[English] 日本語
Yorodumi
- EMDB-64383: PSI-8 FCPI supercomplex from haptophyte Chrysotila roscoffensis -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-64383
TitlePSI-8 FCPI supercomplex from haptophyte Chrysotila roscoffensis
Map dataCryo-EM map of a PSI-8 FCPI supercomplex from a haptophyte Chrysotila roscoffensis.
Sample
  • Complex: Photosystem I (PSI) with 8 fucoxanthin chlorophyll a/c binding protein I (FCPI) supercomplex from haptophyte Chrysotila roscoffensis
    • Protein or peptide: x 1 types
  • Protein or peptide: x 18 types
  • Ligand: x 13 types
Keywordsphotosystem I / photosynthesis / chlorophyll / light-harvesting complex / biogenesis / assembly / LHCI / FCPI / coccolithophore / haptophyte
Biological speciesChrysotila roscoffensis (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.33 Å
AuthorsLa Rocca R / Tsai P-C / Kato K / Nakajima Y / Akita F / Shen J-R
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2026
Title: Multiple structures of photosystem I-FCPI supercomplexes from a coccolithophore alga reveal a modular antenna organization.
Authors: Romain La Rocca / Pi-Cheng Tsai / Koji Kato / Yoshiki Nakajima / Fusamichi Akita / Jian-Ren Shen /
Abstract: Photosystem I (PSI) converts light energy into chemical energy in photosynthesis, and forms supercomplexes with light-harvesting complexes (LHCI) in eukaryotes to enhance energy capture and transfer. ...Photosystem I (PSI) converts light energy into chemical energy in photosynthesis, and forms supercomplexes with light-harvesting complexes (LHCI) in eukaryotes to enhance energy capture and transfer. Various numbers and organizations of both PSI core and LHCI subunits are observed in various organisms. A subgroup of haptophytes named coccolithophores play a major role in marine carbon cycle and CaCO production, and the light-harvesting antennas of them are named FCPs (fucoxanthin-chlorophyll a/c binding protein) because they bind chlorophyll c and fucoxanthin in addition to chlorophyll a. A structure of a large PSI-FCPI supercomplex containing 38 FCPI subunits has been reported from a coccolithophore Emiliania huxleyi recently (L. Shen et al., Science 389, eadv2132, 2025). Here we solved five cryo-electron microscopy (cryo-EM) structures of PSI-FCPI supercomplexes isolated from another coccolithophore Chrysotila roscoffensis with different detergents at resolutions ranging from 2.3 to 1.7 Å. These structures represent discrete PSI-FCPIs containing 1, 4, 6, 8 and 9 FCPI subunits, with FCPIs arranged in a modular fashion. Association of each FCPI module to the PSI core, as well as the arrangement of protein subunits and pigments, are revealed. Contributions of individual antenna modules to excitation energy transfer were calculated and compared with PSI-FCPI supercomplexes from other species of coccolithophores and haptophytes. These results pinpoint the assembly of stable PSI-FCPI supercomplexes in C. roscoffensis and provide insights into how antenna modules contribute to energy transfer in coccolithophores.
History
DepositionApr 26, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_64383.png

Downloads & links

-
Map

FileDownload / File: emd_64383.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of a PSI-8 FCPI supercomplex from a haptophyte Chrysotila roscoffensis.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 600 pix.
= 436.2 Å		0.73 Å/pix.
x 600 pix.
= 436.2 Å		0.73 Å/pix.
x 600 pix.
= 436.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.727 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.232289 - 0.48015362
Average (Standard dev.)0.00003486908 (±0.013909403)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 436.2 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_64383_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-B map.

Fileemd_64383_half_map_1.map
AnnotationHalf-B map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-A map.

Fileemd_64383_half_map_2.map
AnnotationHalf-A map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

+
Entire : Photosystem I (PSI) with 8 fucoxanthin chlorophyll a/c binding pr...

EntireName: Photosystem I (PSI) with 8 fucoxanthin chlorophyll a/c binding protein I (FCPI) supercomplex from haptophyte Chrysotila roscoffensis
Components
  • Complex: Photosystem I (PSI) with 8 fucoxanthin chlorophyll a/c binding protein I (FCPI) supercomplex from haptophyte Chrysotila roscoffensis
    • Protein or peptide: Photosystem I reaction center subunit IX (psaJ)
  • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A1 (psaA)
  • Protein or peptide: Photosystem I P700 chlorophyll a apoprotein A2 (psaB)
  • Protein or peptide: Photosystem I iron-sulfur center (psaC)
  • Protein or peptide: Photosystem I reaction center subunit II (psaD)
  • Protein or peptide: Photosystem I reaction center subunit IV (psaE)
  • Protein or peptide: Photosystem I reaction center subunit III (psaF)
  • Protein or peptide: Photosystem I reaction center subunit VIII (psaI)
  • Protein or peptide: Photosystem I reaction center subunit XI (psaL)
  • Protein or peptide: Photosystem I reaction center subunit XII (psaM)
  • Protein or peptide: Fucoxanthin chlorophyll a/c binding protein III (FCPI-3)
  • Protein or peptide: Fucoxanthin chlorophyll a/c binding protein VI (FCPI-6)
  • Protein or peptide: Fucoxanthin chlorophyll a/c binding protein IV (FCPI-4)
  • Protein or peptide: Photosystem I reaction center subunit psaR
  • Protein or peptide: Fucoxanthin chlorophyll a/c binding protein II (FCPI-2)
  • Protein or peptide: Fucoxanthin chlorophyll a/c binding protein I (FCPI-1)
  • Protein or peptide: Fucoxanthin chlorophyll a/c binding protein VII (FCPI-7)
  • Protein or peptide: Fucoxanthin chlorophyll a/c binding protein VIII (FCPI-8)
  • Protein or peptide: Fucoxanthin chlorophyll a/c binding protein V (FCPI-5)
  • Ligand: CHLOROPHYLL A
  • Ligand: PHYLLOQUINONE
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: BETA-CAROTENE
  • Ligand: CHLOROPHYLL A ISOMER
  • Ligand: IRON/SULFUR CLUSTER
  • Ligand: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • 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: water

+
Supramolecule #1: Photosystem I (PSI) with 8 fucoxanthin chlorophyll a/c binding pr...

SupramoleculeName: Photosystem I (PSI) with 8 fucoxanthin chlorophyll a/c binding protein I (FCPI) supercomplex from haptophyte Chrysotila roscoffensis
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #8 / Details: PSI-8 FCPI supercomplex.
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)

+
Macromolecule #1: Photosystem I P700 chlorophyll a apoprotein A1 (psaA)

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A1 (psaA) / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 83.368938 KDa
SequenceString: MKIGSKELEA KKVQVVVDKD PVVTSFEKWA QPGHFSRTLA KGPKTTTWIW NLHADAHDFD SQTSSLEDIS RKIFSAHFGQ LAIIFLWIS GMYFHGARFS NYSAWLANPT TIKPSAQVVW PIVGQEILNG DVGGGFAGVQ ITSGFFQLWR ASGITSEIEL Y WTAIGGLI ...String:
MKIGSKELEA KKVQVVVDKD PVVTSFEKWA QPGHFSRTLA KGPKTTTWIW NLHADAHDFD SQTSSLEDIS RKIFSAHFGQ LAIIFLWIS GMYFHGARFS NYSAWLANPT TIKPSAQVVW PIVGQEILNG DVGGGFAGVQ ITSGFFQLWR ASGITSEIEL Y WTAIGGLI MSALMVFAGW FHYHKAAPKL EWFQNAESMM NHHLAGLLGL GCLGWAGHQI HVSLPINKLL DAGVSPQEIP LP YELIFNQ DLMAQLYPSF KQGLVPFFTL NWSAYSDFLT FKGGLNPITG SLWLSDTAHH HLALSVLFIF AGHMYRTNWG IGH SMKEIL EAHKGPLTGE GHKGLYEILT TSWHAQLAIN LAMMGSVSII VAHHMYAMPP YPYIGIDYPT QLSLFTHHMW IGGF CVCGA GAHASIFMVR DYSPVQSYNN LLDRVLRHRD AIISHLNWVC IFLGTHSFGL YIHNDTMRAL GRPQDMFSDK AIQLQ PIFA QWVQSLHTLA PGNTAPNALA TTSYAFGGDV VAVNGKIAMM PIALGTADFL VHHIHAFTIH VTVLILLKGT LFARNS RLI PDKANLGFRF PCDGPGRGGT CQVSAWDHVF LGLFWMYNCI SVVIFHFSWK MQSDVWGTVS AAGKISHVTG GNFANSA LT INGWLRDFLW SEASQVIQSY GSALSAYGLI FLGAHFIWAF SLMFLFSGRG YWQELIESIV WAHSKLKLAP AIQPRALS I TQGRAVGLAH YLLGGIGTTW SFFLARIISV G

+
Macromolecule #2: Photosystem I P700 chlorophyll a apoprotein A2 (psaB)

MacromoleculeName: Photosystem I P700 chlorophyll a apoprotein A2 (psaB) / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 82.002906 KDa
SequenceString: MATKFPKFSQ ALAQDPATRR IWYGIATAHD LESHDGMSEE NLYQKIFASH FGHLAIIFLW TSGNLFHVAW QGNFQQWVLN PLKVKPIAH AIWDPHFGQS AIKAFTRAGV SYPVNIATSG VYHWWYTIGM RTNNDLYFGA LGLLILSTAL LFAGWLHLQP K FRPGLAWF ...String:
MATKFPKFSQ ALAQDPATRR IWYGIATAHD LESHDGMSEE NLYQKIFASH FGHLAIIFLW TSGNLFHVAW QGNFQQWVLN PLKVKPIAH AIWDPHFGQS AIKAFTRAGV SYPVNIATSG VYHWWYTIGM RTNNDLYFGA LGLLILSTAL LFAGWLHLQP K FRPGLAWF KNNESRLNHH LSGLFGVSSL AWSGHLIHVA IPESRGQHIG WDNFTSTLPH PDGLTPFFTG NWGLYAENPD TV KHIFGTS EGAGTAILTF LGGFHPQTQS MWLTDIAHHH LAIAVLFIFA GHMYRTNWGI GHSMKEILDA HVPPKGRLGA GHR GLFETI TDSLHMQLGL ALASLGVATS LVAQHMYALP PYAFMAKDYV TQAALYTHHQ YIAGFLMVGA FAHGAIFFVR DYDP EVNKD NVLARMLQHK EAIISHLSWV SLFLGFHTLG LYIHNDVCVA FGTPEKQILF EPVFAQFIQA SSGKAVYGFD VLLSS STSA ATVASSKIWL PGWLEAINSG KNSLFLTIGP GDFLVHHAIA LGLHTTTLIL VKGALDARGS KLMPDKKDFG YSFPCD GPG RGGTCDISAW DAFYLAMFWM LNTIGWVTFY WHFKHMTIWG GNAAAFNESS TYLMGWLRDY LWLNSSPLIN GYNAFGM NA QAVWAWMFLF GHLIWATGFM FLISWRGYWQ ELIETLVWAH ERTPIANLVR WKDKPVALSI VQARLVGLAH FTVGYIFT Y APFVIASTTG KFG

+
Macromolecule #3: Photosystem I iron-sulfur center (psaC)

MacromoleculeName: Photosystem I iron-sulfur center (psaC) / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 8.836194 KDa
SequenceString:
MSHNVRIYDT CIGCTQCVRA CPCDVLEMVP WDGCKAGQIA SAPRAEDCIG CKRCETACPT DFLSVRVYLG SETTRSLGLS Y

+
Macromolecule #4: Photosystem I reaction center subunit II (psaD)

MacromoleculeName: Photosystem I reaction center subunit II (psaD) / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 15.936089 KDa
SequenceString:
MSTDILNLQI PSPTFGGSTG GWLRAAETEE KYAITWTSKK EQVFEMPTSG SAIMQKGENL LYLAKKEQCL ALGSQLRTGF KIQDYKIYR IFPNSEIQYL HPKDGVFPEK LNEGRIGVGN VDHSIGKNKQ PVNVKFSGRN TFD

+
Macromolecule #5: Photosystem I reaction center subunit IV (psaE)

MacromoleculeName: Photosystem I reaction center subunit IV (psaE) / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 7.342328 KDa
SequenceString:
MVSRGSVVRV MRPESYWFQE TGTVATIAKG GDRYPVVVRF DKVNYAGVAT NNFAVDELVE VSAPPAK

+
Macromolecule #6: Photosystem I reaction center subunit III (psaF)

MacromoleculeName: Photosystem I reaction center subunit III (psaF) / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 20.163416 KDa
SequenceString:
MKRILSILFL FSVIGNAPLV ASADVSGLVP CKDSSVFNRR LDGSVKKLTT RLKNYEEGTP AYLALEQQIA QTKTRFAMYA DKGLLCGTD GLPHLIADGR FSHAGEFMIP GVGFLYITGW IGWAGRSYLQ FSKKTDKPNE SEIIINVPVA LSMMSAAFIW P LAAWKELV SGQLLVSADE ITVSPR

+
Macromolecule #7: Photosystem I reaction center subunit VIII (psaI)

MacromoleculeName: Photosystem I reaction center subunit VIII (psaI) / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 3.900682 KDa
SequenceString:
MTASFLPSIL TPVVTLIFPG LCFALFFVLI EQEEI

+
Macromolecule #8: Photosystem I reaction center subunit IX (psaJ)

MacromoleculeName: Photosystem I reaction center subunit IX (psaJ) / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 4.340066 KDa
SequenceString:
MDKNLLTYLS TAPVLLTAWM TITAGFSIEF LRFFPDAAA

+
Macromolecule #9: Photosystem I reaction center subunit XI (psaL)

MacromoleculeName: Photosystem I reaction center subunit XI (psaL) / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 15.045253 KDa
SequenceString:
MSEFVKPYNN DPFVGNLSTP VTTSTATKLY LGNLPIYRKG LSSLRRGLEI GMAHGYFLVG PFYLLGPLRN SESALLIGLF AAFGLILIL TLALTIYGLA SFQDNETGDA LESSSGWQKF TSGFFVGASG GAVVAYVLLA NI

+
Macromolecule #10: Photosystem I reaction center subunit XII (psaM)

MacromoleculeName: Photosystem I reaction center subunit XII (psaM) / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 3.082678 KDa
SequenceString:
MITDGQIFLA LTVALTAAIF AIGLGRQLY

+
Macromolecule #11: Fucoxanthin chlorophyll a/c binding protein III (FCPI-3)

MacromoleculeName: Fucoxanthin chlorophyll a/c binding protein III (FCPI-3)
type: protein_or_peptide / ID: 11 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 21.458887 KDa
SequenceString: MTATAFSGPS LPVGRAAAPA ISMMAERSAS IPFLNKPPAL DGSMVGDVGF DPLGFSTTIT ELGGDLNYVR EAELMHGRQA MLATVGFVF PSIFGKIPSD WSASVSTDPL VAQYQLPGTV LGQLIFSIAV AEGIRASIIF KKDSVPGEHG FDPAGFIPKF C NTPEKMAE ...String:
MTATAFSGPS LPVGRAAAPA ISMMAERSAS IPFLNKPPAL DGSMVGDVGF DPLGFSTTIT ELGGDLNYVR EAELMHGRQA MLATVGFVF PSIFGKIPSD WSASVSTDPL VAQYQLPGTV LGQLIFSIAV AEGIRASIIF KKDSVPGEHG FDPAGFIPKF C NTPEKMAE MKLKELKHCR IAMIAITGFF FQETITGHVV PFL

+
Macromolecule #12: Fucoxanthin chlorophyll a/c binding protein VI (FCPI-6)

MacromoleculeName: Fucoxanthin chlorophyll a/c binding protein VI (FCPI-6)
type: protein_or_peptide / ID: 12 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 24.382199 KDa
SequenceString: MLSLVASAPA FVPPTGLVAP AMQPLTQIRM AEGPMYDAPL APSGMGAEFI NAERAPISSY VGASWEAGDV VYDPLDLCEL WKVSANNPD AAFLREAELK HCRLAMLAFA GIIHTSAGFH IPGEIWAVDD WSAALSTVQA KNPAALGQIF AGIGIIEGYT S KGVFDMWF ...String:
MLSLVASAPA FVPPTGLVAP AMQPLTQIRM AEGPMYDAPL APSGMGAEFI NAERAPISSY VGASWEAGDV VYDPLDLCEL WKVSANNPD AAFLREAELK HCRLAMLAFA GIIHTSAGFH IPGEIWAVDD WSAALSTVQA KNPAALGQIF AGIGIIEGYT S KGVFDMWF GKTTVRAPGK LGFDPLGLMP KDKEGAAKME LSELKNGRMA MIAVAGIACN HYIPGSVPGC PFP

+
Macromolecule #13: Fucoxanthin chlorophyll a/c binding protein IV (FCPI-4)

MacromoleculeName: Fucoxanthin chlorophyll a/c binding protein IV (FCPI-4)
type: protein_or_peptide / ID: 13 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 21.06448 KDa
SequenceString: MLSLVSGSLA FTAPLTPAVT QTRAHAPNML KSQALPFVEA PKALDGSMVG DVGFDPLNLS DGLDLKFMRE AELKHGRICM LAWLGYVVV DLGITAPGAP SVSSLAAHDT AVKEGAMYLL LMLVSGFEAI STPAVYEMMS GQSDRKPGDF QLDPFGWAKG D KAEKMMLS ...String:
MLSLVSGSLA FTAPLTPAVT QTRAHAPNML KSQALPFVEA PKALDGSMVG DVGFDPLNLS DGLDLKFMRE AELKHGRICM LAWLGYVVV DLGITAPGAP SVSSLAAHDT AVKEGAMYLL LMLVSGFEAI STPAVYEMMS GQSDRKPGDF QLDPFGWAKG D KAEKMMLS EVIHCRTAML AFSGVVTQSA LKEIGFPYF

+
Macromolecule #14: Photosystem I reaction center subunit psaR

MacromoleculeName: Photosystem I reaction center subunit psaR / type: protein_or_peptide / ID: 14 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 9.637013 KDa
SequenceString:
MELKAQDTWW GDKDYPDSIV LGIGKGVPSI VYSVSSLIAL ALGSYCVAES NLLNILSGST VNGFYVVGAV LVPYSWGLHV AAWIQKQNG K

+
Macromolecule #15: Fucoxanthin chlorophyll a/c binding protein II (FCPI-2)

MacromoleculeName: Fucoxanthin chlorophyll a/c binding protein II (FCPI-2)
type: protein_or_peptide / ID: 15 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 22.708201 KDa
SequenceString: MAVRTLLLCA AIGSAAALTA PVTRAVRPAV RRTTDVQAVV NFDSAASQWN AEFPYLAKFG FGPSAKAERW NGRHAMFGWV VIVATGYAQ SHGLIPSPDV PLSYSSWGGL AQMGFNEYIT NERAVIMIAH THFLAFSLAA AFGPKVLDSL TLANGESDEE P AGFMPAIQ ...String:
MAVRTLLLCA AIGSAAALTA PVTRAVRPAV RRTTDVQAVV NFDSAASQWN AEFPYLAKFG FGPSAKAERW NGRHAMFGWV VIVATGYAQ SHGLIPSPDV PLSYSSWGGL AQMGFNEYIT NERAVIMIAH THFLAFSLAA AFGPKVLDSL TLANGESDEE P AGFMPAIQ PGLTASAELL NGRMAMLGLV LLVLTSAFTG KEILDVVNIG LGGLLLK

+
Macromolecule #16: Fucoxanthin chlorophyll a/c binding protein I (FCPI-1)

MacromoleculeName: Fucoxanthin chlorophyll a/c binding protein I (FCPI-1)
type: protein_or_peptide / ID: 16 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 20.547621 KDa
SequenceString:
MAAYLISLAS PSFVPGAAVH HIAPTITSQQ QIVAKVDGLV GDSAPLGFFD PLGYTKKASP ADLKKYRECE LKHGRVAMLA SMGMVVADF WHPLYGGGNS ANPLVAITQV PKAGLLQILA FIGFMEVMGQ LNMQRADYEP GNFLGSGQWE TSESWDDYQT R ELNNGRLA MFASIGMLAH AALTGKGPLE LIF

+
Macromolecule #17: Fucoxanthin chlorophyll a/c binding protein VII (FCPI-7)

MacromoleculeName: Fucoxanthin chlorophyll a/c binding protein VII (FCPI-7)
type: protein_or_peptide / ID: 17 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 22.153486 KDa
SequenceString: MLSLVSASFA FNAAPAVVPA TRAGVVSMAI SNPSNAVPFL TAPPSQSSGL PGAETGFDPL YLSEYIDVKW AREAELKHGR ICMLACLGI LVQEFISLPG YPGYDANPVA AFSSVDPQAL AQIFVGMSIV ELVSNKGKYS SMDMFEDGTK TPGDFGFDPL N YGKDPSKR ...String:
MLSLVSASFA FNAAPAVVPA TRAGVVSMAI SNPSNAVPFL TAPPSQSSGL PGAETGFDPL YLSEYIDVKW AREAELKHGR ICMLACLGI LVQEFISLPG YPGYDANPVA AFSSVDPQAL AQIFVGMSIV ELVSNKGKYS SMDMFEDGTK TPGDFGFDPL N YGKDPSKR AELEMKELKN GRLAMLGFSG MIHQVLITGK PLLAGLGDIL S

+
Macromolecule #18: Fucoxanthin chlorophyll a/c binding protein VIII (FCPI-8)

MacromoleculeName: Fucoxanthin chlorophyll a/c binding protein VIII (FCPI-8)
type: protein_or_peptide / ID: 18 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 18.375295 KDa
SequenceString:
VEYSQSMPFL VKRKALNGYV GDVGFDPLGF SEILPMDWLR EAELKHCRVC MLATVGFVFT DFLTLPGSIY QVSTLDAHDV SVASGSMSQ LLLWIGIAEI ISVVAIQQML AGSGRAPGEF GFDPMGFAKD ASKKADLEMK ELANGRLAMM AFSGMVTQAV L TGNSFPYL Y

+
Macromolecule #19: Fucoxanthin chlorophyll a/c binding protein V (FCPI-5)

MacromoleculeName: Fucoxanthin chlorophyll a/c binding protein V (FCPI-5)
type: protein_or_peptide / ID: 19 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chrysotila roscoffensis (eukaryote)
Molecular weightTheoretical: 21.37976 KDa
SequenceString: MISMVNAALA FAGQHAVLNG VARATAPVMQ QKSQSVPFLD RPAALDGTMV GDVGFDPLGI SSGIPMAWLR ESELKHGRVC MLATVGYIA VDMGIRAPYA ETLSVTSLTA HDATVATGQM WLLLIACGVL EVAGAAGIAA TLSGSDRKPG YFAFDPLGFG K DPKQMERM ...String:
MISMVNAALA FAGQHAVLNG VARATAPVMQ QKSQSVPFLD RPAALDGTMV GDVGFDPLGI SSGIPMAWLR ESELKHGRVC MLATVGYIA VDMGIRAPYA ETLSVTSLTA HDATVATGQM WLLLIACGVL EVAGAAGIAA TLSGSDRKPG YFAFDPLGFG K DPKQMERM ELSEIKNGRL AMLAFSGIVT QDALFEHAKN FPYL

+
Macromolecule #20: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 20 / Number of copies: 166 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

+
Macromolecule #21: PHYLLOQUINONE

MacromoleculeName: PHYLLOQUINONE / type: ligand / ID: 21 / Number of copies: 2 / Formula: PQN
Molecular weightTheoretical: 450.696 Da
Chemical component information

ChemComp-PQN:
PHYLLOQUINONE

+
Macromolecule #22: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 22 / Number of copies: 4 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

+
Macromolecule #23: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 23 / Number of copies: 18 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

+
Macromolecule #24: CHLOROPHYLL A ISOMER

MacromoleculeName: CHLOROPHYLL A ISOMER / type: ligand / ID: 24 / Number of copies: 1 / Formula: CL0
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CL0:
CHLOROPHYLL A ISOMER

+
Macromolecule #25: IRON/SULFUR CLUSTER

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

ChemComp-FS1:
IRON/SULFUR CLUSTER

+
Macromolecule #26: (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: 26 / Number of copies: 30 / 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 #27: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 27 / Number of copies: 1 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Macromolecule #28: 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: 28 / Number of copies: 2 / 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 #29: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 29 / Number of copies: 6 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

+
Macromolecule #30: Chlorophyll c1

MacromoleculeName: Chlorophyll c1 / type: ligand / ID: 30 / Number of copies: 10 / Formula: KC1
Molecular weightTheoretical: 610.941 Da
Chemical component information

ChemComp-KC1:
Chlorophyll c1

+
Macromolecule #31: (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: 31 / Number of copies: 7 / Formula: A86
Molecular weightTheoretical: 658.906 Da

+
Macromolecule #32: water

MacromoleculeName: water / type: ligand / ID: 32 / Number of copies: 229 / 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
Component:
ConcentrationFormulaName
25.0 mMMES2-(N-morpholino)ethanesulfonic acid
50.0 mMNaClsodium chloride
1.0 mMEDTA[6-[3,4-dihydroxy-2,5-bis(hydroxymethyl)oxolan-2-yl]oxy-3,4,5-trihydroxyoxan-2-yl]methyl dodecanoate
0.05 %SMLsucrose monolaurate
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Pressure: 0.007 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (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 / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 165000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

9uh3


Details: PSI-9 FCPI supercomplex from haptophyte Chrysotila roscoffensis.
Final reconstructionNumber classes used: 12 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.33 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 17450
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more