[English] 日本語
Yorodumi
- PDB-7vd6: Structure of S1M1-type FCPII complex from diatom -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7vd6
TitleStructure of S1M1-type FCPII complex from diatom
Components
  • Chlorophyll a/b-binding protein
  • Fcpb2, Fucoxanthin chlorophyll a/c-binding protein
  • Fcpb3, Fucoxanthin chlorophyll a/c-binding protein
  • Fcpb4, Fucoxanthin chlorophyll a/c-binding protein
  • Fcpb5, Fucoxanthin chlorophyll a/c-binding protein
  • Fcpb6, Fucoxanthin chlorophyll a/c-binding protein
  • Fcpb7, Fucoxanthin chlorophyll a/c-binding protein
KeywordsELECTRON TRANSPORT / Photosystem / PSII
Function / homology
Function and homology information


light-harvesting complex / photosynthesis, light harvesting / chlorophyll binding / chloroplast / membrane
Similarity search - Function
Chlorophyll A-B binding protein, plant and chromista / Chlorophyll A-B binding protein / Chlorophyll A-B binding protein
Similarity search - Domain/homology
Chem-A86 / CHLOROPHYLL A / Chem-DD6 / Chlorophyll c1 / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE / Chem-SQD / Unknown ligand / Chlorophyll a/b-binding protein
Similarity search - Component
Biological speciesChaetoceros gracilis (Diatom)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsNagao, R. / Kato, K. / Akita, F. / Miyazaki, N. / Shen, J.R.
Funding support1items
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, J.R.
History
DepositionSep 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Sep 14, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jun 19, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-31906
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
11: Chlorophyll a/b-binding protein
12: Fcpb2, Fucoxanthin chlorophyll a/c-binding protein
13: Chlorophyll a/b-binding protein
14: Chlorophyll a/b-binding protein
15: Chlorophyll a/b-binding protein
16: Fcpb3, Fucoxanthin chlorophyll a/c-binding protein
17: Fcpb4, Fucoxanthin chlorophyll a/c-binding protein
18: Chlorophyll a/b-binding protein
19: Fcpb5, Fucoxanthin chlorophyll a/c-binding protein
20: Fcpb6, Fucoxanthin chlorophyll a/c-binding protein
21: Fcpb7, Fucoxanthin chlorophyll a/c-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)383,711207
Polymers251,67111
Non-polymers132,040196
Water23413
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 7 types, 11 molecules 1113141518121617192021

#1: Protein
Chlorophyll a/b-binding protein


Mass: 22098.182 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom) / References: UniProt: A0A679BXP6
#2: Protein Fcpb2, Fucoxanthin chlorophyll a/c-binding protein


Mass: 22162.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#3: Protein Fcpb3, Fucoxanthin chlorophyll a/c-binding protein


Mass: 22627.543 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#4: Protein Fcpb4, Fucoxanthin chlorophyll a/c-binding protein


Mass: 22298.115 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#5: Protein Fcpb5, Fucoxanthin chlorophyll a/c-binding protein


Mass: 29014.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#6: Protein Fcpb6, Fucoxanthin chlorophyll a/c-binding protein


Mass: 23934.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)
#7: Protein Fcpb7, Fucoxanthin chlorophyll a/c-binding protein


Mass: 21143.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Chaetoceros gracilis (Diatom)

-
Sugars , 1 types, 1 molecules

#16: Sugar ChemComp-LMU / DODECYL-ALPHA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

-
Non-polymers , 9 types, 208 molecules

#8: Chemical...
ChemComp-CLA / CHLOROPHYLL A


Mass: 893.489 Da / Num. of mol.: 71 / Source method: obtained synthetically / Formula: C55H72MgN4O5
#9: Chemical...
ChemComp-KC1 / Chlorophyll c1


Mass: 610.941 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: C35H30MgN4O5
#10: Chemical...
ChemComp-A86 / (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 / Fucoxanthin


Mass: 658.906 Da / Num. of mol.: 54 / Source method: obtained synthetically / Formula: C42H58O6
#11: Chemical
ChemComp-LMG / 1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE


Mass: 787.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C45H86O10
#12: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 19 / Source method: obtained synthetically
#13: Chemical
ChemComp-DD6 / (3S,3'R,5R,6S,7cis)-7',8'-didehydro-5,6-dihydro-5,6-epoxy-beta,beta-carotene-3,3'-diol / Diadinoxanthin


Mass: 582.855 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C40H54O3
#14: Chemical ChemComp-SQD / 1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL / SULFOQUINOVOSYLDIACYLGLYCEROL


Mass: 795.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C41H78O12S
#15: Chemical
ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#17: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: S1M1-type FCPII complex / Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL
Molecular weightValue: 0.24 MDa / Experimental value: NO
Source (natural)Organism: Chaetoceros gracilis (Diatom)
Buffer solutionpH: 6.5
Buffer component
IDConc.FormulaBuffer-ID
120 mMMES-NaOH1
20.02 %DDM1
SpecimenConc.: 0.256 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

-
Processing

EM software
IDNameVersionCategory
1RELION3particle selection
4CTFFIND4.1CTF correction
7UCSF Chimera1.12model fitting
9RELION3initial Euler assignment
10RELION3final Euler assignment
11RELION3classification
12RELION33D reconstruction
13PHENIX1.13_2998model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 8093924
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 373897 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 6J40

6j40


Accession code: 6J40 / Source name: PDB / Type: experimental model

+
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