAGAQI FQEGGLDYLG NPNLVHAQSI LAILGTQVLL M GAIEGYRV ...String:
MAFALAKSSA RAAVSRRSTV KVEARRTVKP ASKASTPDSF WYGPERPLFL GAFTGEPPSY LTGEFPGDYG WDTAGLSADP ETFKRYREL ELIHARWAML GALGCIFPEL LGSYGVPFGE AVWFKAGAQI FQEGGLDYLG NPNLVHAQSI LAILGTQVLL M GAIEGYRV NGGPLGEGLD KLYPGGSFDP LGLADDPDTF AELKVKEIKN GRLAMFSMFG FFVQAIVTGK GPLQNLSDHL AN PGTNNAF AYATKFTPQ

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #2: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 2 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 27.405008 KDa
SequenceString: MAFALSFSRK ALQVSAKATG KKGTGKTAAK QAPASSGIEF YGPNRAKWLG PYSENATPAY LTGEFPGDYG WDTAGLSADP ETFKRYREL ELIHARWAML GALGCITPEL LAKSGTQFGE AVWFKAGAQI FSEGGLDYLG NPSLVHAQNI VATLAVQVIL M GLVEGYRV ...String:
MAFALSFSRK ALQVSAKATG KKGTGKTAAK QAPASSGIEF YGPNRAKWLG PYSENATPAY LTGEFPGDYG WDTAGLSADP ETFKRYREL ELIHARWAML GALGCITPEL LAKSGTQFGE AVWFKAGAQI FSEGGLDYLG NPSLVHAQNI VATLAVQVIL M GLVEGYRV NGGPAGEGLD PLYPGESFDP LGLADDPDTF AELKVKEIKN GRLAMFSMFG FFVQAIVTGK GPIQNLDDHL SN PTVNNAF AFATKFTPSA

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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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: 4 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 26.67535 KDa
SequenceString: MAAIMKSAVR SSVRPTVSGR SARVVPRAAI EWYGPDRPKF LGPFSEGDTP AYLTGEFPGD YGWDTAGLSA DPETFKRYRE LELIHARWA MLGALGCITP ELLAKNGIPF GEAVWFKAGA QIFAEGGLNY LGNENLIHAQ SIIATLAFQV VVMGLAEAYR A NGGPLGEG ...String:
MAAIMKSAVR SSVRPTVSGR SARVVPRAAI EWYGPDRPKF LGPFSEGDTP AYLTGEFPGD YGWDTAGLSA DPETFKRYRE LELIHARWA MLGALGCITP ELLAKNGIPF GEAVWFKAGA QIFAEGGLNY LGNENLIHAQ SIIATLAFQV VVMGLAEAYR A NGGPLGEG LDPLHPGGAF DPLGLADDPD TFAELKVKEI KNGRLAMFSM FGFFVQAIVT GKGPIQNLDD HLANPTAVNA FA YATKFTP SA

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #4: Photosystem II protein D1

MacromoleculeName: Photosystem II protein D1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 39.06634 KDa
SequenceString: MTAILERREN SSLWARFCEW ITSTENRLYI GWFGVIMIPC LLTATSVFII AFIAAPPVDI DGIREPVSGS LLYGNNIITG AVIPTSNAI GLHFYPIWEA ASLDEWLYNG GPYQLIVCHF LLGVYCYMGR EWELSFRLGM RPWIAVAYSA PVAAASAVFL V YPIGQGSF ...String:
MTAILERREN SSLWARFCEW ITSTENRLYI GWFGVIMIPC LLTATSVFII AFIAAPPVDI DGIREPVSGS LLYGNNIITG AVIPTSNAI GLHFYPIWEA ASLDEWLYNG GPYQLIVCHF LLGVYCYMGR EWELSFRLGM RPWIAVAYSA PVAAASAVFL V YPIGQGSF SDGMPLGISG TFNFMIVFQA EHNILMHPFH MLGVAGVFGG SLFSAMHGSL VTSSLIRETT ENESANEGYR FG QEEETYN IVAAHGYFGR LIFQYASFNN SRSLHFFLAA WPVIGIWFTA LGLSTMAFNL NGFNFNQSVV DSQGRVLNTW ADI INRANL GMEVMHERNA HNFPLDLAST NSSSNN

UniProtKB: Photosystem II protein D1

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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: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 56.15982 KDa
SequenceString: MGLPWYRVHT VVINDPGRLI SVHLMHTALV SGWAGSMALF EISVFDPSDP VLNPMWRQGM FVLPFMTRLG ITQSWGGWTI SGETATNPG IWSYEGVAAA HIILSGALFL ASVWHWTYWD LELFRDPRTG KTALDLPKIF GIHLFLSGLL CFGFGAFHVT G VFGPGIWV ...String:
MGLPWYRVHT VVINDPGRLI SVHLMHTALV SGWAGSMALF EISVFDPSDP VLNPMWRQGM FVLPFMTRLG ITQSWGGWTI SGETATNPG IWSYEGVAAA HIILSGALFL ASVWHWTYWD LELFRDPRTG KTALDLPKIF GIHLFLSGLL CFGFGAFHVT G VFGPGIWV SDPYGLTGRV QPVAPSWGAD GFDPYNPGGI ASHHIAAGIL GVLAGLFHLC VRPSIRLYFG LSMGSIETVL SS SIAAVFW AAFVVAGTMW YGSAATPIEL FGPTRYQWDQ GFFQQEIQKR VQASLAEGAS LSDAWSRIPE KLAFYDYIGN NPA KGGLFR TGAMNSGDGI AVGWLGHASF KDQEGRELFV RRMPTFFETF PVLLLDKDGI VRADVPFRKA ESKYSIEQVG VSVT FYGGE LDGLTFTDPA TVKKYARKAQ LGEIFEFDRS TLQSDGVFRS SPRGWFTFGH VCFALLFFFG HIWHGARTIF RDVFA GIDD DINDQVEFGK YKKLGDTSSL REAF

UniProtKB: Photosystem II CP47 reaction center protein

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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: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 50.680738 KDa
SequenceString: METLFNGTLT VGGRDQETTG FAWWSGNARL INLSGKLLGA HVAHAGLIVF WAGAMNLFEV SHFVPEKPMY EQGLILLPHI ATLGYGVGP GGEIIDTFPY FVSGVLHLIS SAVLGFGGVY HSLIGPETLE ESYPFFGYVW KDKNKMTNIL GYHLIMLGLG A WLLVWKAM ...String:
METLFNGTLT VGGRDQETTG FAWWSGNARL INLSGKLLGA HVAHAGLIVF WAGAMNLFEV SHFVPEKPMY EQGLILLPHI ATLGYGVGP GGEIIDTFPY FVSGVLHLIS SAVLGFGGVY HSLIGPETLE ESYPFFGYVW KDKNKMTNIL GYHLIMLGLG A WLLVWKAM YFGGVYDTWA PGGGDVRVIT NPTTNAAVIF GYLVKSPFGG DGWICSVDNM EDIIGGHIWI GTLEILGGIW HI YTTPWPW ARRAFVWSGE AYLSYSLGAI GVMGFIACCM SWFNNTAYPS EFYGPTGPEA SQSQAFTFLV RDQRLGANVA SAQ GPTGLG KYLMRSPTGE IIFGGETMRF WDFRGPWLEP LRGPNGLDLN KLKNDIQPWQ ERRAAEYMTH APLGSLNSVG GVAT EINAV NFVSPRSWLA CSHFCLGFFF FIGHLWHAGR ARAAAAGFEK GIDRFDEPVL SMRPLD

UniProtKB: Photosystem II CP43 reaction center protein

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Macromolecule #7: Photosystem II D2 protein

MacromoleculeName: Photosystem II D2 protein / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 39.474031 KDa
SequenceString: MTIAIGTYQE KRTWFDDADD WLRQDRFVFV GWSGLLLFPC AYFALGGWLT GTTFVTSWYT HGLATSYLEG CNFLTAAVST PANSMAHSL LFVWGPEAQG DFTRWCQLGG LWAFVALHGA FGLIGFMLRQ FEIARSVNLR PYNAIAFSAP IAVFVSVFLI Y PLGQSGWF ...String:
MTIAIGTYQE KRTWFDDADD WLRQDRFVFV GWSGLLLFPC AYFALGGWLT GTTFVTSWYT HGLATSYLEG CNFLTAAVST PANSMAHSL LFVWGPEAQG DFTRWCQLGG LWAFVALHGA FGLIGFMLRQ FEIARSVNLR PYNAIAFSAP IAVFVSVFLI Y PLGQSGWF FAPSFGVAAI FRFILFFQGF HNWTLNPFHM MGVAGVLGAA LLCAIHGATV ENTLFEDGDG ANTFRAFNPT QA EETYSMV TANRFWSQIF GVAFSNKRWL HFFMLLVPVT GLWMSAIGVV GLALNLRAYD FVSQEIRAAE DPEFETFYTK NIL LNEGIR AWMAAQDQPH ERLVFPEEVL PRGNAL

UniProtKB: Photosystem II D2 protein

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Macromolecule #8: Cytochrome b559 subunit alpha

MacromoleculeName: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 9.312598 KDa
SequenceString:
MAGKPVERPF SDILTSIRYW VIHSITVPAL FIAGWLFVST GLAYDVFGTP RPNEYFTEDR QEAPLITDRF NALEQVKKLS GN

UniProtKB: Cytochrome b559 subunit alpha

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Macromolecule #9: Cytochrome b559 subunit beta

MacromoleculeName: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 4.986013 KDa
SequenceString:
MTTKKSAEVL VYPIFTVRWL AIHGIAVPTI FFLGAITAMQ FIQR

UniProtKB: Cytochrome b559 subunit beta

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Macromolecule #10: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 9.445063 KDa
SequenceString:
MATGTSKAKP SKVNSDFQEP GLVTPLGTLL RPLNSEAGKV LPGWGTTVLM AVFILLFAAF LLIILEIYNS SLILDDVSMS WETLAKVS

UniProtKB: Photosystem II reaction center protein H

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Macromolecule #11: Photosystem II reaction center protein I

MacromoleculeName: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 4.245035 KDa
SequenceString:
MLTLKIFVYT VVTFFVCLFI FGFLSNDPAR NPGKNLD

UniProtKB: Photosystem II reaction center protein I

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Macromolecule #12: Photosystem II reaction center protein J

MacromoleculeName: Photosystem II reaction center protein J / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 4.291 KDa
SequenceString:
MSNTGTTGRI PLWLVGTVVG TLAIGLLAVF FYGSYVGLGS SL

UniProtKB: Photosystem II reaction center protein J

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Macromolecule #13: Photosystem II reaction center protein K

MacromoleculeName: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 5.062142 KDa
SequenceString:
MTTLALVLAK LPEAYAPFAP IVDVLPVIPV FFILLAFVWQ AAVSFR

UniProtKB: Photosystem II reaction center protein K

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Macromolecule #14: Photosystem II reaction center protein L

MacromoleculeName: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 4.431229 KDa
SequenceString:
MARPNPNKQV VELNRTSLYW GLLLIFVLAV LFSSYIFN

UniProtKB: Photosystem II reaction center protein L

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Macromolecule #15: Photosystem II reaction center protein M

MacromoleculeName: Photosystem II reaction center protein M / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 3.762433 KDa
SequenceString:
MEVNIYGLTA TALFIIIPTS FLLILYVKTA STQD

UniProtKB: Photosystem II reaction center protein M

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Macromolecule #16: Oxygen-evolving enhancer protein 1, chloroplastic

MacromoleculeName: Oxygen-evolving enhancer protein 1, chloroplastic / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 30.557697 KDa
SequenceString: MALRAAQSAK AGVRAARPNR ATAVVCKAQK VGQAAAAAAL ATAMVAGSAN ALTFDEIQGL TYLQVKGSGI ANTCPVLESG TTNLKELKA GSYKLENFCI EPTSFTVKEE SQFKGGETEF VKTKLMTRLT YTLDAMSGSF KVGSDGSAEL KEDDGIDYAA T TVQLPGGE ...String:
MALRAAQSAK AGVRAARPNR ATAVVCKAQK VGQAAAAAAL ATAMVAGSAN ALTFDEIQGL TYLQVKGSGI ANTCPVLESG TTNLKELKA GSYKLENFCI EPTSFTVKEE SQFKGGETEF VKTKLMTRLT YTLDAMSGSF KVGSDGSAEL KEDDGIDYAA T TVQLPGGE RVAFLFTIKQ FDGKGTLDGI KGDFLVPSYR GSSFLDPKGR GGSTGYDNAV ALPARADAEE LLKENVKITK AL KGSAVFS VAKVDPVTGE IAGVFESIQP SDTDLGAKPP KDIKVTGLWY AQLK

UniProtKB: Oxygen-evolving enhancer protein 1, chloroplastic

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Macromolecule #17: Chlorophyll a-b binding protein CP29

MacromoleculeName: Chlorophyll a-b binding protein CP29 / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 29.970846 KDa
SequenceString: MVFKFPTPPG TQKKAGTTAT KPAPKATTKK VATSTGTRSG GVGYRKYQGD ALWLPNTTRP EWLDGSLPGD RGFDPLGLSK PSEFVVIGV DENDQNAAKN NKGSVEAIVQ ATPDEVSSEN RLAPYSEVFG LARFRECELI HGRWAMLACL GALVAEATTG V SWVEAGKV ...String:
MVFKFPTPPG TQKKAGTTAT KPAPKATTKK VATSTGTRSG GVGYRKYQGD ALWLPNTTRP EWLDGSLPGD RGFDPLGLSK PSEFVVIGV DENDQNAAKN NKGSVEAIVQ ATPDEVSSEN RLAPYSEVFG LARFRECELI HGRWAMLACL GALVAEATTG V SWVEAGKV ELDGASYAGL SLPFSITQLI WIEVILVGGA EFYRNSETNP EKRCYPGGVF DPLKLASEDE ERAFRLKTAE IK HARLAMV SFFGYGVQAL STGEGALGSL AKFADGLNNG KGL

UniProtKB: Chlorophyll a-b binding protein CP29

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Macromolecule #18: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 30.74283 KDa
SequenceString: MQIQALFKKT GASAPAKKGT ASTKVVKPSK AGGKATRGWL GGQGGAADLD KWYGPDRKLF LPSGLYDRSE IPEYLNGELA GDYGYDPLG LGKDPETVAK YRENELLHAR WAMLAAAGIL IPEGLQANGA NIKGGTWFET GAEMLNGGTL NYFAVPWGIV S NPLPLFAV ...String:
MQIQALFKKT GASAPAKKGT ASTKVVKPSK AGGKATRGWL GGQGGAADLD KWYGPDRKLF LPSGLYDRSE IPEYLNGELA GDYGYDPLG LGKDPETVAK YRENELLHAR WAMLAAAGIL IPEGLQANGA NIKGGTWFET GAEMLNGGTL NYFAVPWGIV S NPLPLFAV IAVEVGLMGA VEFYRRNGTG PAGYSPGIGK FDSSVFDGLD PLYPGGPFDP LGLADDPEVL QELKVKEIKN GR LAMVSVL GFAVQSYVTG EGPYANWTKH VADPFGYNLL TVLGAEERTP TL

UniProtKB: Chlorophyll a-b binding protein, chloroplastic

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Macromolecule #19: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 3.639438 KDa
SequenceString:
MEALVYTFLL VGTLGIIFFS IFFRDPPRMI K

UniProtKB: Photosystem II reaction center protein T

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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: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 3.333058 KDa
SequenceString:
MNIELALTLV SLVLVVSAGP LVVVLLSARG GNL

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Macromolecule #21: Photosystem II reaction center W protein, chloroplastic

MacromoleculeName: Photosystem II reaction center W protein, chloroplastic
type: protein_or_peptide / ID: 21 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 12.155054 KDa
SequenceString:
MQALSARAPR VAAKPVSRSG ARSAVTVVCK ATTVRSEVAK KVAMLSTLPA TLAAHPAFAL VDERMNGDGT GRPFGVNDPV LGWVLLGVF GTMWAIWFIG QKDLGDFEDA DDGLKL

UniProtKB: Photosystem II reaction center W protein, chloroplastic

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Macromolecule #22: 4.1 kDa photosystem II subunit

MacromoleculeName: 4.1 kDa photosystem II subunit / type: protein_or_peptide / ID: 22 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 9.894716 KDa
SequenceString:
MAAVCVSSKA VAVRPATRVA SRPAARMVVR ASAKPAQISE KAIAAGVSAA AAASLALAPI AEAAVTPSLK NFLGSLIAGA TVLGGIALA ITAVSKFDKT IR

UniProtKB: Uncharacterized protein

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Macromolecule #23: Photosystem II reaction center protein Z

MacromoleculeName: Photosystem II reaction center protein Z / type: protein_or_peptide / ID: 23 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chlamydomonas reinhardtii (plant)
Molecular weightTheoretical: 6.565863 KDa
SequenceString:
MTSILQVALL ALIFVSFALV VGVPVVFATP NGWTDNKGAV FSGLSLWLLL VFVVGILNSF VV

UniProtKB: Photosystem II reaction center protein Z

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Macromolecule #24: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 24 / Number of copies: 122 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B

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Macromolecule #25: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 25 / Number of copies: 254 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #26: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

MacromoleculeName: (3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 26 / Number of copies: 42 / Formula: LUT
Molecular weightTheoretical: 568.871 Da
Chemical component information

ChemComp-LUT:
(3R,3'R,6S)-4,5-DIDEHYDRO-5,6-DIHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

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Macromolecule #27: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BE...

MacromoleculeName: (3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL
type: ligand / ID: 27 / Number of copies: 20 / Formula: XAT
Molecular weightTheoretical: 600.87 Da
Chemical component information

ChemComp-XAT:
(3S,5R,6S,3'S,5'R,6'S)-5,6,5',6'-DIEPOXY-5,6,5',6'- TETRAHYDRO-BETA,BETA-CAROTENE-3,3'-DIOL

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Macromolecule #28: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY...

MacromoleculeName: (1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL
type: ligand / ID: 28 / Number of copies: 22 / Formula: NEX
Molecular weightTheoretical: 600.87 Da
Chemical component information

ChemComp-NEX:
(1R,3R)-6-{(3E,5E,7E,9E,11E,13E,15E,17E)-18-[(1S,4R,6R)-4-HYDROXY-2,2,6-TRIMETHYL-7-OXABICYCLO[4.1.0]HEPT-1-YL]-3,7,12,16-TETRAMETHYLOCTADECA-1,3,5,7,9,11,13,15,17-NONAENYLIDENE}-1,5,5-TRIMETHYLCYCLOHEXANE-1,3-DIOL

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

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 29 / Number of copies: 32 / 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: CA-MN4-O5 CLUSTER

MacromoleculeName: CA-MN4-O5 CLUSTER / type: ligand / ID: 30 / 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 #31: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 31 / Number of copies: 2 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

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Macromolecule #32: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 32 / Number of copies: 2 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #33: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 33 / Number of copies: 4 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

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Macromolecule #34: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 34 / Number of copies: 20 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

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Macromolecule #35: 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: 35 / Number of copies: 8 / 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 #36: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 36 / Number of copies: 14 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #37: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 37 / Number of copies: 10 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #38: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 38 / 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 #39: 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: 39 / Number of copies: 2 / 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 #40: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 40 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 1.31 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 281317
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 118423
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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