[English] 日本語
Yorodumi
- EMDB-9775: Structure of C2S2-type PSII-FCPII supercomplex from diatom -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-9775
TitleStructure of C2S2-type PSII-FCPII supercomplex from diatom
Map data
Sample
  • Complex: C2S2-type PSII-FCPII supercomplex
    • Protein or peptide: x 25 types
  • Ligand: x 14 types
KeywordsPhotosystem / ELECTRON TRANSPORT
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: 3.3 Å
AuthorsNagao R / Kato K
CitationJournal: Nat Plants / Year: 2019
Title: Structural basis for energy harvesting and dissipation in a diatom PSII-FCPII supercomplex.
Authors: Ryo Nagao / Koji Kato / Takehiro Suzuki / Kentaro Ifuku / Ikuo Uchiyama / Yasuhiro Kashino / Naoshi Dohmae / Seiji Akimoto / Jian-Ren Shen / Naoyuki Miyazaki / Fusamichi Akita /
Abstract: Light-harvesting antenna systems in photosynthetic organisms harvest solar energy and transfer it to the photosynthetic reaction centres to initiate charge-separation and electron-transfer reactions. ...Light-harvesting antenna systems in photosynthetic organisms harvest solar energy and transfer it to the photosynthetic reaction centres to initiate charge-separation and electron-transfer reactions. Diatoms are one of the important groups of oxyphototrophs and possess fucoxanthin chlorophyll a/c-binding proteins (FCPs) as light harvesters. The organization and association pattern of FCP with the photosystem II (PSII) core are unknown. Here we solved the structure of PSII-FCPII supercomplexes isolated from a diatom, Chaetoceros gracilis, by single-particle cryoelectron microscopy. The PSII-FCPII forms a homodimer. In each monomer, two FCP homotetramers and three FCP monomers are associated with one PSII core. The structure reveals a highly complicated protein-pigment network that is different from the green-type light-harvesting apparatus. Comparing these two systems allows the identification of energy transfer and quenching pathways. These findings provide structural insights into not only excitation-energy transfer mechanisms in the diatom PSII-FCPII, but also changes of light harvesters between the red- and green-lineage oxyphototrophs during evolution.
History
DepositionJan 7, 2019-
Header (metadata) releaseJun 5, 2019-
Map releaseAug 7, 2019-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6j3y
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6j3y
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9775.png

Downloads & links

-
Map

FileDownload / File: emd_9775.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 512 pix.
= 573.44 Å		1.12 Å/pix.
x 512 pix.
= 573.44 Å		1.12 Å/pix.
x 512 pix.
= 573.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.15498917 - 0.37961861
Average (Standard dev.)0.00055303366 (±0.0068695513)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 573.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.121.121.12
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z573.440573.440573.440
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ344344344
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.1550.3800.001

-
Supplemental data

-
Sample components

+
Entire : C2S2-type PSII-FCPII supercomplex

EntireName: C2S2-type PSII-FCPII supercomplex
Components
  • Complex: C2S2-type PSII-FCPII supercomplex
    • Protein or peptide: Photosystem II reaction center protein D1
    • Protein or peptide: Photosystem II chlorophyll protein CP47
    • Protein or peptide: Photosystem II chlorophyll protein CP43
    • Protein or peptide: Photosystem II reaction center protein D2
    • Protein or peptide: Cytochrome b559 subunit alpha
    • Protein or peptide: Cytochrome b559 subunit beta
    • Protein or peptide: Photosystem II reaction center protein H
    • Protein or peptide: Photosystem II reaction center protein I
    • Protein or peptide: Photosystem II reaction center protein J
    • Protein or peptide: Photosystem II reaction center protein K
    • Protein or peptide: Photosystem II reaction center protein L
    • Protein or peptide: Photosystem II reaction center protein M
    • Protein or peptide: Extrinsic protein in photosystem II
    • Protein or peptide: Photosystem II reaction center protein T
    • Protein or peptide: Extrinsic protein in photosystem II
    • Protein or peptide: Cytochrome c-550
    • Protein or peptide: Photosystem II reaction center protein Ycf12
    • Protein or peptide: Photosystem II reaction center X protein
    • Protein or peptide: Photosystem II reaction center protein Z
    • Protein or peptide: Extrinsic protein in photosystem II
    • Protein or peptide: Photosystem II reaction center protein W
    • Protein or peptide: Unknown protein 0
    • Protein or peptide: Unknown protein 1
    • Protein or peptide: Unknown protein 2
    • Protein or peptide: Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1
  • 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: BICARBONATE ION
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: CA-MN4-O5 CLUSTER
  • Ligand: DIGALACTOSYL DIACYL GLYCEROL (DGDG)
  • 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: 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: DODECYL-ALPHA-D-MALTOSIDE

+
Supramolecule #1: C2S2-type PSII-FCPII supercomplex

SupramoleculeName: C2S2-type PSII-FCPII supercomplex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#25
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 850 KDa

+
Macromolecule #1: Photosystem II reaction center protein D1

MacromoleculeName: Photosystem II reaction center protein D1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 38.1835 KDa
SequenceString: MTATLERREG VSLWERFCAW ITSTENRLYI GWFGCLMFPT LLTATSCFII AFIAAPPVDI DGIREPVAGS LLYGNNIISG AVVPSSNAI GMHFYPIWEA ASIDEWLYNG GPYQLIVLHF LLGVSAYMGR EWELSYRLGM RPWIFVAFSA PVAAASAVFL V YPIGQGSF ...String:
MTATLERREG VSLWERFCAW ITSTENRLYI GWFGCLMFPT LLTATSCFII AFIAAPPVDI DGIREPVAGS LLYGNNIISG AVVPSSNAI GMHFYPIWEA ASIDEWLYNG GPYQLIVLHF LLGVSAYMGR EWELSYRLGM RPWIFVAFSA PVAAASAVFL V YPIGQGSF SDGMPLGISG TFNFMLVFQA EHNILMHPFH MAGVAGVFGG SLFSAMHGSL VTSSLIRETT ENESTNYGYK FG QEEETYN IVAAHGYFGR LIFQYASFNN SRALHFFLAL WPVVGIWITS MGISTMAFNL NGFNFNQSVV DSQGRVINTW ADI LNRANL GIEVMHERNA HNFPLDLA

+
Macromolecule #2: Photosystem II chlorophyll protein CP47

MacromoleculeName: Photosystem II chlorophyll protein CP47 / 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

+
Macromolecule #3: Photosystem II chlorophyll protein CP43

MacromoleculeName: Photosystem II chlorophyll protein CP43 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 51.947262 KDa
SequenceString: MKTLYSLRRY YHVETPFNSS IAGRDIESTG FAWWSGNARL INVSGKLLGA HVAHAGLMVF WAGAMVLFEV SHFVPEKPTY EQGFILIQH LATLGYGIGP GGEITSTVPY FAVGVIHLIS SAILGFGGIY HSLLGPDTLE ESFPFFGYDW RDKNKMTTIL G IHLCLLGL ...String:
MKTLYSLRRY YHVETPFNSS IAGRDIESTG FAWWSGNARL INVSGKLLGA HVAHAGLMVF WAGAMVLFEV SHFVPEKPTY EQGFILIQH LATLGYGIGP GGEITSTVPY FAVGVIHLIS SAILGFGGIY HSLLGPDTLE ESFPFFGYDW RDKNKMTTIL G IHLCLLGL GSFLLVIKAM YLGGVYDTWA PGGGDVRYIT TPTLNPIVIF GYVFRSPFGG DGWVVSVNNM EDVIGGHIWV GI LCITGGI WHIFTKPFAW ARRAFVWSGE AYLSYSLAAI SLMGFTAALY SWYNNTAYPS ELYGPTGPEA SQAQAFTFLV RDQ RLGANV SSAQGPTGLG KYLMRSPSGE IIFGGETMRF WDLRAPWVEP LRGPNGLDIN KIKNDIQPWQ ERRAAEYMTH APLG SLNSV GGVATEINSV NYVSPRSWLC CSHFFLAFFF LVGHWWHSGR ARAAAAGFEK GINRANEPVL SMRPID

+
Macromolecule #4: Photosystem II reaction center protein D2

MacromoleculeName: Photosystem II reaction center protein D2 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 39.06952 KDa
SequenceString: MTIAIGQNQE RGLFDLVDDW LKKDRFVFVG WSGLLLFPTA YLAAGGWMTG TTFVTSWYTH GLASSYLEGC NFLTAAVSTP ANSVGHSLL LLWGPEAQGD FTRWCQIGGL WTFVALHGAF GLIGFCLRQF EIARLVGIRP YNAIAFSGPI AVFVSVFLLY P LGQASWFF ...String:
MTIAIGQNQE RGLFDLVDDW LKKDRFVFVG WSGLLLFPTA YLAAGGWMTG TTFVTSWYTH GLASSYLEGC NFLTAAVSTP ANSVGHSLL LLWGPEAQGD FTRWCQIGGL WTFVALHGAF GLIGFCLRQF EIARLVGIRP YNAIAFSGPI AVFVSVFLLY P LGQASWFF APSFGVAAIF RFLLFLQGFH NWTLNPFHMM GVAGILGGAL LCAIHGATVE NTLFEDGDAA NTFRAFTPTQ SE ETYSMVT ANRFWSQIFG VAFSNKRWLH FFMLFVPVTG LWTSSIGIVG LALNLRAYDF VSQELRAAED PEFETFYTKN HLL DEGIRA WMAAQDQPHE NFVFPEEVLP RGNAL

+
Macromolecule #5: Cytochrome b559 subunit alpha

MacromoleculeName: Cytochrome b559 subunit alpha / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 9.507667 KDa
SequenceString:
MSGGSTGERP FSDIITSVRY WIIHSITIPS LFVSGWLFIS TGLAYDVFGT PRPNEYFTQD RQQVPLVNDR FSAKQELEDL TKGL

+
Macromolecule #6: Cytochrome b559 subunit beta

MacromoleculeName: Cytochrome b559 subunit beta / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 4.912796 KDa
SequenceString:
MTNNINQPVA YPIFTFRWLA IHGLAIPTVF FLGGITAMQF IQR

+
Macromolecule #7: Photosystem II reaction center protein H

MacromoleculeName: Photosystem II reaction center protein H / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 7.418827 KDa
SequenceString:
MALRTRLGEI LRPLNAEYGK VAPGWGTTPI MGIVMLAFLI FLVIILQIYN SSLIIENVDV DWANGIV

UniProtKB: Photosystem II reaction center protein H

+
Macromolecule #8: Photosystem II reaction center protein I

MacromoleculeName: Photosystem II reaction center protein I / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 4.427212 KDa
SequenceString:
MLTLKILVYT TVIFFVSLFI FGFLSSDPSR NPNRKDLE

+
Macromolecule #9: Photosystem II reaction center protein J

MacromoleculeName: Photosystem II reaction center protein J / type: protein_or_peptide / ID: 9 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 4.093833 KDa
SequenceString:
MTNTGRIPLW LVGLVGGLAV ITMLSLFFYG SYSGLGSSL

+
Macromolecule #10: Photosystem II reaction center protein K

MacromoleculeName: Photosystem II reaction center protein K / type: protein_or_peptide / ID: 10 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 4.978028 KDa
SequenceString:
MESLLLARLP EAYVVFSPIV DVLPIIPVFF LLLAFVWQAA IGFR

+
Macromolecule #11: Photosystem II reaction center protein L

MacromoleculeName: Photosystem II reaction center protein L / type: protein_or_peptide / ID: 11 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 4.367076 KDa
SequenceString:
MTGPNPNKQA VELNRTSLYW GLLLIFVLAV LFSSYFFN

+
Macromolecule #12: Photosystem II reaction center protein M

MacromoleculeName: Photosystem II reaction center protein M / type: protein_or_peptide / ID: 12 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 14.180403 KDa
SequenceString:
LHLTVVSEVG KVAVGSIPAA AIASPAFAMD SVVESLPTNM LAGEVQFGAY LAVLLGTFLP ALFLVNLFIQ TEARKAGKAG GQDSDLDGY LCIRVWIAIE AGRLSSHLWC PLVLPHFWRN NRTVSHLYGR YQ

+
Macromolecule #13: Extrinsic protein in photosystem II

MacromoleculeName: Extrinsic protein in photosystem II / type: protein_or_peptide / ID: 13 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 26.762297 KDa
SequenceString: LTKSQINELS YLQVKGTGLA NRCAEVVGED SIKPKPGAKL VDMCIEPKAW AVEEEVGKAG KTEKKFVNSK VMTRQTYTLD AIEGPITVD GGKITFNEKE GIDYAATTVQ LPGGERVPFL FTVKDLVAKG NGDTFKPGFQ MGGDFNTPSY RTGLFLDPKG R GGTTGYDM ...String:
LTKSQINELS YLQVKGTGLA NRCAEVVGED SIKPKPGAKL VDMCIEPKAW AVEEEVGKAG KTEKKFVNSK VMTRQTYTLD AIEGPITVD GGKITFNEKE GIDYAATTVQ LPGGERVPFL FTVKDLVAKG NGDTFKPGFQ MGGDFNTPSY RTGLFLDPKG R GGTTGYDM AVALPALQLG EEGDAELFGE NNKVFDITQG RIEMEVNKVN AEDSEIGGVF VATQLSDTDM GSKTPKKVLT KG IFYAKVD Q

UniProtKB: Extrinsic protein in photosystem II

+
Macromolecule #14: Photosystem II reaction center protein T

MacromoleculeName: Photosystem II reaction center protein T / type: protein_or_peptide / ID: 14 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 3.711547 KDa
SequenceString:
MEALVYTFLL IGTLMVIFFA VFFRETPRIL R

+
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: 10.137501 KDa
SequenceString:
VIDYENIGYL GGSSIVDINN ANVRAYLKMP GMYPTVAGKI VSHGPYSGVA DLYKIPGLSS AEADVIKKYE SRLTAKTPSP DYVIDRINN GLYR

UniProtKB: Photosystem II 12 kDa extrinsic protein

+
Macromolecule #16: Cytochrome c-550

MacromoleculeName: Cytochrome c-550 / type: protein_or_peptide / ID: 16 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 14.893812 KDa
SequenceString:
IDLDEATRTV VVDNAGNTTV LTPEQVKRGK RLFNATCGAC HVGGITKTNP NVGLDPEALS LATPRRDNIS ALVDYIKNPT TYDGLESIA EVHPSIKSAD IYPRMRSLTD EDLYSIAGHI MLSPKIASEK WGGGKIYY

UniProtKB: Photosystem II extrinsic protein V

+
Macromolecule #17: Photosystem II reaction center protein Ycf12

MacromoleculeName: Photosystem II reaction center protein Ycf12 / type: protein_or_peptide / ID: 17 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 3.6095 KDa
SequenceString:
MINWQVIGQL MSTAVIMLAG PAVIVLLALK KGNL

+
Macromolecule #18: Photosystem II reaction center X protein

MacromoleculeName: Photosystem II reaction center X protein / type: protein_or_peptide / ID: 18 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 3.859647 KDa
SequenceString:
MTASLSNFIA SLIAGGVVVG VIAIALIVIS KSDRILRS

UniProtKB: Photosystem II reaction center protein X

+
Macromolecule #19: Photosystem II reaction center protein Z

MacromoleculeName: Photosystem II reaction center protein Z / type: protein_or_peptide / ID: 19 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 6.528887 KDa
SequenceString:
MITLLVALLV LISLGLVVTV PVALATPGEW EIAKGKFNRF FQIWVFLVIV IAAADGISSS I

+
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: 17.088086 KDa
SequenceString:
AVGESPRFSV FGLVGDGTSY SEGAAYGTDQ ADKLYSPYSV YSPEGEKSLY KPDNAEYLAR KKAVLAETKN RLQKIPAYVD KKEWFNVKD ELTRYMYETR GAVRSLSSSV TQKEKAEVFF RALEDTYGAA TLKKGDAVKA SNDKAIAALD AFTATL

UniProtKB: Extrinsic protein in photosystem II

+
Macromolecule #21: Photosystem II reaction center protein W

MacromoleculeName: Photosystem II reaction center protein W / type: protein_or_peptide / ID: 21 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 7.848743 KDa
SequenceString:
MAALAGFMPA ILSSTAAVAT EGTNEWFGVD DLRLLAVLFL GHWAILSLWL GSYGDSNEDE DFFGEIDYSA RK

+
Macromolecule #22: Unknown protein 0

MacromoleculeName: Unknown protein 0 / type: protein_or_peptide / ID: 22 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 2.656265 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)

+
Macromolecule #23: Unknown protein 1

MacromoleculeName: Unknown protein 1 / type: protein_or_peptide / ID: 23 / 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)

+
Macromolecule #24: Unknown protein 2

MacromoleculeName: Unknown protein 2 / type: protein_or_peptide / ID: 24 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 869.063 Da
SequenceString:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

+
Macromolecule #25: Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1

MacromoleculeName: Fucoxanthin chlorophyll a/c-binding protein Lhcf1, FCP1
type: protein_or_peptide / ID: 25 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 22.098182 KDa
SequenceString: MKLAVAALLV ASAAAFAPAP ASKASTSLKV SEIELGVTEP LGVYDPLGWL ESEPEAFERR RAVERKHGRV AMAAVVGTIV HNNHIVFDG YLSPSNNLKF SDIPTGVDGI RAIPTAGLAQ ILAFFALVEL AWMPASKYDG DYGVGYFGTD IKDPEEKARK L NVELNNGR ...String:
MKLAVAALLV ASAAAFAPAP ASKASTSLKV SEIELGVTEP LGVYDPLGWL ESEPEAFERR RAVERKHGRV AMAAVVGTIV HNNHIVFDG YLSPSNNLKF SDIPTGVDGI RAIPTAGLAQ ILAFFALVEL AWMPASKYDG DYGVGYFGTD IKDPEEKARK L NVELNNGR AAMMGIMGNM VAEVLTGQTM YEQYASGHIS PFGDGQGVF

+
Macromolecule #26: FE (II) ION

MacromoleculeName: FE (II) ION / type: ligand / ID: 26 / Number of copies: 2 / Formula: FE2
Molecular weightTheoretical: 55.845 Da

+
Macromolecule #27: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 27 / Number of copies: 158 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

+
Macromolecule #28: PHEOPHYTIN A

MacromoleculeName: PHEOPHYTIN A / type: ligand / ID: 28 / Number of copies: 4 / Formula: PHO
Molecular weightTheoretical: 871.2 Da
Chemical component information

ChemComp-PHO:
PHEOPHYTIN A

+
Macromolecule #29: BETA-CAROTENE

MacromoleculeName: BETA-CAROTENE / type: ligand / ID: 29 / Number of copies: 24 / Formula: BCR
Molecular weightTheoretical: 536.873 Da
Chemical component information

ChemComp-BCR:
BETA-CAROTENE

+
Macromolecule #30: 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: 30 / Number of copies: 6 / Formula: SQD
Molecular weightTheoretical: 795.116 Da
Chemical component information

ChemComp-SQD:
1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL

+
Macromolecule #31: BICARBONATE ION

MacromoleculeName: BICARBONATE ION / type: ligand / ID: 31 / Number of copies: 2 / Formula: BCT
Molecular weightTheoretical: 61.017 Da
Chemical component information

ChemComp-BCT:
BICARBONATE ION

+
Macromolecule #32: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 32 / Number of copies: 8 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

+
Macromolecule #33: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 33 / Number of copies: 14 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

+
Macromolecule #34: CA-MN4-O5 CLUSTER

MacromoleculeName: CA-MN4-O5 CLUSTER / type: ligand / ID: 34 / Number of copies: 2 / Formula: OEX
Molecular weightTheoretical: 339.827 Da
Chemical component information

ChemComp-OEX:
CA-MN4-O5 CLUSTER

+
Macromolecule #35: DIGALACTOSYL DIACYL GLYCEROL (DGDG)

MacromoleculeName: DIGALACTOSYL DIACYL GLYCEROL (DGDG) / type: ligand / ID: 35 / Number of copies: 8 / Formula: DGD
Molecular weightTheoretical: 949.299 Da
Chemical component information

ChemComp-DGD:
DIGALACTOSYL DIACYL GLYCEROL (DGDG)

+
Macromolecule #36: 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: 36 / 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 #37: PROTOPORPHYRIN IX CONTAINING FE

MacromoleculeName: PROTOPORPHYRIN IX CONTAINING FE / type: ligand / ID: 37 / Number of copies: 4 / Formula: HEM
Molecular weightTheoretical: 616.487 Da
Chemical component information

ChemComp-HEM:
PROTOPORPHYRIN IX CONTAINING FE

+
Macromolecule #38: (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: 38 / Number of copies: 48 / Formula: A86
Molecular weightTheoretical: 658.906 Da

+
Macromolecule #39: DODECYL-ALPHA-D-MALTOSIDE

MacromoleculeName: DODECYL-ALPHA-D-MALTOSIDE / type: ligand / ID: 39 / Number of copies: 2 / Formula: LMU
Molecular weightTheoretical: 510.615 Da
Chemical component information

ChemComp-LMU:
DODECYL-ALPHA-D-MALTOSIDE / detergent*YM

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.256 mg/mL
BufferpH: 6.5 / Component:
ConcentrationFormula
20.0 mMMES-NaOH
0.02 %DDM
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 20.0 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 correctionSoftware - Name: CTFFIND (ver. 4.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3jcu

Final reconstructionNumber classes used: 3 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 214939
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

3wu2

source_name: PDB, initial_model_type: experimental model

3jcu

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient
Output model

PDB-6j3y:
Structure of C2S2-type PSII-FCPII supercomplex from diatom

+
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