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- EMDB-62153: Structural insights into photosystem II supercomplex of a a sipho... -

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Basic information

Entry
Database: EMDB / ID: EMD-62153
TitleStructural insights into photosystem II supercomplex of a a siphonous green algae Bryopsis corticulans from intertidal zone
Map data
Sample
  • Complex: Bc-PSII-LHCII
    • Protein or peptide: x 22 types
  • Ligand: x 17 types
KeywordsPSII-LHCII supercomplex / PHOTOSYNTHESIS
Function / homology
Function and homology information


oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / photosynthetic electron transport chain / photosystem II / photosynthetic electron transport in photosystem II / chlorophyll binding / phosphate ion binding / photosynthesis, light reaction ...oxygen evolving activity / photosystem II stabilization / photosystem II reaction center / photosystem II / photosynthetic electron transport chain / photosystem II / photosynthetic electron transport in photosystem II / chlorophyll binding / phosphate ion binding / photosynthesis, light reaction / chloroplast thylakoid membrane / photosynthesis / electron transfer activity / protein stabilization / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbT / Photosystem II PsbL ...Photosystem II reaction centre protein Ycf12 / Photosystem II complex subunit Ycf12 / Photosystem II reaction centre M protein (PsbM) / Photosystem II PsbM superfamily / Photosystem II PsbM / Photosystem II PsbZ, reaction centre / Photosystem II PsbZ superfamily / YCF9 / Photosystem II PsbT / Photosystem II PsbL / Photosystem II PsbL superfamily / Photosystem II PsbT superfamily / Photosystem II reaction centre T protein / PsbL protein / Photosystem II PsbK / Photosystem II CP43 reaction centre protein / Photosystem II PsbK superfamily / Photosystem II CP43 reaction centre protein superfamily / Photosystem II 4 kDa reaction centre component / Photosystem II PsbI / Photosystem II CP47 reaction centre protein / Photosystem II PsbI superfamily / Photosystem II reaction centre I protein (PSII 4.8 kDa protein) / Photosystem II reaction centre protein H / Photosystem II 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. / : / Photosystem antenna protein-like / Photosystem antenna protein-like superfamily / Photosystem II protein / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
Photosystem II reaction center protein L / Photosystem II D2 protein / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein Psb30 / Cytochrome b559 subunit alpha / Photosystem II reaction center protein T / Photosystem II reaction center protein H / Photosystem II reaction center protein I / Photosystem II reaction center protein M / Cytochrome b559 subunit beta ...Photosystem II reaction center protein L / Photosystem II D2 protein / Photosystem II CP47 reaction center protein / Photosystem II reaction center protein Psb30 / Cytochrome b559 subunit alpha / Photosystem II reaction center protein T / Photosystem II reaction center protein H / Photosystem II reaction center protein I / Photosystem II reaction center protein M / Cytochrome b559 subunit beta / Photosystem II reaction center protein Z / Photosystem II CP43 reaction center protein / Photosystem II reaction center protein K
Similarity search - Component
Biological speciesBryopsis corticulans (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsLiu XY / Wang WD
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To Be Published
Title: Structural insights into photosystem II supercomplex of a siphonous green algae Bryopsis corticulans from intertidal zone
Authors: Liu XY / Wang WD
History
DepositionOct 24, 2024-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62153.png

Downloads & links

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Map

FileDownload / File: emd_62153.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 600 pix.
= 624. Å		1.04 Å/pix.
x 600 pix.
= 624. Å		1.04 Å/pix.
x 600 pix.
= 624. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.204
Minimum - Maximum-0.28378534 - 0.9221757
Average (Standard dev.)-0.00013056111 (±0.022548271)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 624.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62153_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_62153_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bc-PSII-LHCII

EntireName: Bc-PSII-LHCII
Components
  • Complex: Bc-PSII-LHCII
    • Protein or peptide: Photosystem II reaction center protein Z
    • Protein or peptide: Cytochrome b559 subunit alpha
    • 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 K
    • Protein or peptide: Photosystem II reaction center protein L
    • Protein or peptide: Photosystem II reaction center protein M
    • Protein or peptide: PsbR
    • Protein or peptide: Cytochrome b559 subunit beta
    • Protein or peptide: Lhcb1
    • Protein or peptide: Lhcb2
    • Protein or peptide: Lhcb3
    • Protein or peptide: LhcbS
    • Protein or peptide: PsbX
    • Protein or peptide: Photosystem II reaction center protein Psb30
    • Protein or peptide: Photosystem II reaction center protein T
    • Protein or peptide: LhcbG
    • Protein or peptide: Photosystem II CP47 reaction center protein
    • Protein or peptide: PsbA
    • Protein or peptide: Photosystem II CP43 reaction center protein
    • Protein or peptide: Photosystem II D2 protein
    • Protein or peptide: PsbW
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: CHLOROPHYLL B
  • Ligand: CHLOROPHYLL A
  • Ligand: Siphonaxanthin
  • 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: Siphonein
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,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: CA-MN4-O5 CLUSTER
  • Ligand: PHEOPHYTIN A
  • Ligand: BICARBONATE ION
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: FE (II) 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

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Supramolecule #1: Bc-PSII-LHCII

SupramoleculeName: Bc-PSII-LHCII / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#22
Source (natural)Organism: Bryopsis corticulans (plant)

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Macromolecule #1: Photosystem II reaction center protein Z

MacromoleculeName: Photosystem II reaction center protein Z / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 6.736073 KDa
SequenceString:
MILLFQVAVF ALISLSFLLV VGVPVAFAYP NGWSENKGTI FSGVGLWFIL VFLVGILNSF VV

UniProtKB: Photosystem II reaction center protein Z

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Macromolecule #2: Cytochrome b559 subunit alpha

MacromoleculeName: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 9.306461 KDa
SequenceString:
MSGTTGERPF SDILTSIRYW VIHSITIPSL FIAGWLFVST GLAYDVFGSP RPNEYFTEDR QQAPLITDRF NALEQVKSLS EI

UniProtKB: Cytochrome b559 subunit alpha

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Macromolecule #3: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 8.05639 KDa
SequenceString:
MPKNSGKDTG MVTGLGTLLS PLNSEYGKVA PGWGTTVLMA VFMALFAVFL VIILEIYNSD VLIDDIAMSW ESLAQ

UniProtKB: Photosystem II reaction center protein H

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Macromolecule #4: Photosystem II reaction center protein I

MacromoleculeName: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 4.055739 KDa
SequenceString:
MLTLKIFVYI VVTFFVSLFI FGFLSDDPGR NPGQGN

UniProtKB: Photosystem II reaction center protein I

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Macromolecule #5: Photosystem II reaction center protein K

MacromoleculeName: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 4.874861 KDa
SequenceString:
MEILISKLPE AYAPFDPLVD VLPIIPVLFL LLAFVWQASV SFR

UniProtKB: Photosystem II reaction center protein K

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Macromolecule #6: Photosystem II reaction center protein L

MacromoleculeName: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 4.405188 KDa
SequenceString:
MAKPNPNKQT VELNRTSLYW GLLLIFVLAV LFSSYIFN

UniProtKB: Photosystem II reaction center protein L

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Macromolecule #7: Photosystem II reaction center protein M

MacromoleculeName: Photosystem II reaction center protein M / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 3.652409 KDa
SequenceString:
MEVNILGLIA TTLFIIIPTS FLLILYVKTA SQN

UniProtKB: Photosystem II reaction center protein M

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Macromolecule #8: PsbR

MacromoleculeName: PsbR / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 28.733895 KDa
SequenceString: MMSSSLQFGV ANGSRVFMAK KGTKKVAKKP AGTKKASGGA KSSDTLWMPG LTRPAWLDGT MAGDRGFDPL CLSKPVEFLQ FDIDELDQN AAVNKKGGVT GSFTTTTDEV STETLQPYSE VFGIQRFREC ELIHGRWCML ATTGCLVQEL VTGVPWQKAG E VILQDGGS ...String:
MMSSSLQFGV ANGSRVFMAK KGTKKVAKKP AGTKKASGGA KSSDTLWMPG LTRPAWLDGT MAGDRGFDPL CLSKPVEFLQ FDIDELDQN AAVNKKGGVT GSFTTTTDEV STETLQPYSE VFGIQRFREC ELIHGRWCML ATTGCLVQEL VTGVPWQKAG E VILQDGGS YFGLGLPFSV SQLVWIEVLL VGGAELYRNS ELDTTKRCYP GGLFDPLNFG SGDPAKVDRL KEAEVKHGRL AM IAFLGFS VQALATGEGI FGSLSRAVTL

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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: Bryopsis corticulans (plant)
Molecular weightTheoretical: 4.783679 KDa
SequenceString:
MASKKSSYTY PIFTVRWLAV HGLAVPTIFF LGSITAMQFI QR

UniProtKB: Cytochrome b559 subunit beta

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Macromolecule #10: Lhcb1

MacromoleculeName: Lhcb1 / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 22.832611 KDa
SequenceString: VEFYGPDRAL WLGPYSEGAV PSYLTGEFPG DYGWDSAGLS ADPETFAANR ELELIHARWA MLGTVGCLTP EALEKYGGVE FGEAVWFKA GSQIFAEGGL DYLGNPSLVH AQSILAICWT QVVLMGLAEG YRCSGGPLGE ATDPLYPGEA FDPMGMADDP E TFAELKTK ...String:
VEFYGPDRAL WLGPYSEGAV PSYLTGEFPG DYGWDSAGLS ADPETFAANR ELELIHARWA MLGTVGCLTP EALEKYGGVE FGEAVWFKA GSQIFAEGGL DYLGNPSLVH AQSILAICWT QVVLMGLAEG YRCSGGPLGE ATDPLYPGEA FDPMGMADDP E TFAELKTK EIKNGRLAMF AMFGFFVQSL QTGKGPVECW AEHIADPVAN NGFV

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Macromolecule #11: Lhcb2

MacromoleculeName: Lhcb2 / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 27.946504 KDa
SequenceString: MASALASKTF VGVQKPSVST QQSKQVTRAA VEWYGPGREL WLGPYSSGAV PSYLTGEFPG DYGWDTAGLS ADPESFRRYR EIELIHARW AMMGTVGCLT PEALERYTGA TFGESVWFKA GAQIFSDDGL NYLGKPELIH AQSILAIVWT QVLIMGFAEG Y RVNGGPAG ...String:
MASALASKTF VGVQKPSVST QQSKQVTRAA VEWYGPGREL WLGPYSSGAV PSYLTGEFPG DYGWDTAGLS ADPESFRRYR EIELIHARW AMMGTVGCLT PEALERYTGA TFGESVWFKA GAQIFSDDGL NYLGKPELIH AQSILAIVWT QVLIMGFAEG Y RVNGGPAG EGLDRLYPGE AFDPLGLADD PETFAELKIK EIKNGRLAMF AMFGFFVQAI QTGKGPVECW AEHVADPFGS NG FNVDQMS KFLFFSPSA

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Macromolecule #12: Lhcb3

MacromoleculeName: Lhcb3 / type: protein_or_peptide / ID: 12 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 27.448963 KDa
SequenceString: MASTMMAKSL VGVTVHTPAV RGKASRHVTK AATEWYGPNR ALWLGPYSGG DVPDYLTGEF PGDYGWDTAG LSADPEMFKQ NRELEVIHS RWAMLGTVGC LTPELLAKYG NVDLPSPVWF SAGSQIFSDG GIDYLGNPNF VHAQSILAIC GIQAVLMSLC E GYRCSGGP ...String:
MASTMMAKSL VGVTVHTPAV RGKASRHVTK AATEWYGPNR ALWLGPYSGG DVPDYLTGEF PGDYGWDTAG LSADPEMFKQ NRELEVIHS RWAMLGTVGC LTPELLAKYG NVDLPSPVWF SAGSQIFSDG GIDYLGNPNF VHAQSILAIC GIQAVLMSLC E GYRCSGGP LGEPTDSLYP GESFDPFNFA ADPETFSELK VKEIKNGRLA MFSMFGYFVQ AIVTGKGPVE NWAAHIADPA NN NIFTDGV ITRFAPN

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Macromolecule #13: LhcbS

MacromoleculeName: LhcbS / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 32.80027 KDa
SequenceString: MQVQAFFDRF TKPTTKKVSK AAGTKKAVPK KAAPASRKAA PAPKPASSGS GGFLSKGWFG ESTNQANLDK WYGPDRALWL PSGLLDRSD VPSYLSGELP GDYGYDPLGI GKDPENVATL RAFELIHCRW AMLGAAGMLI PEALKANGAD LKAGNWLDAG A EMLNGGTL ...String:
MQVQAFFDRF TKPTTKKVSK AAGTKKAVPK KAAPASRKAA PAPKPASSGS GGFLSKGWFG ESTNQANLDK WYGPDRALWL PSGLLDRSD VPSYLSGELP GDYGYDPLGI GKDPENVATL RAFELIHCRW AMLGAAGMLI PEALKANGAD LKAGNWLDAG A EMLNGGTL DYFAVPWAVV ANPLPLAVIA VIEVVLVGAA ENYRRTGAGP KGYAPGIGQF ESSAFDGLDS LYPGGPLDPF DL ARDPEVF QELKIKEIKN GRLAMMATLG FYVQAAVTGE GPYANWSKHI ADPFGYNLFT VIGNSDRVPT L

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Macromolecule #14: PsbX

MacromoleculeName: PsbX / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 10.899735 KDa
SequenceString:
MASFAAASTT RALVTRKTVG MPAMPAVRSR SARATQTVRA SAQKENFVVP VVAATVVAAS LVVPEIASAT EATPSVKALL GSVVNGGLV LLGIAGAISL VSGFDPVARK

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Macromolecule #15: Photosystem II reaction center protein Psb30

MacromoleculeName: Photosystem II reaction center protein Psb30 / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 3.520295 KDa
SequenceString:
MNLEVIFQLL ALLVVLTAGP LVIVLLASRD GNL

UniProtKB: Photosystem II reaction center protein Psb30

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Macromolecule #16: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 3.68347 KDa
SequenceString:
MEALVYTFFL IGTLGILFFS IFFREPPRII K

UniProtKB: Photosystem II reaction center protein T

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Macromolecule #17: LhcbG

MacromoleculeName: LhcbG / type: protein_or_peptide / ID: 17 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 29.898654 KDa
SequenceString: MASAAMAQNA IGFQVSTRVS LEAELNSVGA SMGLSCTNMV VDASARTQAT KQVTRAAVEF YGPDRALWLG PYSEGAVPSY LTGEFPGDY GWDSAGLSAD PETFAANREL ELIHARWAML GTVGCLTPEA LEKYGGVEFG EAVWFKAGSQ IFAEGGLDYL G NPSLVHAQ ...String:
MASAAMAQNA IGFQVSTRVS LEAELNSVGA SMGLSCTNMV VDASARTQAT KQVTRAAVEF YGPDRALWLG PYSEGAVPSY LTGEFPGDY GWDSAGLSAD PETFAANREL ELIHARWAML GTVGCLTPEA LEKYGGVEFG EAVWFKAGSQ IFAEGGLDYL G NPSLVHAQ SILAICWTQV VLMGLAEGYR CSGGPLGEAT DPLYPGEAFD PMGMADDPET FAELKTKEIK NGRLAMFAMF GF FVQSLQT GKGPVECWAE HIADPVANNG FVYATKFFGA QIF

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Macromolecule #18: Photosystem II CP47 reaction center protein

MacromoleculeName: Photosystem II CP47 reaction center protein / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 56.062527 KDa
SequenceString: MGLPWYRVHT VVLNDPGRLI AVHLMHTSLV SGWAGSMAFY ELAVFDPSDP VLNPMWRQGM FVLPFMTRLG ITQSWGGWTI SGETATNPG IWSYEGVATS HILLSGALFA AALWHWVYWD LELFRDPRTG KPALDLPKIF GIHLFLSGLL CFGFGAFHVT G LFGPGIWV ...String:
MGLPWYRVHT VVLNDPGRLI AVHLMHTSLV SGWAGSMAFY ELAVFDPSDP VLNPMWRQGM FVLPFMTRLG ITQSWGGWTI SGETATNPG IWSYEGVATS HILLSGALFA AALWHWVYWD LELFRDPRTG KPALDLPKIF GIHLFLSGLL CFGFGAFHVT G LFGPGIWV SDPFGITGSV QAIKPSWGAD GFDPFNPGGI ASHHIAAGIL GILAGLFHLC VRPPQRLYNA LSMGNIETVL SS SIAAVFW SAFVVCGTMW YGSAATPIEL FGPTRYQWDN GFFANEIEKR VSESVASGKT LSEAWSQIPE KLAFYDYIGN NPA KGGLFR AGAMNSGDGI AVGWLGHSVF KDKNGTELHV RRMPTFFETF PVVLLDDDGI VRADIPFRRA ESKYSIEQVG VSVT FYGGE LDGVTFSDPS TVKKYARRSQ LGEIFEFDRA TLQSDGVFRS SPRGWFTFGH LCFGLLFFFG HIWHGARTIF RDVFA GIDT DLDEQVEFGA FQKVGDTSTR RQSV

UniProtKB: Photosystem II CP47 reaction center protein

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Macromolecule #19: PsbA

MacromoleculeName: PsbA / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 36.192219 KDa
SequenceString: EGVSVWERFC AWITSTENRL YIGWFGCTRL PTLLTATSVF IIAFIAAPPV DIDGIREPVS GSLLYGNNII SGAIIPTSNA IGLHFYPIW EAASLDEWLY NGGPYQLIVC HFFLGICAYM GREWELSFRL GMRPWIAVAY SAPVAAATAV FIIYPIGQGS F SDGMPLGI ...String:
EGVSVWERFC AWITSTENRL YIGWFGCTRL PTLLTATSVF IIAFIAAPPV DIDGIREPVS GSLLYGNNII SGAIIPTSNA IGLHFYPIW EAASLDEWLY NGGPYQLIVC HFFLGICAYM GREWELSFRL GMRPWIAVAY SAPVAAATAV FIIYPIGQGS F SDGMPLGI SGTFNFMIVF QAEHNILMHP FHMLGVAGVF GGSLFSAMHG SLVTSSLIRE TTENESTNAG YKFGQETETY NI VAAHGYF GRLIFQYASF NNSRSLHFFL ALWPVVGIWF TALGISTMAF NLNGFNFNQS VVDSQGRVVN TWADIINRAN LGM EVMHER N

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Macromolecule #20: Photosystem II CP43 reaction center protein

MacromoleculeName: Photosystem II CP43 reaction center protein / type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 50.338395 KDa
SequenceString: VETLFNGTLT VGGRDQESTG FAWWAGNARL INLSGKLLGA HVAHAGLIVF WAGAMNLFEV AHFVPEKPMY EQGLILLPHL AGLGYGIGP GGEVVDTFPY FVSGVLHLIS SAVLGFGGVY HSLIGPETLE ESFPFFGYVW KDKNKMTTIL GIHLIILGIG A WLLVWKAL ...String:
VETLFNGTLT VGGRDQESTG FAWWAGNARL INLSGKLLGA HVAHAGLIVF WAGAMNLFEV AHFVPEKPMY EQGLILLPHL AGLGYGIGP GGEVVDTFPY FVSGVLHLIS SAVLGFGGVY HSLIGPETLE ESFPFFGYVW KDKNKMTTIL GIHLIILGIG A WLLVWKAL YFGGVYDTWA PGGGDVRLIT NPTVSPAVVF GYILKSPFGG DGWIVSVDNM EDIIGGHIWI GTLNIFGGIW HI LTKPWAW ARRAFVWSGE AYLSYSLAAI SLMGFIACCM SWFNNTAYPS EFYGPTGPEA SQAQAFTFLV RDQRLGANVA SAQ GPTGLG KYLMRSPTGE IIFGGETMRF WDFRGPWLEP LRGPNGLDLN KLKNDIQPWQ ERRAAEYMTH APLGSLNSVG GVAT EINAV NFVSPRSWLA TSHFSLGFFF FVGHLWHAGR ARAAAAGFEK GIDRDNEPVL SLKPLD

UniProtKB: Photosystem II CP43 reaction center protein

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Macromolecule #21: Photosystem II D2 protein

MacromoleculeName: Photosystem II D2 protein / type: protein_or_peptide / ID: 21 / Number of copies: 2 / Enantiomer: LEVO / EC number: photosystem II
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 39.575414 KDa
SequenceString: MTIALGKSQT ERGWFDLVDD WLRRDRFVFV GWSGLLLFPC AYLALGGWLT GITFITSWYT HGLASSFLEG CNFLTVAVST PANSMGHSL LLLWGPEAQA DFTRWFQLGG LWSFVALHGS FALIGFMLRQ FEIARSLKLR PYNAIAFSAP ISVFVSVFLI Y PLGQQGWF ...String:
MTIALGKSQT ERGWFDLVDD WLRRDRFVFV GWSGLLLFPC AYLALGGWLT GITFITSWYT HGLASSFLEG CNFLTVAVST PANSMGHSL LLLWGPEAQA DFTRWFQLGG LWSFVALHGS FALIGFMLRQ FEIARSLKLR PYNAIAFSAP ISVFVSVFLI Y PLGQQGWF FAPSFGVAAI FRFILFFQGF HNWTLNPFHM MGVAGVLGAA LLCAIHGATV ENTLFEDGDG ANTFRAFNPT QA EETYSMV TANRFWSQIF GVAFSNKRWL HFFMLFVPVT GLWMSAIGVL GLALNLRAYD FVSQEIRAAE DPEFETFYTK NIL LNEGIR AWMAAQDQPH EKLVFPEEVL PRGNAL

UniProtKB: Photosystem II D2 protein

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Macromolecule #22: PsbW

MacromoleculeName: PsbW / type: protein_or_peptide / ID: 22 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Bryopsis corticulans (plant)
Molecular weightTheoretical: 12.285922 KDa
SequenceString:
MASVSNPFII RGAALPSTAN RTAFKPAARV AVHASMREDV KKFVAAGTCA PVLLASNPAF AAFVEERMNG DGTGRALGID DSSLGLALV ATFSLVWALF YVSQKDLGGD ENDESGLTL

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Macromolecule #23: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 23 / Number of copies: 2 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

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Macromolecule #24: CHLOROPHYLL B

MacromoleculeName: CHLOROPHYLL B / type: ligand / ID: 24 / Number of copies: 170 / 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: 208 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #26: Siphonaxanthin

MacromoleculeName: Siphonaxanthin / type: ligand / ID: 26 / Number of copies: 31 / Formula: 0IE
Molecular weightTheoretical: 600.87 Da
Chemical component information

ChemComp-0IE:
Siphonaxanthin

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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: 2 / 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

+
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: 20 / 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: Siphonein

MacromoleculeName: Siphonein / type: ligand / ID: 29 / Number of copies: 18 / Formula: 0UR
Molecular weightTheoretical: 781.157 Da
Chemical component information

ChemComp-0UR:
Siphonein

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

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 30 / Number of copies: 23 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #31: (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta...

MacromoleculeName: (6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene
type: ligand / ID: 31 / Number of copies: 22 / Formula: 8CT
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-8CT:
(6'R,11cis,11'cis,13cis,15cis)-4',5'-didehydro-5',6'-dihydro-beta,beta-carotene

+
Macromolecule #32: 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: 32 / Number of copies: 6 / 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 #33: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 33 / Number of copies: 10 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #34: CA-MN4-O5 CLUSTER

MacromoleculeName: CA-MN4-O5 CLUSTER / type: ligand / ID: 34 / 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 #35: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 35 / Number of copies: 4 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

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Macromolecule #36: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 36 / 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 #37: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 37 / Number of copies: 4 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Macromolecule #38: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 38 / Number of copies: 2 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

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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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Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TECNAI 10
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 140758
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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