[English] 日本語
Yorodumi
- EMDB-31906: Structure of S1M1-type FCPII complex from diatom -

+
Open data


ID or keywords:

Loading...

-
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 / plastid / chlorophyll binding / 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

-
Structure visualization

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

emd_31906.png

Downloads & links

-
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

-
Supplemental data

-
Sample components

+
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

+
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

+
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

+
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

+
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

+
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

+
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

+
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

+
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

+
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

+
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

+
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

+
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

+
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

+
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

+
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

+
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

+
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

+
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

-
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
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

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)

-
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

+
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