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- EMDB-9839: Structure of PSII-FCP supercomplex from a centric diatom Chaetoce... -

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Basic information

Entry
Database: EMDB / ID: EMD-9839
TitleStructure of PSII-FCP supercomplex from a centric diatom Chaetoceros gracilis at 3.02 angstrom resolution
Map dataPSII-FCP
Sample
  • Complex: PSII-FCP supercomplex
    • Protein or peptide: x 28 types
  • Ligand: x 18 types
KeywordsPSII-FCP supercomplex / PLANT PROTEIN
Function / homology
Function and homology information


thylakoid / photosystem II assembly / photosystem II stabilization / photosystem II / extrinsic component of membrane / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis, light reaction / photosynthesis / respiratory electron transport chain ...thylakoid / photosystem II assembly / photosystem II stabilization / photosystem II / extrinsic component of membrane / phosphate ion binding / chloroplast thylakoid membrane / photosynthesis, light reaction / photosynthesis / respiratory electron transport chain / electron transfer activity / protein stabilization / iron ion binding / heme binding
Similarity search - Function
PsbQ-like domain superfamily / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide ...PsbQ-like domain superfamily / Photosystem II PsbU, oxygen evolving complex / Photosystem II 12 kDa extrinsic protein (PsbU) / Photosystem II PsbV, cytochrome c-550 precursor / Photosystem II cytochrome c-550 precursor / Cytochrome c-550 domain / Cytochrome c-550 domain / Photosystem II PsbX, type 1 subfamily / Photosystem II PsbO, manganese-stabilising / Manganese-stabilising protein / photosystem II polypeptide / Photosystem II PsbX / Photosystem II reaction centre X protein (PsbX) / Photosystem II reaction centre protein H / Photosystem II reaction centre protein H superfamily / Photosystem II 10 kDa phosphoprotein / Outer membrane protein/outer membrane enzyme PagP, beta-barrel / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily
Similarity search - Domain/homology
Extrinsic protein in photosystem II / Extrinsic protein in photosystem II / Photosystem II 12 kDa extrinsic protein / Photosystem II reaction center protein X / Photosystem II extrinsic protein V / Photosystem II reaction center protein H
Similarity search - Component
Biological speciesChaetoceros gracilis (Diatom)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.02 Å
AuthorsPi X / Zhao S
CitationJournal: Science / Year: 2019
Title: The pigment-protein network of a diatom photosystem II-light-harvesting antenna supercomplex.
Authors: Xiong Pi / Songhao Zhao / Wenda Wang / Desheng Liu / Caizhe Xu / Guangye Han / Tingyun Kuang / Sen-Fang Sui / Jian-Ren Shen /
Abstract: Diatoms play important roles in global primary productivity and biogeochemical cycling of carbon, in part owing to the ability of their photosynthetic apparatus to adapt to rapidly changing light ...Diatoms play important roles in global primary productivity and biogeochemical cycling of carbon, in part owing to the ability of their photosynthetic apparatus to adapt to rapidly changing light intensity. We report a cryo-electron microscopy structure of the photosystem II (PSII)-fucoxanthin (Fx) chlorophyll (Chl) a/c binding protein (FCPII) supercomplex from the centric diatom The supercomplex comprises two protomers, each with two tetrameric and three monomeric FCPIIs around a PSII core that contains five extrinsic oxygen-evolving proteins at the lumenal surface. The structure reveals the arrangement of a huge pigment network that contributes to efficient light energy harvesting, transfer, and dissipation processes in the diatoms.
History
DepositionMar 6, 2019-
Header (metadata) releaseJul 31, 2019-
Map releaseJul 31, 2019-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6jlu
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9839.png

Downloads & links

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Map

FileDownload / File: emd_9839.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPSII-FCP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 340 pix.
= 444.224 Å		1.31 Å/pix.
x 340 pix.
= 444.224 Å		1.31 Å/pix.
x 340 pix.
= 444.224 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.30654 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.057114918 - 0.12278585
Average (Standard dev.)0.000024796067 (±0.00480418)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 444.2236 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.30654117647061.30654117647061.3065411764706
M x/y/z340340340
origin x/y/z0.0000.0000.000
length x/y/z444.224444.224444.224
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS340340340
D min/max/mean-0.0570.1230.000

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Supplemental data

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Sample components

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Entire : PSII-FCP supercomplex

EntireName: PSII-FCP supercomplex
Components
  • Complex: PSII-FCP supercomplex
    • 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: Psb31
    • Protein or peptide: Photosystem II reaction center protein H
    • 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: Extrinsic protein in photosystem II
    • Protein or peptide: FCP-D
    • Protein or peptide: Extrinsic protein in photosystem II
    • Protein or peptide: PsbG
    • Protein or peptide: PsbT
    • Protein or peptide: Extrinsic protein in photosystem II
    • Protein or peptide: Cytochrome c-550
    • Protein or peptide: PsbW
    • Protein or peptide: Photosystem II reaction center X protein
    • Protein or peptide: PsbY
    • Protein or peptide: PsbZ
    • Protein or peptide: FCP-E
    • Protein or peptide: FCP-A
    • Protein or peptide: FCP-F
  • Ligand: CA-MN4-O5 CLUSTER
  • Ligand: FE (II) ION
  • Ligand: CHLOROPHYLL A
  • Ligand: PHEOPHYTIN A
  • Ligand: BETA-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: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: CHLORIDE ION
  • Ligand: BICARBONATE ION
  • Ligand: PROTOPORPHYRIN IX CONTAINING FE
  • Ligand: Chlorophyll c1
  • 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: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol
  • Ligand: Chlorophyll c2
  • Ligand: water

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Supramolecule #1: PSII-FCP supercomplex

SupramoleculeName: PSII-FCP supercomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#28
Source (natural)Organism: Chaetoceros gracilis (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: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 39.575062 KDa
SequenceString: MTATLERREG VSLWERFCAW ITSTENRLYI GWFGCLMFPT LLTATSCFII AFIAAPPVDI DGIREPVSGS LLYGNNIISG AVVPSSNAI GMHFYPIWEA ASVDEWLYNG GPYQLIVLHF LLGVSAYMGR EWELSYRLGM RPWIFVAFSA PVAAASAVFL V YPIGQGSF ...String:
MTATLERREG VSLWERFCAW ITSTENRLYI GWFGCLMFPT LLTATSCFII AFIAAPPVDI DGIREPVSGS LLYGNNIISG AVVPSSNAI GMHFYPIWEA ASVDEWLYNG GPYQLIVLHF LLGVSAYMGR EWELSYRLGM RPWIFVAFSA PVAAASAVFL V YPIGQGSF SDGMPLGISG TFNFMLVFQA EHNILMHPFH MAGVAGVFGG SLFSAMHGSL VTSSLIRETT ENESTNYGYK FG QEEETYN IVAAHGYFGR LIFQYASFNN SRALHFFLAL WPVVGIWITA MGISTMAFNL NGFNFNQSVV DSQGRVINTW ADI LNRANL GIEVMHERNA HNFPLDLASG DVLPVALTAP AVN

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Macromolecule #2: PsbB

MacromoleculeName: PsbB / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 56.475301 KDa
SequenceString: MALPWYRVHT VVLNDPGRLI AVHLMHTALV AGWAGSMALY ELAVFDPSDP VLNPMWRQGM FVMPFMTRLG ITDSWGGWSI TGESVSNPG IWSFEGVALS HIILSGMCFL AAIWHWVYWD LELFRDPRTG EPALDLPKIF GIHLFLSGLL CFGFGAFHVT G LFGPGIWV ...String:
MALPWYRVHT VVLNDPGRLI AVHLMHTALV AGWAGSMALY ELAVFDPSDP VLNPMWRQGM FVMPFMTRLG ITDSWGGWSI TGESVSNPG IWSFEGVALS HIILSGMCFL AAIWHWVYWD LELFRDPRTG EPALDLPKIF GIHLFLSGLL CFGFGAFHVT G LFGPGIWV SDAYGITGKV QPVAPAWGAD GFNPFNPGGI AAHHIAAGIF GIFAGIFHLT VRPPQRLYRA LRMGNIETVL SS SISAVFF AAFVTSGTMW YGAAATPIEL FGPTRYQWDS GYFQQEIERQ VETSVSEGLS ESQAWSRIPD KLAFYDYIGN NPA KGGLFR AGPMNKGDGI AEAWLGHPIF RDKEGRELTV RRMPAFFETF PVILVDKDGI IRADIPFRRA ESKYSIEQVG VTVD FYGGK LNGQTFKDAP TVKKFARKAQ LGEVFEFDRT SLESDGVFRS SPRGWYTYGH ANFALLFFFG HLWHGGRTIF RDVFT GIGA EVTEQVEFGA FQKLGDKSTK KQGAV

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Macromolecule #3: PsbC

MacromoleculeName: PsbC / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (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: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 37.983301 KDa
SequenceString: RGLFDLVDDW LKKDRFVFVG WSGLLLFPTA YLAAGGWMTG TTFVTSWYTH GLASSYLEGC NFLTAAVSTP ANSVGHSLLL LWGPEAQGD FTRWCQIGGL WTFVALHGAF GLIGFCLRQF EIARLVGIRP YNAIAFSGPI AVFVSVFLLY PLGQASWFFA P SFGVAAIF ...String:
RGLFDLVDDW LKKDRFVFVG WSGLLLFPTA YLAAGGWMTG TTFVTSWYTH GLASSYLEGC NFLTAAVSTP ANSVGHSLLL LWGPEAQGD FTRWCQIGGL WTFVALHGAF GLIGFCLRQF EIARLVGIRP YNAIAFSGPI AVFVSVFLLY PLGQASWFFA P SFGVAAIF RFLLFLQGFH NWTLNPFHMM GVAGILGGAL LCAIHGATVE NTLFEDGDAA NTFRAFTPTQ SEETYSMVTA NR FWSQIFG VAFSNKRWLH FFMLFVPVTG LWTSSIGIVG LALNLRAYDF VSQELRAAED PEFETFYTKN HLLDEGIRAW MAA QDQPHE NFVFPEEVLP RGNAL

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Macromolecule #5: PsbE

MacromoleculeName: PsbE / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 9.062132 KDa
SequenceString:
STGERPFSDI ITSVRYWIIH SITIPSLFVS GWLFISTGLA YDVFGTPRPN EYFTQDRQQV PLVNDRFSAK QELEDLTKG

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Macromolecule #6: PsbF

MacromoleculeName: PsbF / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 3.652377 KDa
SequenceString:
PIFTFRWLAV HGLAIPTVFF LGGITAMQFI QR

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Macromolecule #7: Psb31

MacromoleculeName: Psb31 / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 18.733262 KDa
SequenceString:
MKLSIAALLV TSVAAFAPST VERTSTALNM DRRSAFAQIA TAGAVLAGIP SIASADGSVS AATINRARGL YGDRIAALKD AVAAGDFKA IAEEKNAFIL FNSGAYPTNK AKKNAAIAQT NEIFKAIRSG DKAAVKSAYD AYMAANDIRP LPEINANIGQ G YSSDFDFR VRTKAGAIYV R

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Macromolecule #8: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 7.188501 KDa
SequenceString:
ALRTRLGEIL RPLNAEYGKV APGWGTTPIM GIVMLAFLIF LVIILQIYNS SLIIENVDVD WANGI

UniProtKB: Photosystem II reaction center protein H

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Macromolecule #9: PsbI

MacromoleculeName: PsbI / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 3.940673 KDa
SequenceString:
MLTLKILVYT TVIFFVSLFI FGFLSSDPSR NPNR

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Macromolecule #10: PsbJ

MacromoleculeName: PsbJ / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 3.487078 KDa
SequenceString:
GRVPLWLVGL VGGFAVITIV SLFIYGSYSG LGSS

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Macromolecule #11: PsbK

MacromoleculeName: PsbK / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 4.225085 KDa
SequenceString:
KLPEAYAFLN PIVDVMPVIP VLFFLLAFVW QAAVSFR

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Macromolecule #12: PsbL

MacromoleculeName: PsbL / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 4.367076 KDa
SequenceString:
MTGPNPNKQA VELNRTSLYW GLLLIFVLAV LFSSYFFN

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Macromolecule #13: PsbM

MacromoleculeName: PsbM / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 4.358022 KDa
SequenceString:
EVQFGAYLAV LLGTFLPALF LVNLFIQTEA RKAGKAGGQD S

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Macromolecule #14: Psb34

MacromoleculeName: Psb34 / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (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 #15: Extrinsic protein in photosystem II

MacromoleculeName: Extrinsic protein in photosystem II / type: protein_or_peptide / ID: 15 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 26.820375 KDa
SequenceString: ALTKSQINEL SYLQVKGTGL ANRCAEVVGE DSIKPKPGAK LVDMCIEPKA WAVEEEVGKA GKTEKKFVNS KVMTRQTYTL DAIEGPITV DGGKITFSEK EGIDYAATTV QLPGGERVPF LFTVKDLVAK GNGDTFKPGF QMGGDFNTPS YRTGLFLDPK G RGGTTGYD ...String:
ALTKSQINEL SYLQVKGTGL ANRCAEVVGE DSIKPKPGAK LVDMCIEPKA WAVEEEVGKA GKTEKKFVNS KVMTRQTYTL DAIEGPITV DGGKITFSEK EGIDYAATTV QLPGGERVPF LFTVKDLVAK GNGDTFKPGF QMGGDFNTPS YRTGLFLDPK G RGGTTGYD MAVALPALQL GEEGDAELFG ENNKVFDITQ GRIEMEVNKV NAEDSEIGGV FVATQLSDTD MGSKTPKKVL TK GIFYAKV EQ

UniProtKB: Extrinsic protein in photosystem II

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Macromolecule #16: FCP-D

MacromoleculeName: FCP-D / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 24.667848 KDa
SequenceString: PSADAWANSV ESKALPFARA PATLDGTMLG DFGFDPLGFS TVPVGPWFTG IQGRNGEIGN LKWYREAELI HGRIAQVAVV GFIAPGLFG TLPGNEWTGV DAYSNLNPLE AFSQVPGLAI LQIFLFMSYL EIRRINIIKE EGENYMPGDL RIGQGEGRWN P FGLDYSPE ...String:
PSADAWANSV ESKALPFARA PATLDGTMLG DFGFDPLGFS TVPVGPWFTG IQGRNGEIGN LKWYREAELI HGRIAQVAVV GFIAPGLFG TLPGNEWTGV DAYSNLNPLE AFSQVPGLAI LQIFLFMSYL EIRRINIIKE EGENYMPGDL RIGQGEGRWN P FGLDYSPE AYEEKRLQEL KHCRLAMIGV FGLWAQAQAS GVGVTEQIGA ALTTPDYYAK AGYFLPEG

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Macromolecule #17: Extrinsic protein in photosystem II

MacromoleculeName: Extrinsic protein in photosystem II / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 22.585391 KDa
SequenceString: MKSAICFVAL AASASAFAPE ANNARVATSV NAEARREVFG KIAAAGAAFL PVAANAAVGE SPRFSVFGLI GDGTSYSEGA AYGTDQADK LYSPYSVYSP EGEKSLYKPD SAEYLARKKA VLAETKNRLQ KIPGYVDKKE WFNVKDELTR YMYETRGAVR S LSSSVTQK ...String:
MKSAICFVAL AASASAFAPE ANNARVATSV NAEARREVFG KIAAAGAAFL PVAANAAVGE SPRFSVFGLI GDGTSYSEGA AYGTDQADK LYSPYSVYSP EGEKSLYKPD SAEYLARKKA VLAETKNRLQ KIPGYVDKKE WFNVKDELTR YMYETRGAVR S LSSSVTQK EKAEVFFRAL EDTYGAATLK KGDAVKASND KAIAALDAFT ATL

UniProtKB: Extrinsic protein in photosystem II

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Macromolecule #18: PsbG

MacromoleculeName: PsbG / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 6.230672 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)

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Macromolecule #19: PsbT

MacromoleculeName: PsbT / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 3.711547 KDa
SequenceString:
MEALVYTFLL IGTLMVIFFA VFFRETPRIL R

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Macromolecule #20: Extrinsic protein in photosystem II

MacromoleculeName: Extrinsic protein in photosystem II / type: protein_or_peptide / ID: 20 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 10.167527 KDa
SequenceString:
VIDYENIGYL GGSSIVDINN ANIRAYLKMP GMYPTVAGKI VSHGPYSGVS DLYKIPGLSS AEADVIKKYE SRLTAKTPSP DYVIDRINN GLYR

UniProtKB: Photosystem II 12 kDa extrinsic protein

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Macromolecule #21: Cytochrome c-550

MacromoleculeName: Cytochrome c-550 / type: protein_or_peptide / ID: 21 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 14.920837 KDa
SequenceString:
IDLDEATRTV VVDNAGNTTV LTPEQVKRGK RLFNATCGAC HVGGITKTNP NVGLDPEALS LATPRRDNIN ALVDYIKNPT TYDGLESIA EVHPSIKSAD IYPRMRSLTD EDLYSIAGHI MLSPKIASEK WGGGKIYY

UniProtKB: Photosystem II extrinsic protein V

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Macromolecule #22: PsbW

MacromoleculeName: PsbW / type: protein_or_peptide / ID: 22 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 5.720508 KDa
SequenceString:
NARFANGKPQ SIEAKYIMRS PAEWDRFMRF MDRYAEANGL GFSS(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)

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Macromolecule #23: Photosystem II reaction center X protein

MacromoleculeName: Photosystem II reaction center X protein / type: protein_or_peptide / ID: 23 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 3.502219 KDa
SequenceString:
MTASLSNFIA SLIAGGVVVG VIAIALIVIS KSDRI

UniProtKB: Photosystem II reaction center protein X

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Macromolecule #24: PsbY

MacromoleculeName: PsbY / type: protein_or_peptide / ID: 24 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 3.634343 KDa
SequenceString:
DTRLLVIAAP VLVAASWALF NIGRLAIQQI QRL

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Macromolecule #25: PsbZ

MacromoleculeName: PsbZ / type: protein_or_peptide / ID: 25 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 6.417546 KDa
SequenceString:
MITALTALFV LVSLALVVTV PVALATPGEW ETSKDQFNKI FQLWVGLVVA IATADGISTA I

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Macromolecule #26: FCP-E

MacromoleculeName: FCP-E / type: protein_or_peptide / ID: 26 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 18.781801 KDa
SequenceString: AFEDELGAQP PLGFFDPLGL V(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)DG DQEKFDRLRY VEIKHGRISM LA VVGYLVQ EAGVRLPGTI DYSGKTFAEI PNGFAAFKEI PAGGLVQLLF FIGVLESSVM RDLT(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK) ...String:
AFEDELGAQP PLGFFDPLGL V(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)DG DQEKFDRLRY VEIKHGRISM LA VVGYLVQ EAGVRLPGTI DYSGKTFAEI PNGFAAFKEI PAGGLVQLLF FIGVLESSVM RDLT(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) TFDEETQFKK RAIELNQGRA AQMGILALM VHEQLGVSLL P(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)

+
Macromolecule #27: FCP-A

MacromoleculeName: FCP-A / type: protein_or_peptide / ID: 27 / Number of copies: 16 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 18.98884 KDa
SequenceString:
ENELGAQPPL GFFDPLGLVE DGNQAKFDRL RYVELKHGRI SMLAVVGYLI EKAGIRLPGN ISYDGTTFAD IPDGFAALSK IPDAGLFQL FAFIGFLEVF VMKDITGGEF VGDFRNGFID FGWDSFDEET KLKKRAIELN QGRAAMMGIL ALMVHEKLIP L GYDADLPI IGHL

+
Macromolecule #28: FCP-F

MacromoleculeName: FCP-F / type: protein_or_peptide / ID: 28 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 18.214701 KDa
SequenceString:
AFEDELGAQP PLGFFDPLGL VADGDQEKFD RLRYVEIKHG RISMLAVVGY LVQEAGVRLP GTIDYSGKTF AEIPNGFAAF KEIPAGGLV QLLFFIGVLE SSVMRDLTGE AEFVGDFRNG AIDFGWDTFD EETQFKKRAI ELNQGRAAQM GILALMVHEQ L GVSLLP

+
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: 230 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
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

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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

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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: 10 / 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

+
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

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

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 36 / Number of copies: 22 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 37 / Number of copies: 36 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #38: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 38 / Number of copies: 14 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

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Macromolecule #39: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 39 / Number of copies: 2 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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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

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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

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Macromolecule #42: Chlorophyll c1

MacromoleculeName: Chlorophyll c1 / type: ligand / ID: 42 / Number of copies: 22 / Formula: KC1
Molecular weightTheoretical: 610.941 Da
Chemical component information

ChemComp-KC1:
Chlorophyll c1

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Macromolecule #43: (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: 43 / Number of copies: 124 / Formula: A86
Molecular weightTheoretical: 658.906 Da

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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: 2 / 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

+
Macromolecule #45: Chlorophyll c2

MacromoleculeName: Chlorophyll c2 / type: ligand / ID: 45 / Number of copies: 36 / Formula: KC2
Molecular weightTheoretical: 608.926 Da
Chemical component information

ChemComp-KC2:
Chlorophyll c2

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Macromolecule #46: water

MacromoleculeName: water / type: ligand / ID: 46 / Number of copies: 1 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 6.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: NONE
Startup modelType of model: PDB ENTRY
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.02 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 42033
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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