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- EMDB-31906: Structure of S1M1-type FCPII complex from diatom -

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Basic information

Entry
Database: EMDB / ID: EMD-31906
TitleStructure of S1M1-type FCPII complex from diatom
Map data
Sample
  • Complex: S1M1-type FCPII complex
    • Protein or peptide: x 7 types
  • Ligand: x 10 types
KeywordsPhotosystem / PSII / ELECTRON TRANSPORT
Function / homologylight-harvesting complex / photosynthesis, light harvesting / Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein / photosystem II / chlorophyll binding / chloroplast thylakoid membrane / Chlorophyll a/b-binding protein
Function and homology information
Biological speciesChaetoceros gracilis (Diatom)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsNagao R / Kato K
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for different types of hetero-tetrameric light-harvesting complexes in a diatom PSII-FCPII supercomplex
Authors: Nagao R / Kato K / Kumazawa M / Ifuku K / Yokono M / Suzuki T / Dohmae N / Akita F / Akimoto S / Miyazaki N / Shen JR
History
DepositionSep 6, 2021-
Header (metadata) releaseMar 2, 2022-
Map releaseMar 2, 2022-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7vd6
  • Surface level: 0.055
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31906.png

Downloads & links

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Map

FileDownload / File: emd_31906.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.)
1.11 Å/pix.
x 512 pix.
= 569.856 Å		1.11 Å/pix.
x 512 pix.
= 569.856 Å		1.11 Å/pix.
x 512 pix.
= 569.856 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.113 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.055 / Movie #1: 0.055
Minimum - Maximum-0.10695298 - 0.2962924
Average (Standard dev.)0.00012687691 (±0.0032981518)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 569.856 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1131.1131.113
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z569.856569.856569.856
α/β/γ90.00090.00090.000
start NX/NY/NZ535455
NX/NY/NZ134138134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.1070.2960.000

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Supplemental data

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Sample components

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Entire : S1M1-type FCPII complex

EntireName: S1M1-type FCPII complex
Components
  • Complex: S1M1-type FCPII complex
    • Protein or peptide: Chlorophyll a/b-binding protein
    • Protein or peptide: Fcpb2, Fucoxanthin chlorophyll a/c-binding protein
    • Protein or peptide: Fcpb3, Fucoxanthin chlorophyll a/c-binding protein
    • Protein or peptide: Fcpb4, Fucoxanthin chlorophyll a/c-binding protein
    • Protein or peptide: Fcpb5, Fucoxanthin chlorophyll a/c-binding protein
    • Protein or peptide: Fcpb6, Fucoxanthin chlorophyll a/c-binding protein
    • Protein or peptide: Fcpb7, Fucoxanthin chlorophyll a/c-binding protein
  • Ligand: CHLOROPHYLL A
  • 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: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
  • Ligand: UNKNOWN LIGAND
  • Ligand: (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol
  • Ligand: 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL
  • Ligand: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
  • Ligand: DODECYL-ALPHA-D-MALTOSIDE
  • Ligand: water

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Supramolecule #1: S1M1-type FCPII complex

SupramoleculeName: S1M1-type FCPII complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 240 KDa

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Macromolecule #1: Chlorophyll a/b-binding protein

MacromoleculeName: Chlorophyll a/b-binding protein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / 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

UniProtKB: Chlorophyll a/b-binding protein

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Macromolecule #2: Fcpb2, Fucoxanthin chlorophyll a/c-binding protein

MacromoleculeName: Fcpb2, Fucoxanthin chlorophyll a/c-binding protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 22.162188 KDa
SequenceString: MKLAIAALLC ASAAAFAPAP ASKVSTALNV NELEIGATAP LGVYDPLGWL DGEPENFERR RAVERKHGRV AMAAVVGTIV HNNHITFDG YLSPSANLKF SDIPTGVDGI RAIPTAGLLQ ILFFFALVEL AWMPASKYDG DYGVGWFGSN IEDPEEKARK L NVELNNGR ...String:
MKLAIAALLC ASAAAFAPAP ASKVSTALNV NELEIGATAP LGVYDPLGWL DGEPENFERR RAVERKHGRV AMAAVVGTIV HNNHITFDG YLSPSANLKF SDIPTGVDGI RAIPTAGLLQ ILFFFALVEL AWMPASKYDG DYGVGWFGSN IEDPEEKARK L NVELNNGR AAMMGIMGNM VTECITGQTM YEQYAAGHFS PFGDGQGAF

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Macromolecule #3: Fcpb3, Fucoxanthin chlorophyll a/c-binding protein

MacromoleculeName: Fcpb3, Fucoxanthin chlorophyll a/c-binding protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 22.627543 KDa
SequenceString: MKTAILAAML GSAAAFVPAQ QSKVSTSLAA SELEDGIGAV APLGYFDPLG YIKDEETFIR YRAVERKHGR VAMMAMLGTF VHNNGWTFD GYLSPSQGLK FSDIDSGIGG LFQVPPAGLA QIILLCGFVE LAWWPASNLS GDYGVRLGTL NDWEEQPAKY Y RQKNAELN ...String:
MKTAILAAML GSAAAFVPAQ QSKVSTSLAA SELEDGIGAV APLGYFDPLG YIKDEETFIR YRAVERKHGR VAMMAMLGTF VHNNGWTFD GYLSPSQGLK FSDIDSGIGG LFQVPPAGLA QIILLCGFVE LAWWPASNLS GDYGVRLGTL NDWEEQPAKY Y RQKNAELN NGRAAMMGIL GTFTHEVITG QNFAEQAAAG HFSPFGDGQG FF

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Macromolecule #4: Fcpb4, Fucoxanthin chlorophyll a/c-binding protein

MacromoleculeName: Fcpb4, Fucoxanthin chlorophyll a/c-binding protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 22.298115 KDa
SequenceString: MKLAIAALLA TSAAAFTTSP ASRATTSLQV SEIELGATEP LGVFDPLGWL ETEPEAFERR RAVERKHGRV AMAAVVGTIV HNNHIVFDG YISPSNNLKF SDIPTGIDGI FSVPTAGLAQ IIAFLGFVEL AWLPASQYDG DYGVGYFGND ILDPEEKARK L NAELNNGR ...String:
MKLAIAALLA TSAAAFTTSP ASRATTSLQV SEIELGATEP LGVFDPLGWL ETEPEAFERR RAVERKHGRV AMAAVVGTIV HNNHIVFDG YISPSNNLKF SDIPTGIDGI FSVPTAGLAQ IIAFLGFVEL AWLPASQYDG DYGVGYFGND ILDPEEKARK L NAELNNGR AAMMGIMGNM VAEKITGQTM YEQYAAGHFN PFNDGEGFF

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Macromolecule #5: Fcpb5, Fucoxanthin chlorophyll a/c-binding protein

MacromoleculeName: Fcpb5, Fucoxanthin chlorophyll a/c-binding protein / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 29.014037 KDa
SequenceString: MKLALAALLA TSAAAFQAPT MTFSLGKKAA AKKAVKAPAP SGASPSADAW ANSIESKALP FARAPATLDG TMLGDFGFDP LGFSTVPVG PWFTGIEGRN GQIGNLNWYR EAELIHGRIA QVAVVGFIAP GLFGTLPGNE WTGVDAYSNL NPLEAFSQVP G LAILQIFL ...String:
MKLALAALLA TSAAAFQAPT MTFSLGKKAA AKKAVKAPAP SGASPSADAW ANSIESKALP FARAPATLDG TMLGDFGFDP LGFSTVPVG PWFTGIEGRN GQIGNLNWYR EAELIHGRIA QVAVVGFIAP GLFGTLPGNE WTGVDAYSNL NPLEAFSQVP G LAILQIFL FMSYLEVRRI NIIKEEGENY MPGDLRIGQG EGRWNPFGLD YSPEAYEEKR LQELKHCRLA MIGVFGLWAQ AQ ASGVGVT EQIGAALTTP DYYAKAGYFL PEGI

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Macromolecule #6: Fcpb6, Fucoxanthin chlorophyll a/c-binding protein

MacromoleculeName: Fcpb6, Fucoxanthin chlorophyll a/c-binding protein / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 23.934375 KDa
SequenceString: MKSIAALLAL ASAAAAFTPQ SQSTSSTALK ERISPLDPSI GVTEPLGLYD PLGWLDPEKD PASKFATFHA NFERRRAVER KHGRIAMVA VVGMLFHNAD IEFPGYLSKE LGIRFSDVPN GMNGLFSIPL AGLTQIVFAI GVMELAIWPA SNYSGDYGTG Y GRPFVPNV ...String:
MKSIAALLAL ASAAAAFTPQ SQSTSSTALK ERISPLDPSI GVTEPLGLYD PLGWLDPEKD PASKFATFHA NFERRRAVER KHGRIAMVA VVGMLFHNAD IEFPGYLSKE LGIRFSDVPN GMNGLFSIPL AGLTQIVFAI GVMELAIWPA SNYSGDYGTG Y GRPFVPNV LEGDELKYKL DMEINQGRAA MMGIMGALVG EAVTGQTLAE QIASNNLGLF SALFE

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Macromolecule #7: Fcpb7, Fucoxanthin chlorophyll a/c-binding protein

MacromoleculeName: Fcpb7, Fucoxanthin chlorophyll a/c-binding protein / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Molecular weightTheoretical: 21.143453 KDa
SequenceString: MKLALLASLV ASAAAFAPSK VAQTSTALKA FENELGAQPP LGFFDPLGLV EDGNQAKFDR LRYVELKHGR ISMLAVVGYL IEKAGIRLP GNISYDGTSF ADIPDGFAAL SKIPDAGLFQ LFAFIGFLEV FVMKDITGGE FVGDFRNGFI DFGWDSFDEE T KLKKRAIE ...String:
MKLALLASLV ASAAAFAPSK VAQTSTALKA FENELGAQPP LGFFDPLGLV EDGNQAKFDR LRYVELKHGR ISMLAVVGYL IEKAGIRLP GNISYDGTSF ADIPDGFAAL SKIPDAGLFQ LFAFIGFLEV FVMKDITGGE FVGDFRNGFI DFGWDSFDEE T KLKKRAIE LNQGRAAMMG ILALMVHEKL GVSLLPQ

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Macromolecule #8: CHLOROPHYLL A

MacromoleculeName: CHLOROPHYLL A / type: ligand / ID: 8 / Number of copies: 71 / Formula: CLA
Molecular weightTheoretical: 893.489 Da
Chemical component information

ChemComp-CLA:
CHLOROPHYLL A

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Macromolecule #9: Chlorophyll c1

MacromoleculeName: Chlorophyll c1 / type: ligand / ID: 9 / Number of copies: 35 / Formula: KC1
Molecular weightTheoretical: 610.941 Da
Chemical component information

ChemComp-KC1:
Chlorophyll c1

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Macromolecule #10: (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: 10 / Number of copies: 54 / Formula: A86
Molecular weightTheoretical: 658.906 Da

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Macromolecule #11: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE

MacromoleculeName: 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / type: ligand / ID: 11 / Number of copies: 4 / Formula: LMG
Molecular weightTheoretical: 787.158 Da
Chemical component information

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

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Macromolecule #12: UNKNOWN LIGAND

MacromoleculeName: UNKNOWN LIGAND / type: ligand / ID: 12 / Number of copies: 19 / Formula: UNL
Chemical component information


ChemComp, No image

ChemComp-UNL:
Unknown ligand

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Macromolecule #13: (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: 13 / Number of copies: 6 / 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

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Macromolecule #14: 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: 14 / 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

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Macromolecule #15: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE

MacromoleculeName: 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / type: ligand / ID: 15 / Number of copies: 4 / Formula: LHG
Molecular weightTheoretical: 722.97 Da
Chemical component information

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

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Macromolecule #16: DODECYL-ALPHA-D-MALTOSIDE

MacromoleculeName: DODECYL-ALPHA-D-MALTOSIDE / type: ligand / ID: 16 / Number of copies: 1 / Formula: LMU
Molecular weightTheoretical: 510.615 Da
Chemical component information

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

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Macromolecule #17: water

MacromoleculeName: water / type: ligand / ID: 17 / Number of copies: 13 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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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

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Image processing

Particle selectionNumber selected: 8093924
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 373897
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationSoftware - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6j40


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Correlation coefficient
Output model

PDB-7vd6:
Structure of S1M1-type FCPII complex from diatom

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