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- EMDB-35987: Structural insights into photosystem II supercomplex and trimeric... -

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Entry
Database: EMDB / ID: EMD-35987
TitleStructural insights into photosystem II supercomplex and trimeric FCP antennae of a centric diatom Cyclotella meneghiniana
Map data
Sample
  • Complex: Cm-PSII-FCPII
    • Protein or peptide: x 28 types
  • Ligand: x 16 types
KeywordsPSII-FCPII supercomplex / PHOTOSYNTHESIS
Biological speciesStephanocyclus meneghinianus (Diatom)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 Å
AuthorsShen LL / Li ZH / Shen JR / Wang WD
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: Nat Commun / Year: 2023
Title: Structural insights into photosystem II supercomplex and trimeric FCP antennae of a centric diatom Cyclotella meneghiniana.
Authors: Songhao Zhao / Lili Shen / Xiaoyi Li / Qiushuang Tao / Zhenhua Li / Caizhe Xu / Cuicui Zhou / Yanyan Yang / Min Sang / Guangye Han / Long-Jiang Yu / Tingyun Kuang / Jian-Ren Shen / Wenda Wang /
Abstract: Diatoms are dominant marine algae and contribute around a quarter of global primary productivity, the success of which is largely attributed to their photosynthetic capacity aided by specific ...Diatoms are dominant marine algae and contribute around a quarter of global primary productivity, the success of which is largely attributed to their photosynthetic capacity aided by specific fucoxanthin chlorophyll-binding proteins (FCPs) to enhance the blue-green light absorption under water. We purified a photosystem II (PSII)-FCPII supercomplex and a trimeric FCP from Cyclotella meneghiniana (Cm) and solved their structures by cryo-electron microscopy (cryo-EM). The structures reveal detailed organizations of monomeric, dimeric and trimeric FCP antennae, as well as distinct assemblies of Lhcx6_1 and dimeric FCPII-H in PSII core. Each Cm-PSII-FCPII monomer contains an Lhcx6_1, an FCP heterodimer and other three FCP monomers, which form an efficient pigment network for harvesting energy. More diadinoxanthins and diatoxanthins are found in FCPs, which may function to quench excess energy. The trimeric FCP contains more chlorophylls c and fucoxanthins. These diversified FCPs and PSII-FCPII provide a structural basis for efficient light energy harvesting, transfer, and dissipation in C. meneghiniana.
History
DepositionApr 23, 2023-
Header (metadata) releaseDec 20, 2023-
Map releaseDec 20, 2023-
UpdateDec 20, 2023-
Current statusDec 20, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35987.png

Downloads & links

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Map

FileDownload / File: emd_35987.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.158
Minimum - Maximum-0.31446657 - 0.7089361
Average (Standard dev.)-0.00015652567 (±0.018221822)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 542.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35987_half_map_1.map
Projections & Slices
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Histogram (log scale)

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Half map: #1

Fileemd_35987_half_map_2.map
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Sample components

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Entire : Cm-PSII-FCPII

EntireName: Cm-PSII-FCPII
Components
  • Complex: Cm-PSII-FCPII
    • Protein or peptide: PsbA
    • Protein or peptide: PsbB
    • Protein or peptide: PsbC
    • Protein or peptide: PsbD
    • Protein or peptide: PsbE
    • Protein or peptide: PsbF
    • Protein or peptide: PsbH
    • Protein or peptide: PsbI
    • Protein or peptide: PsbJ
    • Protein or peptide: PsbK
    • Protein or peptide: PsbL
    • Protein or peptide: PsbM
    • Protein or peptide: Psb34
    • Protein or peptide: PsbO
    • Protein or peptide: PsbQ'
    • Protein or peptide: PsbT
    • Protein or peptide: PsbU
    • Protein or peptide: PsbV
    • Protein or peptide: PsbW
    • Protein or peptide: PsbX
    • Protein or peptide: PsbY
    • Protein or peptide: PsbZ
    • Protein or peptide: FCPII-G, fucoxanthin chlorophyll a/c binding protein
    • Protein or peptide: FCPII-H2, fucoxanthin chlorophyll a/c binding protein
    • Protein or peptide: FCPII-H1, fucoxanthin chlorophyll a/c binding protein
    • Protein or peptide: FCPII-I, fucoxanthin chlorophyll a/c binding protein
    • Protein or peptide: FCPII-K, fucoxanthin chlorophyll a/c binding protein
    • Protein or peptide: FCPII-J, fucoxanthin chlorophyll a/c binding protein
  • Ligand: CA-MN4-O5 CLUSTER
  • Ligand: FE (II) ION
  • Ligand: CHLOROPHYLL A
  • Ligand: PHEOPHYTIN APheophytin
  • Ligand: BETA-CAROTENEΒ-Carotene
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • 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: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: CHLORIDE IONChloride
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: BICARBONATE IONBicarbonate
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate
  • Ligand: (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol
  • Ligand: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol

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Supramolecule #1: Cm-PSII-FCPII

SupramoleculeName: Cm-PSII-FCPII / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#28
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)

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Macromolecule #1: PsbA

MacromoleculeName: PsbA / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 36.951098 KDa
SequenceString: VSLWERFCAW ITSTENRLYI GWFGCLMFPT LLTATSCFII AFIAAPPVDI DGIREPVSGS LLYGNNIISG AVVPSSNAIG MHFYPIWEA ASVDEWLYNG GPYQLIVLHF LLGVSAYMGR EWELSYRLGM RPWIFVAFSA PVAAASAVFL VYPIGQGSFS D GMPLGISG ...String:
VSLWERFCAW ITSTENRLYI GWFGCLMFPT LLTATSCFII AFIAAPPVDI DGIREPVSGS LLYGNNIISG AVVPSSNAIG MHFYPIWEA ASVDEWLYNG GPYQLIVLHF LLGVSAYMGR EWELSYRLGM RPWIFVAFSA PVAAASAVFL VYPIGQGSFS D GMPLGISG TFNFMLVFQA EHNILMHPFH MAGVAGVFGG SLFSAMHGSL VTSSLIRETT ENESTNYGYK FGQEEETYNI VA AHGYFGR LIFQYASFNN SRALHFFLAL WPVVGIWITA MGISTMAFNL NGFNFNQSVV DSQGRVINTW ADILNRANLG IEV MHERNA HNFPLDL

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Macromolecule #2: PsbB

MacromoleculeName: PsbB / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 53.504957 KDa
SequenceString: ALPWYRVHTV VLNDPGRLIA VHLMHTALVA GWAGSMALYE LAVFDPSDPV LNPMWRQGMF VMPFMTRLGI TDSWGGWSIT GESVSNPGI WSFEGVALSH IILSGMCFLA AIWHWVYWDL ELFRDPRTGE PALDLPKIFG IHLFLSGLLC FGFGAFHVTG L FGPGIWVS ...String:
ALPWYRVHTV VLNDPGRLIA VHLMHTALVA GWAGSMALYE LAVFDPSDPV LNPMWRQGMF VMPFMTRLGI TDSWGGWSIT GESVSNPGI WSFEGVALSH IILSGMCFLA AIWHWVYWDL ELFRDPRTGE PALDLPKIFG IHLFLSGLLC FGFGAFHVTG L FGPGIWVS DAYGITGKVQ PVAPAWGADG FNPFNPGGIA AHHIAAGIFG IFAGIFHLTV RPPQRLYRAL RMGNIETVLS SS ISAVFFA AFVTSGTMWY GAAATPIELF GPTRYQWDSG YFQQEIERQV ETSVSEGLSE SQAWSRIPDK LAFYDYIGNN PAK GGLFRA GPMNKGDGIA EAWLGHPIFR DKEGRELTVR RMPAFFETFP VILVDKDGII RADIPFRRAE SKYSIEQVGV TVDF YGGKL NGQTFKDAPT VKKFARKAQL GEVFEFDRTS LESDGVFRSS PRGWYTYGHA NFALLFFFGH LWHGGRTIFR DVFTG I

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Macromolecule #3: PsbC

MacromoleculeName: PsbC / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 49.357348 KDa
SequenceString: IAGRDIESTG FAWWSGNARL INVSGKLLGA HVAHAGLMVF WAGAMVLFEV SHFVPEKPTY EQGFILIQHL ATLGYGIGPG GEITSTVPY FAVGVIHLIS SAILGFGGIY HSLLGPDTLE ESFPFFGYDW RDKNKMTTIL GIHLCLLGLG SFLLVIKAMY L GGVYDTWA ...String:
IAGRDIESTG FAWWSGNARL INVSGKLLGA HVAHAGLMVF WAGAMVLFEV SHFVPEKPTY EQGFILIQHL ATLGYGIGPG GEITSTVPY FAVGVIHLIS SAILGFGGIY HSLLGPDTLE ESFPFFGYDW RDKNKMTTIL GIHLCLLGLG SFLLVIKAMY L GGVYDTWA PGGGDVRYIT TPTLNPIVIF GYVFRSPFGG DGWVVSVNNM EDVIGGHIWV GILCIVGGIW HIFTKPFAWA RR AFVWSGE AYLSYSLAAI SLMGFTAALY SWYNNTAYPS ELYGPTGPEA SQAQAFTFLV RDQRLGANVS SAQGPTGLGK YLM RSPSGE IIFGGETMRF WDLRAPWVEP LRGPNGLDIN KIKNDIQPWQ ERRAAEYMTH APLGSLNSVG GVATEINSVN YVSP RSWLC CSHFFLAFFF LVGHWWHAGR ARAAAAGFEK GIDRDFEPVL SMTPL

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Macromolecule #4: PsbD

MacromoleculeName: PsbD / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 37.826109 KDa
SequenceString: GLFDLVDDWL KKDRFVFVGW SGLLLFPTAY LAAGGWMTGT TFVTSWYTHG LASSYLEGCN FLTAAVSTPA NSVGHSLLLL WGPEAQGDF TRWCQIGGLW TFVALHGAFG LIGFCLRQFE IARLVGIRPY NAIAFSGPIA VFVSVFLLYP LGQASWFFAP S FGVAAIFR ...String:
GLFDLVDDWL KKDRFVFVGW SGLLLFPTAY LAAGGWMTGT TFVTSWYTHG LASSYLEGCN FLTAAVSTPA NSVGHSLLLL WGPEAQGDF TRWCQIGGLW TFVALHGAFG LIGFCLRQFE IARLVGIRPY NAIAFSGPIA VFVSVFLLYP LGQASWFFAP S FGVAAIFR FLLFLQGFHN WTLNPFHMMG VAGILGGALL CAIHGATVEN TLFEDGDAAN TFRAFTPTQS EETYSMVTAN RF WSQIFGV AFSNKRWLHF FMLFVPVTGL WTSSIGIVGL ALNLRAYDFV SQELRAAEDP EFETFYTKNH LLDEGIRAWM AAQ DQPHEN FVFPEEVLPR GNAL

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Macromolecule #5: PsbE

MacromoleculeName: PsbE / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 8.687784 KDa
SequenceString:
RPFSDIITSV RYWIIHSITI PSLFVSGWLF ISTGLAYDVF GTPRPNEYFT QDRQQVPLVN DRFSAKQELE DLTKG

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Macromolecule #6: PsbF

MacromoleculeName: PsbF / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 3.555263 KDa
SequenceString:
IFTFRWLAVH GLAIPTVFFL GGITAMQFIQ R

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Macromolecule #7: PsbH

MacromoleculeName: PsbH / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 7.188501 KDa
SequenceString:
ALRTRLGEIL RPLNAEYGKV APGWGTTPIM GIVMLAFLIF LVIILQIYNS SLIIENVDVD WANGI

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Macromolecule #8: PsbI

MacromoleculeName: PsbI / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 3.940673 KDa
SequenceString:
MLTLKILVYT TVIFFVSLFI FGFLSSDPSR NPNR

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Macromolecule #9: PsbJ

MacromoleculeName: PsbJ / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 3.487078 KDa
SequenceString:
GRVPLWLVGL VGGFAVITIV SLFIYGSYSG LGSS

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Macromolecule #10: PsbK

MacromoleculeName: PsbK / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 4.225085 KDa
SequenceString:
KLPEAYAFLN PIVDVMPVIP VLFFLLAFVW QAAVSFR

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Macromolecule #11: PsbL

MacromoleculeName: PsbL / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 4.23588 KDa
SequenceString:
TGPNPNKQAV ELNRTSLYWG LLLIFVLAVL FSSYFFN

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Macromolecule #12: PsbM

MacromoleculeName: PsbM / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 4.358022 KDa
SequenceString:
EVQFGAYLAV LLGTFLPALF LVNLFIQTEA RKAGKAGGQD S

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Macromolecule #13: Psb34

MacromoleculeName: Psb34 / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 2.571161 KDa
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)

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Macromolecule #14: PsbO

MacromoleculeName: PsbO / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 26.749297 KDa
SequenceString: LTKSQINELS YLQVKGTGLA NRCAEVVGED SIKPKPGAKL VDMCIEPKAW AVEEEVGKAG KTEKKFVNSK VMTRQTYTLD AIEGPITVD GGKITFSEKE GIDYAATTVQ LPGGERVPFL FTVKDLVAKG NGDTFKPGFQ MGGDFNTPSY RTGLFLDPKG R GGTTGYDM ...String:
LTKSQINELS YLQVKGTGLA NRCAEVVGED SIKPKPGAKL VDMCIEPKAW AVEEEVGKAG KTEKKFVNSK VMTRQTYTLD AIEGPITVD GGKITFSEKE GIDYAATTVQ LPGGERVPFL FTVKDLVAKG NGDTFKPGFQ MGGDFNTPSY RTGLFLDPKG R GGTTGYDM AVALPALQLG EEGDAELFGE NNKVFDITQG RIEMEVNKVN AEDSEIGGVF VATQLSDTDM GSKTPKKVLT KG IFYAKVE Q

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Macromolecule #15: PsbQ'

MacromoleculeName: PsbQ' / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 16.001864 KDa
SequenceString:
SVFGLIGDGT SYSEGAAYGT DQADKLYSPY SVYSPEGEKS LYKPDSAEYL ARKKAVLAET KNRLQKIPGY VDKKEWFNVK DELTRYMYE TRGAVRSLSS SVTQKEKAEV FFRALEDTYG AATLKKGDAV KASNDKAIAA LDAFTA

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Macromolecule #16: PsbT

MacromoleculeName: PsbT / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 3.441195 KDa
SequenceString:
MEALVYTFLL IGTLMVIFFA VFFRETPRI

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Macromolecule #17: PsbU

MacromoleculeName: PsbU / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 10.010334 KDa
SequenceString:
VIDYENIGYL GGSSIVDINN ANIRAYLKMP GMYPTVAGKI VSHGPYSGVS DLYKIPGLSS AEADVIKKYE SRLTAKTPSP DYVIDRINN GLY

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Macromolecule #18: PsbV

MacromoleculeName: PsbV / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 14.757663 KDa
SequenceString:
IDLDEATRTV VVDNAGNTTV LTPEQVKRGK RLFNATCGAC HVGGITKTNP NVGLDPEALS LATPRRDNIN ALVDYIKNPT TYDGLESIA EVHPSIKSAD IYPRMRSLTD EDLYSIAGHI MLSPKIASEK WGGGKIY

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Macromolecule #19: PsbW

MacromoleculeName: PsbW / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 5.606405 KDa
SequenceString:
ARFANGKPQS IEAKYIMRSP AEWDRFMRFM DRYAEANGLG FSS(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #20: PsbX

MacromoleculeName: PsbX / type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 3.389061 KDa
SequenceString:
MTASLSNFIA SLIAGGVVVG VIAIALIVIS KSDR

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Macromolecule #21: PsbY

MacromoleculeName: PsbY / type: protein_or_peptide / ID: 21 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 3.634343 KDa
SequenceString:
DTRLLVIAAP VLVAASWALF NIGRLAIQQI QRL

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Macromolecule #22: PsbZ

MacromoleculeName: PsbZ / type: protein_or_peptide / ID: 22 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 6.233312 KDa
SequenceString:
MITALTALFV LVSLALVVTV PVALATPGEW ETSKDQFNKI FQLWVGLVVA IATADGIST

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Macromolecule #23: FCPII-G, fucoxanthin chlorophyll a/c binding protein

MacromoleculeName: FCPII-G, fucoxanthin chlorophyll a/c binding protein / type: protein_or_peptide / ID: 23 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 18.512004 KDa
SequenceString:
APPGLVGALP PVGFFDPAGF AAKASPEELS RYREVEIMHG RFAQLAVLGF IIPEKCAYDG SFGDDFLAPT GRALEVFNTD PLWLGLTLA VISALETVRL IETEPGTRTD AKIESLGWRP KTESEYINYQ VRELQQGRLA MLAFAGEVAQ ELVNDKPLLV N LQDSGFVS W

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Macromolecule #24: FCPII-H2, fucoxanthin chlorophyll a/c binding protein

MacromoleculeName: FCPII-H2, fucoxanthin chlorophyll a/c binding protein / type: protein_or_peptide / ID: 24 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 18.251734 KDa
SequenceString:
FENELGVIAP TGFFDPLGLS KNISKEKFDE YRTAELKHGR AAMLAVLGYI APETYRFGFD IAPGVSTYDI PNGVAAIDYI PALGWAQII FLIGAVDYWG VLGDFSFGKP DLGDKEEERK LQELQHGRLA MLAFLELLRH DSQNFVSPGF DGYDKMITGL P FMYG

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Macromolecule #25: FCPII-H1, fucoxanthin chlorophyll a/c binding protein

MacromoleculeName: FCPII-H1, fucoxanthin chlorophyll a/c binding protein / type: protein_or_peptide / ID: 25 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 18.085545 KDa
SequenceString:
FENELGVIAP TGFFDPLGFT QDIDQEKFDQ YRTAELKHGR VAQLAVVGYV VPEFFRWGFD IAPGIACADV PNGVAAINAI PALGWAQII FAIGAVDVRG WFGNFDIGKP DLKGKEEERA LQELQHGRLA MLAILELLRH DSQNLVKPGF DGLDNLITGL P FLYN

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Macromolecule #26: FCPII-I, fucoxanthin chlorophyll a/c binding protein

MacromoleculeName: FCPII-I, fucoxanthin chlorophyll a/c binding protein / type: protein_or_peptide / ID: 26 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 23.27917 KDa
SequenceString: SPRALPFGSA PATLDGSLVG DVGFDPIGFS TAPFASFNNP LYKEGDFMSD LEWLREAELT HGRIAQLAVL GFIWPALFGT FPGNENFGG ADAFSYVNPL EAITHVPDLA IYQIVGGMAW VEYQRVIRIK EQGKNRVSGD IGLGYPGGWN PFNLNYSPEE Y AEKQLQEI ...String:
SPRALPFGSA PATLDGSLVG DVGFDPIGFS TAPFASFNNP LYKEGDFMSD LEWLREAELT HGRIAQLAVL GFIWPALFGT FPGNENFGG ADAFSYVNPL EAITHVPDLA IYQIVGGMAW VEYQRVIRIK EQGKNRVSGD IGLGYPGGWN PFNLNYSPEE Y AEKQLQEI KHCRLAMIGA FGLFFQALNS GTDIVSQLSP AFAAPDYAAK AGYFLP

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Macromolecule #27: FCPII-K, fucoxanthin chlorophyll a/c binding protein

MacromoleculeName: FCPII-K, fucoxanthin chlorophyll a/c binding protein / type: protein_or_peptide / ID: 27 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 13.039064 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

+
Macromolecule #28: FCPII-J, fucoxanthin chlorophyll a/c binding protein

MacromoleculeName: FCPII-J, fucoxanthin chlorophyll a/c binding protein / type: protein_or_peptide / ID: 28 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Stephanocyclus meneghinianus (Diatom)
Molecular weightTheoretical: 17.850197 KDa
SequenceString:
ENEIGALAPT GFFDPAKLSD GISQEKFDQY RLAELKHGRA AMLAVLGYVA PETYRFGYDL IPGELSTRDI PNGVAALNAI PFGGWVQMI AFVGTVEAYG WFTSPTGVLD LPADILAKRQ TSELQHGRLA MLAFLELIRH DSQNLAQPGF DGYDNLITGL P FLY

+
Macromolecule #29: CA-MN4-O5 CLUSTER

MacromoleculeName: CA-MN4-O5 CLUSTER / type: ligand / ID: 29 / 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 #30: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 30 / Number of copies: 2 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

+
Macromolecule #31: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 31 / Number of copies: 206 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

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Macromolecule #32: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 32 / Number of copies: 4 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A / Pheophytin

+
Macromolecule #33: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 33 / Number of copies: 20 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE / Β-Carotene

+
Macromolecule #34: 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: 34 / 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 #35: 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: 35 / Number of copies: 4 / 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 / Plastoquinone

+
Macromolecule #36: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 36 / Number of copies: 14 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

+
Macromolecule #37: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 37 / Number of copies: 22 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

+
Macromolecule #38: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 38 / Number of copies: 2 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #39: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 39 / Number of copies: 8 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Macromolecule #40: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 40 / Number of copies: 2 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION / pH buffer*YM / Bicarbonate

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Macromolecule #41: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 41 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE / Heme B

+
Macromolecule #42: (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5...

MacromoleculeName: (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5,5',6,6',7,8-hexahydro-5,6-epoxy-beta,beta-caroten-3'- yl acetate
type: ligand / ID: 42 / Number of copies: 24 / Formula: A86
Molecular weightTheoretical: 658.906 Da

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Macromolecule #43: (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},...

MacromoleculeName: (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen- ...Name: (1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol
type: ligand / ID: 43 / Number of copies: 2 / Formula: ET4
Molecular weightTheoretical: 566.856 Da
Chemical component information

ChemComp-ET4:
(1~{R})-3,5,5-trimethyl-4-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E})-3,7,12,16-tetramethyl-18-[(4~{R})-2,6,6-trimethyl-4-oxidanyl-cyclohexen-1-yl]octadeca-1,3,5,7,9,11,13,15-octaen-17-ynyl]cyclohex-3-en-1-ol

+
Macromolecule #44: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,be...

MacromoleculeName: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol
type: ligand / ID: 44 / Number of copies: 12 / Formula: DD6
Molecular weightTheoretical: 582.855 Da
Chemical component information

ChemComp-DD6:
(3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol / Diadinoxanthin

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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 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: 2.5 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 153326
FSC plot (resolution estimation)

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