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- EMDB-33401: PSI-LHCI-LHCII-Lhcb9 supercomplex of Physcomitrella patens -

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Basic information

Entry
Database: EMDB / ID: EMD-33401
TitlePSI-LHCI-LHCII-Lhcb9 supercomplex of Physcomitrella patens
Map data
Sample
  • Complex: PSI-LHCI-LHCII-Lhcb9 supercomplex of Physcomitrella patens
    • Protein or peptide: x 18 types
  • Protein or peptide: x 2 types
  • Ligand: x 12 types
KeywordsSupercomplex / Membrane protein / State transitions / PHOTOSYNTHESIS
Function / homology
Function and homology information


photosynthesis, light harvesting in photosystem I / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / : / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane ...photosynthesis, light harvesting in photosystem I / photosynthesis, light harvesting / photosystem I reaction center / photosystem I / photosynthetic electron transport in photosystem I / : / photosystem I / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / response to light stimulus / photosynthesis / 4 iron, 4 sulfur cluster binding / electron transfer activity / membrane => GO:0016020 / magnesium ion binding / membrane / metal ion binding
Similarity search - Function
: / Photosystem I PsaO / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre ...: / Photosystem I PsaO / Photosystem I PsaH, reaction centre subunit VI / Photosystem I reaction centre subunit VI / Photosystem I reaction center subunit V / Photosystem I reaction center subunit psaK, plant / Photosystem I reaction center subunit V/PsaK, plant / Photosystem I PsaG/PsaK domain, chloroplastic / Photosystem I PsaM, reaction centre superfamily / Photosystem I PsaM, reaction centre / Photosystem I protein M (PsaM) / Photosystem I psaG and psaK proteins signature. / Photosystem I reaction center subunit V/PsaK / Photosystem I psaG / psaK / Photosystem I PsaL, reaction centre subunit XI / Photosystem I, reaction centre subunit XI / Photosystem I PsaL, reaction centre subunit XI superfamily / Photosystem I reaction centre subunit XI / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII / Photosystem I reaction centre subunit VIII superfamily / Photosystem I PsaF, reaction centre subunit III / Photosystem I PsaF, reaction centre subunit III superfamily / Photosystem I reaction centre subunit III / Photosystem I PsaJ, reaction centre subunit IX / Photosystem I PsaD / Photosystem I PsaJ, reaction centre subunit IX superfamily / Photosystem I, reaction centre subunit PsaD superfamily / Photosystem I reaction centre subunit IX / PsaJ / PsaD / Chlorophyll A-B binding protein, plant and chromista / Photosystem I PsaE, reaction centre subunit IV / Photosystem I reaction centre subunit IV / PsaE / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / Photosystem I protein PsaC / Photosystem I PsaA / Photosystem I PsaB / Photosystem I PsaA/PsaB, conserved site / Photosystem I psaA and psaB proteins signature. / Photosystem I PsaA/PsaB / Photosystem I PsaA/PsaB superfamily / Photosystem I psaA/psaB protein / Electron transport accessory-like domain superfamily / 4Fe-4S dicluster domain / 4Fe-4S ferredoxin, iron-sulphur binding, conserved site / 4Fe-4S ferredoxin-type iron-sulfur binding region signature. / 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. / 4Fe-4S ferredoxin-type, iron-sulphur binding domain
Similarity search - Domain/homology
PSI subunit V / Uncharacterized protein / PSI-F / Photosystem I reaction center subunit V, chloroplastic / Photosystem I subunit O / Uncharacterized protein / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic ...PSI subunit V / Uncharacterized protein / PSI-F / Photosystem I reaction center subunit V, chloroplastic / Photosystem I subunit O / Uncharacterized protein / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / PSI-K / Chlorophyll a-b binding protein, chloroplastic / Chlorophyll a-b binding protein, chloroplastic / PsaH photosystem I reaction center subunit / Photosystem I reaction center subunit XII / Photosystem I reaction center subunit IX / Photosystem I iron-sulfur center / Photosystem I reaction center subunit VIII / Photosystem I P700 chlorophyll a apoprotein A2 / Photosystem I P700 chlorophyll a apoprotein A1
Similarity search - Component
Biological speciesPhyscomitrium patens (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsZhang S / Tang KL / Li XY / Wang WD / Yan QJ / Shen LL / Kuang TY / Han GY / Shen JR / Zhang X
Funding support China, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2020YFA0907600 China
Chinese Academy of SciencesYSBR-004 China
CitationJournal: Nat Plants / Year: 2023
Title: Structural insights into a unique PSI-LHCI-LHCII-Lhcb9 supercomplex from moss Physcomitrium patens.
Authors: Song Zhang / Kailu Tang / Qiujing Yan / Xingyue Li / Liangliang Shen / Wenda Wang / Yi-Kun He / Tingyun Kuang / Guangye Han / Jian-Ren Shen / Xing Zhang /
Abstract: Photosystem I (PSI) possesses a variable supramolecular organization among different photosynthetic organisms to adapt to different light environments. Mosses are evolutionary intermediates that ...Photosystem I (PSI) possesses a variable supramolecular organization among different photosynthetic organisms to adapt to different light environments. Mosses are evolutionary intermediates that diverged from aquatic green algae and evolved into land plants. The moss Physcomitrium patens (P. patens) has a light-harvesting complex (LHC) superfamily more diverse than those of green algae and higher plants. Here, we solved the structure of a PSI-LHCI-LHCII-Lhcb9 supercomplex from P. patens at 2.68 Å resolution using cryo-electron microscopy. This supercomplex contains one PSI-LHCI, one phosphorylated LHCII trimer, one moss-specific LHC protein, Lhcb9, and one additional LHCI belt with four Lhca subunits. The complete structure of PsaO was observed in the PSI core. One Lhcbm2 in the LHCII trimer interacts with PSI core through its phosphorylated N terminus, and Lhcb9 mediates assembly of the whole supercomplex. The complicated pigment arrangement provided important information for possible energy-transfer pathways from the peripheral antennae to the PSI core.
History
DepositionMay 8, 2022-
Header (metadata) releaseApr 26, 2023-
Map releaseApr 26, 2023-
UpdateJun 7, 2023-
Current statusJun 7, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33401.png

Downloads & links

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Map

FileDownload / File: emd_33401.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.014 Å
Density
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-1.757525 - 4.399902
Average (Standard dev.)-0.00048363657 (±0.10490938)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-240-240-240
Dimensions480480480
Spacing480480480
CellA=B=C: 486.72003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33401_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_33401_half_map_2.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : PSI-LHCI-LHCII-Lhcb9 supercomplex of Physcomitrella patens

EntireName: PSI-LHCI-LHCII-Lhcb9 supercomplex of Physcomitrella patens
Components
  • Complex: PSI-LHCI-LHCII-Lhcb9 supercomplex of Physcomitrella patens
    • 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 iron-sulfur center
    • Protein or peptide: Predicted protein PsaDPrediction
    • Protein or peptide: PsaE
    • Protein or peptide: PSI-F
    • Protein or peptide: PSI-G
    • Protein or peptide: PsaH photosystem I reaction center subunit
    • Protein or peptide: Photosystem I reaction center subunit VIII
    • Protein or peptide: Photosystem I reaction center subunit IX
    • Protein or peptide: PsaK
    • Protein or peptide: PSI subunit V
    • Protein or peptide: Photosystem I reaction center subunit XII
    • Protein or peptide: PsaO
    • 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: Chlorophyll a-b binding protein, chloroplastic
  • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Protein or peptide: Chlorophyll a-b binding protein, chloroplastic
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONEPhytomenadione
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: BETA-CAROTENEΒ-Carotene
  • Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
  • Ligand: DODECYL-ALPHA-D-MALTOSIDE
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: CHLOROPHYLL B
  • 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

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Supramolecule #1: PSI-LHCI-LHCII-Lhcb9 supercomplex of Physcomitrella patens

SupramoleculeName: PSI-LHCI-LHCII-Lhcb9 supercomplex of Physcomitrella patens
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#18
Source (natural)Organism: Physcomitrium patens (plant)

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Macromolecule #1: Photosystem I P700 chlorophyll a apoprotein A1

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 82.313422 KDa
SequenceString: EVKIMVEKDP VKTSFEKWAK PGHFSRTLAK GPNTTTWIWN LHADAHDFDS HTNDLEEISR KVFSAHFGQL AVIFIWLSGM YFHGARFSN YEAWLSDPTH IKPSAQVVWP IVGQKILNGD VGGGFQGIQI TSGFFQLWRA SGITSELQLY TTAIGGLIFA A LMLFAGWF ...String:
EVKIMVEKDP VKTSFEKWAK PGHFSRTLAK GPNTTTWIWN LHADAHDFDS HTNDLEEISR KVFSAHFGQL AVIFIWLSGM YFHGARFSN YEAWLSDPTH IKPSAQVVWP IVGQKILNGD VGGGFQGIQI TSGFFQLWRA SGITSELQLY TTAIGGLIFA A LMLFAGWF HYHKAAPKLA WFQNVESMLN HHLAGLLGLG SLAWAGHQVH VSLPINRLLD AGVDPKEIPL PHEFILNRDL LA QLYPSFS KGLTPFFTLN WSEYSDFLTF RGGLNPVTGG LWLTDTAHHH LAIAVLFLVA GHMYRTNFGI GHSMKEILEA HKG PFTGEG HKGLYEILTT SWHAQLAINL AMLGSLTIIV AHHMYAMPPY PYLATDYATQ LSLFTHHMWI GGFLVVGAAA HAAI FMVRD YDPTTQYNNL LDRVLRHRDA IISHLNWVCI FLGFHSFGLY IHNDTMSALG RPQDMFSDTA IQLQPVFAQW IQNTH ALAP SLTAPNATAS TSLTWGGGDL VAVGGKVALL PIPLGTADFL VHHIHAFTIH VTVLILLKGV LFARSSRLIP DKANLG FRF PCDGPGRGGT CQVSAWDHVF LGLFWMYNAI SVVIFHFSWK MQSDVWGSIS DQGVVTHITG GNFAQSSITI NGWLRDF LW AQASQVIQSY GSSLSAYGLL FLGAHFVWAF SLMFLFSGRG YWQELIESIV WAHNKLKVAP AIQPRALSIV QGRAVGVA H YLLGGIATTW AFFLARIISV G

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Macromolecule #2: Photosystem I P700 chlorophyll a apoprotein A2

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 82.316547 KDa
SequenceString: ASRFPKFSRG LSQDPTTRRI WFGIATAHDF ESHDDMTEER LYQKIFASHF GQLAIIFLWT SGNLFHVAWQ GNFEAWGQDP LHVRPIAHA IWDPHFGQPA VEAFTRGGAS GPVNIAYSGV YQWWYTIGLR TNQDLYGGSI FLLFVSALFL IAGWLHLQPK W KPSVSWFK ...String:
ASRFPKFSRG LSQDPTTRRI WFGIATAHDF ESHDDMTEER LYQKIFASHF GQLAIIFLWT SGNLFHVAWQ GNFEAWGQDP LHVRPIAHA IWDPHFGQPA VEAFTRGGAS GPVNIAYSGV YQWWYTIGLR TNQDLYGGSI FLLFVSALFL IAGWLHLQPK W KPSVSWFK NAESRLNHHL SGLFGVSSLA WTGHLVHVAI PESRGEHVRW NNLLTALPHP QGLGPFFAGQ WNVYAQNPDS NS HLFGTSE GAGTAILTFL GGFHPQTQSL WLTDMAHHHL AIAVIFIIAG HMYRTNFGIG HSMKEILEAH TPPGGRLGRG HKG LYDTIN NSLHFQLGLA LASLGVITSL VAQHMYSLPP YAFLAQDFTT QAALYTHHQY IAGFIMTGAF AHGAIFFIRD YNPE QNKDN VLARMLEHKE AIISHLSWAS LFLGFHTLGL YVHNDVMLAF GTPEKQILIE PVFAQWIQSA HGKALYGFDV LLSSA DSPA FNAGQTLWLP GWLDAINNNS NSLFLTIGPG DFLVHHAIAL GLHTTTLILV KGALDARGSK LMPDKKEFGY SFPCDG PGR GGTCDISAWD AFYLAVFWML NTIGWVTFYW HWKHITLWQG NVAQFNESST YLMGWLRDYL WLNSSQLING YNPFGMN SL SVWAWMFLFG HLVWATGFMF LISWRGYWQE LIETLAWAHE RTPLANLVRW KDKPVALSIV QARLVGLAHF SVGYIFTY A AFLIASTSGK FG

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Macromolecule #3: Photosystem I iron-sulfur center

MacromoleculeName: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: photosystem I
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 8.649957 KDa
SequenceString:
AHSVKIYDTC IGCTQCVRAC PTDVLEMVPW DGCKASQIAS APRTEDCVGC KRCESACPTD FLSVRVYLGA ETTRSMGLAY

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Macromolecule #4: Predicted protein PsaD

MacromoleculeName: Predicted protein PsaD / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 15.654927 KDa
SequenceString:
TPPTLNADTP APIFGGSTGG LLRKAQVEEF YVITWESPKE QIFEMPTGGA AIMRSGPNLL KLARKEQCLA LGARLRTKFK IQYQFYRVF PNGEVQYLHP KDGVYPEKVN AGRSPVGVNN RSIGKNANPA ELKFAHKQAY DL

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Macromolecule #5: PsaE

MacromoleculeName: PsaE / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 6.895725 KDa
SequenceString:
GPKRGSIVKV LRRESYWFND TGKVVAVDQA PGVRYPVVVR FDKVNYAGVS TNNYSPDELE AA

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Macromolecule #6: PSI-F

MacromoleculeName: PSI-F / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 17.465363 KDa
SequenceString:
DVAGLTPCKE SKGFAKREKQ EIKKLESRLK LYAPDSAPAL ALNATIEKTK RRFAFYGNEG LLCGTDGLPH LIVDGDQAHL GEFVYPGLV FLYIAGWIGW VGRAYLIDVR TSKKPTEKEI IIDVPLALRI MSKGLTWPVA AIGELRSGKL VEKSANITVS

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Macromolecule #7: PSI-G

MacromoleculeName: PSI-G / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 10.564831 KDa
SequenceString:
EANTALTITL STGALLFLGR FVFLPFQRDN VSRQGLPVQN GVTHFDAGDS RAQEVTSFLK TNDPAGFTIV DVLAWGALGH AVGFFILAT INNGYNPQF

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Macromolecule #8: PsaH photosystem I reaction center subunit

MacromoleculeName: PsaH photosystem I reaction center subunit / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 10.468787 KDa
SequenceString:
KYGEKSVYFD LGEIDNTTGN WDLYGNDDPN RYNGFQNKFF ETFAGAFTKR GLLLKFLVLG GATTIGYLGS TSSPDLLAIK NGPKQVPVM GPRGRK

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Macromolecule #9: Photosystem I reaction center subunit VIII

MacromoleculeName: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 3.791472 KDa
SequenceString:
MTASYLPSIF VPLIGLVFPA ITMASLFIYI EQDE

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Macromolecule #10: Photosystem I reaction center subunit IX

MacromoleculeName: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 4.59746 KDa
SequenceString:
MQDVKTYLST APVLATLWFG FLAGLLIEIN RFFPDALVLP L

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Macromolecule #11: PsaK

MacromoleculeName: PsaK / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 8.088327 KDa
SequenceString:
YIGSSTNLIM VASTTLMLFA GRFGLAPSAN RKSTAGLKLV DRDSGLQTGD PAGFTATDTL ACGALGHVIG VGIVLGLKAT A

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Macromolecule #12: PSI subunit V

MacromoleculeName: PSI subunit V / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 17.346957 KDa
SequenceString:
EKYQVIEPLN GDPFIGGFET PVTSSPLIAW YLSNLPAYRT AVAPLLRGVE IGLAHGYLLV GPFVLTGPLR NSAVRGEAGS LAAAGLVTI LTMCLTIYGI ASFKEGEPSK APSLTLTGRQ KDADKLQTAE GWASFTGGWF FGGLSGVAWA YILLYVLNLP Y PVK

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Macromolecule #13: Photosystem I reaction center subunit XII

MacromoleculeName: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 3.412051 KDa
SequenceString:
MTSISDSQII VALVSAFITG ILALRLGKSL YQ

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Macromolecule #14: PsaO

MacromoleculeName: PsaO / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 9.863429 KDa
SequenceString:
FNRDWLRKDL SVIGFGLIGW LAPSSLPVIN GNSLTGLFLG SIGPELAHFP TGPALTSPFW LWMVTWHVGL FIVLTLGQIG FKGRQDGYW

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Macromolecule #15: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 20.833689 KDa
SequenceString: EWLPGNPRPS YLDGSAPGDF GFDPLGLGEV PENLERFKES ELIHARWAML AIPGVLIPEA LGYGNWVSAQ KWAATPGGQA TYLGNPVPW GNLPIILAVE FIAIAFVESQ RNGESDPEKR KYPGGPFDPL GFSKGANLEE LKLKEIKNGR LALVAFLGFV V QAVAYPGT ...String:
EWLPGNPRPS YLDGSAPGDF GFDPLGLGEV PENLERFKES ELIHARWAML AIPGVLIPEA LGYGNWVSAQ KWAATPGGQA TYLGNPVPW GNLPIILAVE FIAIAFVESQ RNGESDPEKR KYPGGPFDPL GFSKGANLEE LKLKEIKNGR LALVAFLGFV V QAVAYPGT GPLENLKTHL ADPWHNTIAH VLIP

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Macromolecule #16: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 23.039275 KDa
SequenceString: NDRPLWFPGS KAPEWLDGSL PGDFGFDPLG LGSDPELLKW FVQAELVHCR WAMLGAAGIF IPEALTKAGI LNTPSWNVAG DQQYFADPT TLFVIELILF AWAEGRRWAD IVNPGCVNVD PVFPNNKLTG TDVGYPGGLW FDPLGWGQTK DAKKLKELRT K EIKNGRLA ...String:
NDRPLWFPGS KAPEWLDGSL PGDFGFDPLG LGSDPELLKW FVQAELVHCR WAMLGAAGIF IPEALTKAGI LNTPSWNVAG DQQYFADPT TLFVIELILF AWAEGRRWAD IVNPGCVNVD PVFPNNKLTG TDVGYPGGLW FDPLGWGQTK DAKKLKELRT K EIKNGRLA MLAVLGAVVQ ANYTHTGPID NLLAHLADPG HNTIFALSNL VGK

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Macromolecule #17: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 23.606 KDa
SequenceString: FASKQSLSYL DGTLPGDYGF DPLGLMDPEG AGGFIDPQWL PYAEIINGRF AMLGAAGAIA PEVLGRIGLI PQETAIPWFQ SGVIPPVGN YSYWADPYTL FVLEMALMGF AEHRRAQDYY KPGSMGKQYF LGLEKFLGGS GNPAYPGGPI FNFLGFGKNE K ELQELKVK ...String:
FASKQSLSYL DGTLPGDYGF DPLGLMDPEG AGGFIDPQWL PYAEIINGRF AMLGAAGAIA PEVLGRIGLI PQETAIPWFQ SGVIPPVGN YSYWADPYTL FVLEMALMGF AEHRRAQDYY KPGSMGKQYF LGLEKFLGGS GNPAYPGGPI FNFLGFGKNE K ELQELKVK EVKNGRLAMM AVLGYFTQAI FTGVGPFQNL LDHLADPVHN NVLTNLKI

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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: Physcomitrium patens (plant)
Molecular weightTheoretical: 22.521654 KDa
SequenceString: TDRPLWLPGS EAPKWLDGSL PGDYGFDPLD LAAEPGRLNW MVQAELVHCR WAMLGAAGIF IPELLTKIGI LNTPSWYKAG DATYFADQG TLFIVELLLM AWAESRRWAD IARPGSVNTD PIFPNNKLTG TDVGYPGGLW FDPLGWGSGS EDKLKEIRTK E VKNGRLAM ...String:
TDRPLWLPGS EAPKWLDGSL PGDYGFDPLD LAAEPGRLNW MVQAELVHCR WAMLGAAGIF IPELLTKIGI LNTPSWYKAG DATYFADQG TLFIVELLLM AWAESRRWAD IARPGSVNTD PIFPNNKLTG TDVGYPGGLW FDPLGWGSGS EDKLKEIRTK E VKNGRLAM LAVLGAFVQA NVTHVGPIDN LFAHLADPYH TTILQSL

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Macromolecule #19: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 24.760443 KDa
SequenceString: MTGIAEWYKV YGKSVAPDQD ARAPYYGPNR PLWKGPFTKP KDVPEYLKGE YPGDYGCDIF KLARLPANYA RLRTQELMNG RWAMLGITG CLTPELINSN STPGFEPVWF NTGAQIFSDA GIDYLGVPGF INAHSLFAVI VVQALLMGLA EYARIKFVPE G ADPFYPGG ...String:
MTGIAEWYKV YGKSVAPDQD ARAPYYGPNR PLWKGPFTKP KDVPEYLKGE YPGDYGCDIF KLARLPANYA RLRTQELMNG RWAMLGITG CLTPELINSN STPGFEPVWF NTGAQIFSDA GIDYLGVPGF INAHSLFAVI VVQALLMGLA EYARIKFVPE G ADPFYPGG KTFDPLGFSS DPEILAELKV KEIKNGRLAM MAMAGLFAQG AVTGVSPLQN LHDWLHL

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Macromolecule #20: Chlorophyll a-b binding protein, chloroplastic

MacromoleculeName: Chlorophyll a-b binding protein, chloroplastic / type: protein_or_peptide / ID: 20 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Physcomitrium patens (plant)
Molecular weightTheoretical: 24.457379 KDa
SequenceString: RR(TPO)VKSTSDS IWYGADRPKY LGPFSGETPS YLTGEFAGDY GWDTAGLSSD PETFARNREL EVIHARWAML GALGCL TPE LLAKSGVKFG EAVWFKAGAQ IFSEGGLDYL GNPSLVHAQS ILAIWASQVV LMGAVEGYRV AGGPLGEITD PIYPGGS FD PLGLADDPDT ...String:
RR(TPO)VKSTSDS IWYGADRPKY LGPFSGETPS YLTGEFAGDY GWDTAGLSSD PETFARNREL EVIHARWAML GALGCL TPE LLAKSGVKFG EAVWFKAGAQ IFSEGGLDYL GNPSLVHAQS ILAIWASQVV LMGAVEGYRV AGGPLGEITD PIYPGGS FD PLGLADDPDT FAELKVKEIK NGRLAMFSMF GFFVQAIVTG KGPLENLNDH LADPVANNAW AYATNFVPG

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Macromolecule #21: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 21 / Number of copies: 221 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

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Macromolecule #22: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 22 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE / Phytomenadione

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Macromolecule #23: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 23 / Number of copies: 15 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #24: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 24 / Number of copies: 33 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE / Β-Carotene

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Macromolecule #25: IRON/SULFUR CLUSTER

MacromoleculeName: IRON/SULFUR CLUSTER / type: ligand / ID: 25 / Number of copies: 3 / Formula: SF4
Molecular weightTheoretical: 351.64 Da
Chemical component information

ChemComp-FS1:
IRON/SULFUR CLUSTER / Iron–sulfur cluster

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Macromolecule #26: DODECYL-ALPHA-D-MALTOSIDE

MacromoleculeName: DODECYL-ALPHA-D-MALTOSIDE / type: ligand / ID: 26 / Number of copies: 5 / Formula: LMU
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMU:
DODECYL-ALPHA-D-MALTOSIDE / detergent*YM

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Macromolecule #27: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 27 / 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 #28: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 28 / Number of copies: 4 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #29: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 29 / Number of copies: 50 / Formula: CHL
Molecular weightTheoretical: 907.472 Da
Chemical component information

ChemComp-CHL:
CHLOROPHYLL B / Chlorophyll b

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Macromolecule #30: (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: 30 / Number of copies: 16 / 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 / Lutein

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Macromolecule #31: (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: 31 / Number of copies: 11 / 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 / Violaxanthin

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Macromolecule #32: (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: 32 / Number of copies: 3 / 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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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 / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 1.6 µm
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 78.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: COMMON LINE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 83777

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