EMDB-0835: Structure of the PSI-FCPI supercomplex from diatom

Basic information

• Entry: Database: EMDB / ID: EMD-0835
• Title: Structure of the PSI-FCPI supercomplex from diatom

Sample

• Complex: PSI-FCPI
  • Protein or peptide: x 28 types
• Ligand: x 12 types

• Biological species: Chaetoceros gracilis (Diatom)
• Method: single particle reconstruction / cryo EM / Resolution: 2.4 Å
• Authors: Nagao R / Kato K / Miyazaki N / Akita F / Shen JR
• Citation: Journal: Nat Commun / Year: 2020; Title: Structural basis for assembly and function of a diatom photosystem I-light-harvesting supercomplex.; Authors: Ryo Nagao / Koji Kato / Kentaro Ifuku / Takehiro Suzuki / Minoru Kumazawa / Ikuo Uchiyama / Yasuhiro Kashino / Naoshi Dohmae / Seiji Akimoto / Jian-Ren Shen / Naoyuki Miyazaki / Fusamichi Akita / ; Abstract: Photosynthetic light-harvesting complexes (LHCs) play a pivotal role in collecting solar energy for photochemical reactions in photosynthesis. One of the major LHCs are fucoxanthin chlorophyll a/c-binding proteins (FCPs) present in diatoms, a group of organisms having important contribution to the global carbon cycle. Here, we report a 2.40-Å resolution structure of the diatom photosystem I (PSI)-FCPI supercomplex by cryo-electron microscopy. The supercomplex is composed of 16 different FCPI subunits surrounding a monomeric PSI core. Each FCPI subunit showed different protein structures with different pigment contents and binding sites, and they form a complicated pigment-protein network together with the PSI core to harvest and transfer the light energy efficiently. In addition, two unique, previously unidentified subunits were found in the PSI core. The structure provides numerous insights into not only the light-harvesting strategy in diatom PSI-FCPI but also evolutionary dynamics of light harvesters among oxyphototrophs.

History

Deposition	Oct 21, 2019	-
Header (metadata) release	May 20, 2020	-
Map release	May 20, 2020	-
Update	May 20, 2020	-
Current status	May 20, 2020	Processing site: PDBj / Status: Released

Map

• File: Download / File: emd_0835.map.gz / Format: CCP4 / Size: 488.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
• Voxel size: X=Y=Z: 1.113 Å

Density

Contour Level	By AUTHOR: 0.045 / Movie #1: 0.045
Minimum - Maximum	-0.14095047 - 0.4005023
Average (Standard dev.)	0.00030691022 (±0.00532834)

• Symmetry: Space group: 1

Details

EMDB XML:

Map geometry	Axis order X Y Z Origin 0 0 0 Dimensions 504 504 504 Spacing 504 504 504
Cell	A=B=C: 560.952 Å α=β=γ: 90.0 °

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	1.113	1.113	1.113
M x/y/z	504	504	504
origin x/y/z	0.000	0.000	0.000
length x/y/z	560.952	560.952	560.952
α/β/γ	90.000	90.000	90.000
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	504	504	504
D min/max/mean	-0.141	0.401	0.000

Supplemental data

Sample components

Entire : PSI-FCPI

• Entire: Name: PSI-FCPI

Components

• Complex: PSI-FCPI
  • 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: Photosystem I reaction center subunit II
  • Protein or peptide: Photosystem I reaction center subunit IV
  • Protein or peptide: Photosystem I reaction center subunit III
  • Protein or peptide: Photosystem I reaction center subunit VIII
  • Protein or peptide: Photosystem I reaction center subunit IX
  • Protein or peptide: Photosystem I reaction center subunit XI
  • Protein or peptide: Photosystem I reaction center subunit XII
  • Protein or peptide: Unknown protein 1
  • Protein or peptide: Photosystem I reaction center subunit Psa28
  • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcr15
  • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcr8
  • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcr2
  • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcr9
  • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcr11
  • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcr12
  • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcr10
  • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcr4
  • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcf6
  • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcr3
  • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcq13
  • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcq3
  • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcq11
  • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcq10
  • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcq8
  • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcq5
• Ligand: CHLOROPHYLL A ISOMER
• Ligand: CHLOROPHYLL A
• Ligand: PHYLLOQUINONEPhytomenadione
• Ligand: IRON/SULFUR CLUSTERIron–sulfur cluster
• Ligand: BETA-CAROTENEΒ-Carotene
• Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
• Ligand: DODECYL-BETA-D-MALTOSIDE
• Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
• 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: Chlorophyll c1Chlorophyll c
• Ligand: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol
• Ligand: water

Supramolecule #1: PSI-FCPI

• Supramolecule: Name: PSI-FCPI / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#28
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 640 KDa

Macromolecule #1: Photosystem I P700 chlorophyll a apoprotein A1

• Macromolecule: Name: Photosystem I P700 chlorophyll a apoprotein A1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 83.648672 KDa

Sequence

String:

AISSTERRTK NVQIFVEKDA VETSFEKWAQ PGHFSRTLAK GPKTTTWIWN LHADAHDFDS QTNSLEEVSR KIFSAHFGQL AAIFLWISG MHFHGAYFSN YSAWLSDPIG IKQSSQVVWP IVGQEILNAD VGGNFQGVQT TSGWFQMWRA EGITSEVELY W IAIGGLIM SALMLFAGWF HYHKAAPKLE WFQNAESMMN HHLAGLLGLG CLSWSGHQIH IALPINKLLD AGVSPQEIPL PH EFLINRE LMAQLYPSFG KGLAPFFSGH WGEYSDFLTF KGGLNPVTGG LWLSDIAHHH LALSVLFIVA GHMYRTNWGI GHS MKEILE AHKGPFTGEG HKGLYEILTT SWHAQLAINL AMMGSLSIIV AHHMYAMPPY PYIATDYATQ LSLFTHHMWI GGFC VTGGA AHAAIFMVRD YTPANNYNNL LDRVLRHRDA IISHLNWVCI FLGCHAFGFY IHNDTMRALG RPQDMFSDKA IQLQP IFAQ WIQNIHLLAP GTTAPNALAT TSYAFGGDVV EVGGKIAMMP IKLGTADFMV HHIHAFTIHV TVLILLKGVL YARSSK LIP DKANLGFRFP CDGPGRGGTC QSSSWDHVFL GLFWMYNSIS VVIFHFSWKM QSDVWGTVTP DGSISHITGG NFAQSSI TI NGWLRDFLWS QASQVIQSYG SASSAYGLIF LGAHFIWAFS LMFLFSGRGY WQELIESIVW AHNKLNFAPA IQPRALSI T QGRAVGLAHY LLGGIGTTWA FFLARSLSIT

Macromolecule #2: Photosystem I P700 chlorophyll a apoprotein A2

• Macromolecule: Name: Photosystem I P700 chlorophyll a apoprotein A2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 81.897477 KDa

Sequence

String:

MATKFPKFSQ ALAQDPATRR IWYGIATAHD LEAHDGMTEE NLYQKIFASH FGHLAIIFLW TAGNLFHVAW QGNFEQWVAK PLKTKPIAH SIWDPHFGES ALKAFSKGNT YPVNIAFSGV YQWWYTIGFR TNQELYAGSI GLLALSCVLL FAGWLHLQPK F RPSLSWFK NNESRLNHHL SGLLGVSSLA WTGHIVHVAI PASRGVHVGW DNFLTTPPHP AGLTPFFTGN WTVYAENPDS AS HVYGTSE GAGTAILTFL GGFHPQTQSL WLSDIAHHQL AIAVVFIIAG HMYRTNFGIG HNMKEILDAH RPPGGRLGAG HVG LFETIT NSLHMQLGLA LASLGVATSL TAQHMYALTP YAYLSKDFTT EAALYTHHQY IAGFLMVGAF AHGAIFFVRD YDPE LNKNN VLARMLEHKE AIISHLSWAS LFLGFHTLGL YIHNDTVVAF GQPEKQILFE PVFAEYIQAA SGKAVYQFNV LLSSP TSPA TVAGNQVWLP GWLDAINNPK NDLFLKIGPG DFLVHHAIAL GLHVTALILV KGALDARGSK LMPDKKDFGY SFPCDG PGR GGTCDISAWD AFYLAMFWML NTIGWVTFYW HWKHMTIWGG NPGQFDESSN YIMGWLRDYL WLNSSPLING YNPFGMN NL SVWSWMFLFG HLIWATGFMF LISWRGYWQE LIETLVWAHE RTPLANLIRW RDKPVALSIV QARLVGLAHF SVGYILTY A AFVIASTSGK FG

Macromolecule #3: Photosystem I iron-sulfur center

• Macromolecule: Name: Photosystem I iron-sulfur center / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 8.807169 KDa

Sequence

String:

MSHTVKIYDT CIGCTQCVRA CPTDVLEMVP WDGCKSGQIA SSPRVEDCVG CKRCETACPT DFLSVRVYLG AETTRSLGLA Y

Macromolecule #4: Photosystem I reaction center subunit II

• Macromolecule: Name: Photosystem I reaction center subunit II / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 15.594646 KDa

Sequence

String:

MTLNLQTPFP TFGGSTGGWL RSAEVEEKYA ITWTSKKEQI FEMPTGGAAI MRNGENLLYL ARKEQCLALG TQLRTFKIND YKIYRIFPS GEVQYLHPKD GVFPEKVNPG RTSVNSRDFS IGKNPNPASI KFSGTTTYES

Macromolecule #5: Photosystem I reaction center subunit IV

• Macromolecule: Name: Photosystem I reaction center subunit IV / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 7.621467 KDa

Sequence

String:

MVGRGSKVRI LRKESYWFNQ VGTVATIDQS GIRYPALVRF ESVNYAGTNS NNFALDELKE VVEETEE

Macromolecule #6: Photosystem I reaction center subunit III

• Macromolecule: Name: Photosystem I reaction center subunit III / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 20.445615 KDa

Sequence

String:

MKRFNILTLL VAVLITLTPN IASAEIGGLT KCSDSPAFAK REKASIKKLE QRKSTYEAGT PPALALQQQI ERTEARFDKY SRSELLCGA DGLPHLIADG RWSHAAEFML PGFGFIYISG WIGWVGRKYL RAVSTTKNPA ESEIIINVPL ALKIMTTGYI W PISAWEEL VSGDLVALDE EVTVSPR

Macromolecule #7: Photosystem I reaction center subunit VIII

• Macromolecule: Name: Photosystem I reaction center subunit VIII / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 3.94474 KDa

Sequence

String:

MAAAFLPSIL VPIVGLIFPA FSMALFFLYI QQDDIA

Macromolecule #8: Photosystem I reaction center subunit IX

• Macromolecule: Name: Photosystem I reaction center subunit IX / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 4.882824 KDa

Sequence

String:

MKNFQKYLST APVLLTIWMT FTAGFIIEIN RFFPDMLGLY F

Macromolecule #9: Photosystem I reaction center subunit XI

• Macromolecule: Name: Photosystem I reaction center subunit XI / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 16.148812 KDa

Sequence

String:

MANFIKPYND DPFVGHLATP ITSSAVTRAL LKNLPAYRFG LTPLLRGLEI GLAHGYFLIG PFVKLGPLRN SDIALIAGFL STIGLILIL TLGLTIYGAA VFNSDKESLE TTETTLQTRK AWDQFKGGFF VGACGSAGFA LICLSSIPQS IL

Macromolecule #10: Photosystem I reaction center subunit XII

• Macromolecule: Name: Photosystem I reaction center subunit XII / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 3.241863 KDa

Sequence

String:

MIYDSQVYIA LVIAVVASVL AIRLGATLYN

Macromolecule #11: Unknown protein 1

• Macromolecule: Name: Unknown protein 1 / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 11.081651 KDa

Sequence

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)

Macromolecule #12: Photosystem I reaction center subunit Psa28

• Macromolecule: Name: Photosystem I reaction center subunit Psa28 / type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 12.899798 KDa

Sequence

String:

FAPMPRAAIS TTQARTASMP SAPFTSLSMA SEDMTWEGEY PPSKVLGPIM SKMPSGLLGL ISIACAAVCA YSIAQSGVLQ QQPGAYENG SWVKWYYVLG SFGGPLAWGT HVASWIQRKN GM

Macromolecule #13: Fucoxanthin chlorophyll a/c-binding protein Lhcr15

• Macromolecule: Name: Fucoxanthin chlorophyll a/c-binding protein Lhcr15 / type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 24.881914 KDa

Sequence

String:

MILQYFNTFP PPKRSYKKVY NIIIHYFIIM VRSVLLAALV GTAAAFAPAT SMTRRSPAVA LKAEMSESLP FLPRPEKLDG SMAGDRGFD PMGLSEIQQD LTYARWAELK HGRIAMLAIV GMIVQEYIHL PGEAYQNSDP FGAVSTVGLG VNGQIFAAIG C VELINFNK HYDGSEPGDI GWTGGLLKNK SEAEIMKAKE QEITHCRLAM IAITGATVQT LLFHQPLLG

Macromolecule #14: Fucoxanthin chlorophyll a/c-binding protein Lhcr8

• Macromolecule: Name: Fucoxanthin chlorophyll a/c-binding protein Lhcr8 / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 21.727959 KDa

Sequence

String:

MKLALLASLI ASAAAFAPSS STGARASTAL DAGKQSQALP FLPYPENLSG YVGDAGFDPL RFSDYFPMDY LREAEIKHGR ICMLATVGW IAVDMGLRVY PVPAGLEGVT AATAHDASVA QGGLGQVFGW VAVAEMASWI GVSQMLQGSG REPGYFGFDP L GLMKGKSE AEVNNMKLKE IKNGRLAMLA FSGICTQSVL FDKTFPF

Macromolecule #15: Fucoxanthin chlorophyll a/c-binding protein Lhcr2

• Macromolecule: Name: Fucoxanthin chlorophyll a/c-binding protein Lhcr2 / type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 21.558555 KDa

Sequence

String:

MKTVAILSLL TASAAAFAPA STTQTSSSTA LAGSVFDNYV GAKDFRGAEF KFDPLKLSET YEPFQGWFRE SELRHGRTAM LAVVGYIAT DFVRIPGEMY SFEAIPKSAD AHDALIASGP MSQLLLWIGL FDLVVTAPAV QAMGKGEREP GDFGLKWFAP S SKDAFDKK REAELLNGRL AMFAIGGIAT QSVLNGHGFP YL

Macromolecule #16: Fucoxanthin chlorophyll a/c-binding protein Lhcr9

• Macromolecule: Name: Fucoxanthin chlorophyll a/c-binding protein Lhcr9 / type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 22.933426 KDa

Sequence

String:

MAKLSIALTT AAALASSANA FAPSKGARSV TSALSATGFE EVGGKPWDPL SLGKLEDAND TFPNMFPKSQ YLQESEIKHG RMCMLAWTG VWATHVGGMG LGMHIPGMPV ESDWTKALGV FAAEQPALFG AILLFISIAE GESVGHSGDN WRNMSTKEPG N LGFDWMGL TKKLSEEKVA RYKIVELKNG RAAMIAMASL FAMEAIPGSV PIMNVFN

Macromolecule #17: Fucoxanthin chlorophyll a/c-binding protein Lhcr11

• Macromolecule: Name: Fucoxanthin chlorophyll a/c-binding protein Lhcr11 / type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 29.512191 KDa

Sequence

String:

MVVCHLILSR ITNFLPLSLA HYRTCTSPTP TTPPKKTVVS SALHAEMSKA VPFVKAPANT AGYVGDVGFD PLGFSDYFDM KWLRESEIK HGRASMLACL GFVVQEYITI PGYTHVDDSN LAPQAVGVSA MLQIVLWMGV LEFWTNKGNV TMETMFSSPD R IPGNLGFD PMGLSVGKSQ AEKDEMALKE IKNGRLAMLA IGGMIHHNWR KRHGALTSRE RERNVLQTLD AFLKVHMHTV LC VSCSIWD VNSIFIMRDG IESSFGFPD

Macromolecule #18: Fucoxanthin chlorophyll a/c-binding protein Lhcr12

• Macromolecule: Name: Fucoxanthin chlorophyll a/c-binding protein Lhcr12 / type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 22.362646 KDa

Sequence

String:

MKLALLASLI ASAAAFAPSS STGAARASTA LDAGKKSQAL PFLPYPENLA GYVGDAGFDP FRFSDFAPMD FLREAEIKHG RICMLAWLG FVAVDLGARI YPLPEAYEGL TAVTAHDALV QQGAMSQIFL WCSVFEAIST VSVIQMLYEE SGREPGYFGF D PLGFLNGK SEAEVNEMKL KEIKNGRLAM LAFSGVVTQA VLTQGPFPYV

Macromolecule #19: Fucoxanthin chlorophyll a/c-binding protein Lhcr10

• Macromolecule: Name: Fucoxanthin chlorophyll a/c-binding protein Lhcr10 / type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 32.238152 KDa

Sequence

String:

LLQGFSRWLV FFVSIRIIRH PCRPPYHETY SSSNTFLSIQ YIEQSHSARQ TSLSLLLITP LTLVLYLAIY TILKMFKTAA AITSLLAAS ASAFAPSSFN GRISTAVAAE KSQSLPFMNR PPLLDGSMAG DVGFDPLGLS NIDDVGIDLY WLREAEIKHC R VAMLAVVG ILQVEIFGPA PGCEMATDKC QMDAFWQIWG AHPQYIAFGL IMIMMIEMIS GIATTQGRES GERAPGDFGL DP LGYGKGD AAGYARLQAQ EIANGRLAMF AAAGEIMQGC TTHQGALENL MTALRDNSF

Macromolecule #20: Fucoxanthin chlorophyll a/c-binding protein Lhcr4

• Macromolecule: Name: Fucoxanthin chlorophyll a/c-binding protein Lhcr4 / type: protein_or_peptide / ID: 20 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 29.70415 KDa

Sequence

String:

LRSIHHLIAS HRRLFKFIRH YTINKMKSAL IATALLAGSA AAFTSNAGSQ STSALKAMPE RLWDSMVDKT ERSKAVPFLP RAVNLDGSL PGDVGFDPFY LSSIPKDFSG FIQPPQWEEK GIPTLYWMRE AELKHCRVAM LAWFGWLATD GAFGVTLRFP G EIYSVENI PTAYEAHNAL VSQGSMGFLL LAVGFIEFCT GAVLVEVAKG ASDREAGDFK LDPLSFLKGK SEEEIKRMKT RE IANGRLA MLAFGGVATQ TALEGGNHAF PYF

Macromolecule #21: Fucoxanthin chlorophyll a/c-binding protein Lhcf6

• Macromolecule: Name: Fucoxanthin chlorophyll a/c-binding protein Lhcf6 / type: protein_or_peptide / ID: 21 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 23.517385 KDa

Sequence

String:

LLLPYSPYLK SSLTHFDISS HSQPPLFSTN PHSSAFAPSS QTNVRSTSSL QAWKDENIIG ITAPMGFFDP LGLSSGKSDE VMNLYREAE LKHGRVAMAA CLGWYITAAG VHPAFNSALS SDPLEAAKQL PTVGWLQFVL GCGAIEWLAQ QIKARPGYQP G DILGAAYW VDNSDEGWVD YQNKEINNGR LAMVAFMGIF VQDLYFGNYG DQIFRN

Macromolecule #22: Fucoxanthin chlorophyll a/c-binding protein Lhcr3

• Macromolecule: Name: Fucoxanthin chlorophyll a/c-binding protein Lhcr3 / type: protein_or_peptide / ID: 22 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 22.216549 KDa

Sequence

String:

MKSVAILAAL FGSATAFVPS QVSRTAASTS VKASLADMVG AEGPEPIPFA PSKTSKNFDP VGFAERSPEW LPWYREAELK HGRAAMLAT VGFVVPEFIR VPGEQFSFEA IPKVIDAHDA LPESMIQIFG WISFLEACTF PAMAGLGGKY DRKPGDFSFD P LGLYPTDP EKQKQMQLAE LKNGRLAMIA IGGMVTGAAV TGHGFPYLP

Macromolecule #23: Fucoxanthin chlorophyll a/c-binding protein Lhcq13

• Macromolecule: Name: Fucoxanthin chlorophyll a/c-binding protein Lhcq13 / type: protein_or_peptide / ID: 23 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 24.842496 KDa

Sequence

String:

MKTAAIFALL AGSAAAFAPT TVSPRASTVA HMSSINEAFG ISIETGNKCP PLGARILEDA QPSAIKWFQN AEIKHGRIAM VATIGYLVQ KLGVHFPLYL GPSGSNCFHP ESETAWLLSS STGVTFSDIA KAAPLDAIQM VPVAGWMQIF FVAGWFESVA Y YRQWVKNS PIPGDYGYDP LGFTKREGGW DSEELTSLRL KEIKNGRLAM MTIAAWVSDE MIPGALPVWH P

Macromolecule #24: Fucoxanthin chlorophyll a/c-binding protein Lhcq3

• Macromolecule: Name: Fucoxanthin chlorophyll a/c-binding protein Lhcq3 / type: protein_or_peptide / ID: 24 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 21.318404 KDa

Sequence

String:

MKSVLFLALA GSAAAFAPST QSRSNTLLKA DLSSLPGSTA PVGPFDPLNL ADSGSEETLA WFRASELKHG RVAMLATTGY LVQGAGIHF PGMLSSDVSF ESLSAMKPLE AWDAVPDAGK AQILGTIFIA EMITESKPVH YTKGGPMPTM VFPAIDFSGV D AATLKRKQ DSELNNGRLA MIAIMSFISA ANIPGSVPAL TNNPAF

Macromolecule #25: Fucoxanthin chlorophyll a/c-binding protein Lhcq11

• Macromolecule: Name: Fucoxanthin chlorophyll a/c-binding protein Lhcq11 / type: protein_or_peptide / ID: 25 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 25.994562 KDa

Sequence

String:

MKLAILTTLL AGASAFTTPN ARPAFATKLS MSEEAAAEEA PAADAPEEVV EPASPSYTCI SKEAILSSPD TTEIGRVWDP LGLAEIGSA ETLAWYRHSE VKHGRIAMAA FVGWWAVGAG LRFPGELSHG LEFSSIPSKG LEAWDAVPGW GKAQMLLFAG L IEFHDELF HTRRTEGGHY LRGGTPGKNM VPGLFDPFGF SKGKSEEELA KGRDREIKNG RLAMIGVAGL YCAATIPGSV PL QPPC

Macromolecule #26: Fucoxanthin chlorophyll a/c-binding protein Lhcq10

• Macromolecule: Name: Fucoxanthin chlorophyll a/c-binding protein Lhcq10 / type: protein_or_peptide / ID: 26 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 26.875781 KDa

Sequence

String:

MKIILSGLAL LASSVAAFAP QSIISANANN KNANVVLEAA KDDLIAIAEK SNPVLKYYDP LQLGSTTIWG ETNSATIGFL RQSEIKHGR IAMAAFVGYI VQANGIHFPW PMSFDGTPFP ADAGSPPEQW DALSDAAKWQ IILFIGFLEW FSEAAGKHYM R GGKPGAFP NFSDSDLIPH PVPLNLYDPF GFSKGKTEAQ KADGLIKELN NGRLAMIGIM GFLAEQKVEG SVPLLKGVVP HY DGEVMAP FM

Macromolecule #27: Fucoxanthin chlorophyll a/c-binding protein Lhcq8

• Macromolecule: Name: Fucoxanthin chlorophyll a/c-binding protein Lhcq8 / type: protein_or_peptide / ID: 27 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 30.545674 KDa

Sequence

String:

MDNKIAGYNI IIHTIISSIN MKFSLVVLSS LVVASSNGVT AFAPSSSTTS TSTTALSSSA SKAELEAIAK KANPTLGYYD PLSLADKDF WGKGNDATIA FLRQSEIKHG RIAMFAFVGY IVQSNFVFPW AQTLAGAPHP SADLSPEAQW DAIPLGAKWQ I FAVISALE LWDECGGGGV LPHYTKGRKP GQYPPFTLFR DNVHFVLDLY DPFGFNKNMS EETKERRLVS ELNNGRLAML GI FGFLCAD TIPGSVPLLN DIAIPYSGQV MQPFEGQFSY FGSL

Macromolecule #28: Fucoxanthin chlorophyll a/c-binding protein Lhcq5

• Macromolecule: Name: Fucoxanthin chlorophyll a/c-binding protein Lhcq5 / type: protein_or_peptide / ID: 28 / Number of copies: 1 / Enantiomer: LEVO
• Source (natural): Organism: Chaetoceros gracilis (Diatom)
• Molecular weight: Theoretical: 23.533191 KDa

Sequence

String:

MKIATLFLAL ASSAAAFAPS QQVRSMTNEK MKPRQARNNF ALNMKVDEMP GATAPLGKFD PLNLATLGSE STLAWFRAAE LKHSRVAML ATTGYLVQAA GIHFPGMLSS DVSFESLSAM KPLDAWDAVP EGGKNQIYFT IFLAEFITEC KGTHYTKGGP L PTIVFPPI DFSTVNPEQL KTRQNRELNN GRLAMIAIMS FVAAANIPGS VPALAGNPMF

Macromolecule #29: CHLOROPHYLL A ISOMER

• Macromolecule: Name: CHLOROPHYLL A ISOMER / type: ligand / ID: 29 / Number of copies: 1 / Formula: CL0
• Molecular weight: Theoretical: 893.489 Da

Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER / Chlorophyll a

Macromolecule #30: CHLOROPHYLL A

• Macromolecule: Name: CHLOROPHYLL A / type: ligand / ID: 30 / Number of copies: 221 / Formula: CLA
• Molecular weight: Theoretical: 893.489 Da

Chemical component information

ChemComp-CLA:
CHLOROPHYLL A / Chlorophyll a

Macromolecule #31: PHYLLOQUINONE

• Macromolecule: Name: PHYLLOQUINONE / type: ligand / ID: 31 / Number of copies: 2 / Formula: PQN
• Molecular weight: Theoretical: 450.696 Da

Chemical component information

ChemComp-PQN:
PHYLLOQUINONE / Phytomenadione

Macromolecule #32: IRON/SULFUR CLUSTER

• Macromolecule: Name: IRON/SULFUR CLUSTER / type: ligand / ID: 32 / Number of copies: 3 / Formula: SF4
• Molecular weight: Theoretical: 351.64 Da

Chemical component information

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

Macromolecule #33: BETA-CAROTENE

• Macromolecule: Name: BETA-CAROTENE / type: ligand / ID: 33 / Number of copies: 20 / Formula: BCR
• Molecular weight: Theoretical: 536.873 Da

Chemical component information

ChemComp-BCR:
BETA-CAROTENE / Β-Carotene

Macromolecule #34: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

• Macromolecule: Name: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 34 / Number of copies: 7 / Formula: LHG
• Molecular weight: Theoretical: 722.97 Da

Chemical component information

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

Macromolecule #35: DODECYL-BETA-D-MALTOSIDE

• Macromolecule: Name: DODECYL-BETA-D-MALTOSIDE / type: ligand / ID: 35 / Number of copies: 21 / Formula: LMT
• Molecular weight: Theoretical: 510.615 Da

Chemical component information

ChemComp-LMT:
DODECYL-BETA-D-MALTOSIDE / detergent*YM

Macromolecule #36: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

• Macromolecule: Name: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 36 / Number of copies: 13 / Formula: LMG
• Molecular weight: Theoretical: 787.158 Da

Chemical component information

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

Macromolecule #37: (3S,3'S,5R,5'R,6S,6'R,8'R)-3,5'-dihydroxy-8-oxo-6',7'-didehydro-5...

• Macromolecule: Name: (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: 37 / Number of copies: 54 / Formula: A86
• Molecular weight: Theoretical: 658.906 Da

Macromolecule #38: Chlorophyll c1

• Macromolecule: Name: Chlorophyll c1 / type: ligand / ID: 38 / Number of copies: 54 / Formula: KC1
• Molecular weight: Theoretical: 610.941 Da

Chemical component information

ChemComp-KC1:
Chlorophyll c1 / Chlorophyll c

Macromolecule #39: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,be...

• Macromolecule: Name: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol; type: ligand / ID: 39 / Number of copies: 31 / Formula: DD6
• Molecular weight: Theoretical: 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

Macromolecule #40: water

• Macromolecule: Name: water / type: ligand / ID: 40 / Number of copies: 156 / Formula: HOH
• Molecular weight: Theoretical: 18.015 Da

Chemical component information

ChemComp-HOH:
WATER / Water

Experimental details

Structure determination

• Method: cryo EM
• Processing: single particle reconstruction
• Aggregation state: particle

Sample preparation

• Concentration: 2 mg/mL

Buffer

pH: 6.5
Component:

Concentration	Formula	Name
20.0 mM	MES-NaOH	MES-NaOH
0.02 %	DDM	DDM

• Grid: Model: Quantifoil R1.2/1.3 / Material: MOLYBDENUM / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: PLASMA CLEANING
• Vitrification: Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

Electron microscopy

• Microscope: FEI TITAN KRIOS
• Electron beam: Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
• Electron optics: Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
• Image recording: Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Ų
• Experimental equipment: Model: Titan Krios / Image courtesy: FEI Company

Image processing

• Particle selection: Number selected: 2689965
• CTF correction: Software - Name: CTFFIND (ver. 4)

Startup model

Type of model: EMDB MAP
EMDB ID:

9853

• Initial angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
• Final 3D classification: Number classes: 6 / Software - Name: RELION (ver. 3)
• Final angle assignment: Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3)
• Final reconstruction: Applied symmetry - Point group: C₁ (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3) / Number images used: 470801

Atomic model buiding 1

• Refinement: Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient

Output model

PDB-6l4u:
Structure of the PSI-FCPI supercomplex from diatom