[English] 日本語
Yorodumi
- EMDB-31089: Cryo-EM structure of the octameric state of C-phycocyanin from Th... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-31089
TitleCryo-EM structure of the octameric state of C-phycocyanin from Thermoleptolyngbya sp. O-77
Map data
Sample
  • Complex: CPC octamer
    • Protein or peptide: C-phycocyanin alpha chain
    • Protein or peptide: C-phycocyanin beta chain
Function / homology
Function and homology information


: / phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Phycocyanin, alpha subunit / Phycocyanin, beta subunit / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
C-phycocyanin alpha chain / C-phycocyanin beta chain
Similarity search - Component
Biological speciesLeptolyngbya sp. O-77 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.71 Å
AuthorsMinato T / Teramoto T / Adachi N / Hung NK / Yamada K / Kawasaki M / Akutsu M / Moriya T / Senda T / Ogo S ...Minato T / Teramoto T / Adachi N / Hung NK / Yamada K / Kawasaki M / Akutsu M / Moriya T / Senda T / Ogo S / Kakuta Y / Yoon KS
Funding support Japan, 4 items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP20am0101071 Japan
Japan Science and TechnologyJPMJCR18R2 Japan
Japan Society for the Promotion of Science (JSPS)JP18H02091 Japan
Japan Society for the Promotion of Science (JSPS)JP18J00191 Japan
CitationJournal: Commun Biol / Year: 2021
Title: Non-conventional octameric structure of C-phycocyanin.
Authors: Takuo Minato / Takamasa Teramoto / Naruhiko Adachi / Nguyen Khac Hung / Kaho Yamada / Masato Kawasaki / Masato Akutsu / Toshio Moriya / Toshiya Senda / Seiji Ogo / Yoshimitsu Kakuta / Ki-Seok Yoon /
Abstract: C-phycocyanin (CPC), a blue pigment protein, is an indispensable component of giant phycobilisomes, which are light-harvesting antenna complexes in cyanobacteria that transfer energy efficiently to ...C-phycocyanin (CPC), a blue pigment protein, is an indispensable component of giant phycobilisomes, which are light-harvesting antenna complexes in cyanobacteria that transfer energy efficiently to photosystems I and II. X-ray crystallographic and electron microscopy (EM) analyses have revealed the structure of CPC to be a closed toroidal hexamer by assembling two trimers. In this study, the structural characterization of non-conventional octameric CPC is reported for the first time. Analyses of the crystal and cryogenic EM structures of the native CPC from filamentous thermophilic cyanobacterium Thermoleptolyngbya sp. O-77 unexpectedly illustrated the coexistence of conventional hexamer and novel octamer. In addition, an unusual dimeric state, observed via analytical ultracentrifugation, was postulated to be a key intermediate structure in the assemble of the previously unobserved octamer. These observations provide new insights into the assembly processes of CPCs and the mechanism of energy transfer in the light-harvesting complexes.
History
DepositionMar 23, 2021-
Header (metadata) releaseNov 17, 2021-
Map releaseNov 17, 2021-
UpdateNov 17, 2021-
Current statusNov 17, 2021Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.041
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.041
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7eh7
  • Surface level: 0.041
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7eh7
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31089.png

Downloads & links

-
Map

FileDownload / File: emd_31089.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.88 Å
Density
Contour LevelBy AUTHOR: 0.041 / Movie #1: 0.041
Minimum - Maximum-0.07355838 - 0.14411008
Average (Standard dev.)9.987986e-06 (±0.0047511766)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.880.880.88
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z352.000352.000352.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0740.1440.000

-
Supplemental data

-
Mask #1

Fileemd_31089_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_31089_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_31089_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : CPC octamer

EntireName: CPC octamer
Components
  • Complex: CPC octamer
    • Protein or peptide: C-phycocyanin alpha chain
    • Protein or peptide: C-phycocyanin beta chain

-
Supramolecule #1: CPC octamer

SupramoleculeName: CPC octamer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: homo octamer
Source (natural)Organism: Leptolyngbya sp. O-77 (bacteria)
Molecular weightTheoretical: 320 KDa

-
Macromolecule #1: C-phycocyanin alpha chain

MacromoleculeName: C-phycocyanin alpha chain / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Leptolyngbya sp. O-77 (bacteria)
SequenceString:
MKTPITEAIA AADTQGRFLS NTELQAVNGR FERAAASMEA ARALTNNAQQ LIDGAANAVY QKFPYTTQM QGANFASDSR GKSKCARDIG YYLRIITYSL VAGGTGPLDE YLIAGLDEIN R TFDLSPSW YVEALKYIKA NHGLSGQAAN EANTYIDYAI NALS

-
Macromolecule #2: C-phycocyanin beta chain

MacromoleculeName: C-phycocyanin beta chain / type: protein_or_peptide / ID: 2 / Details: MEN: N-METHYL ASPARAGINE / Enantiomer: LEVO
Source (natural)Organism: Leptolyngbya sp. O-77 (bacteria)
SequenceString:
MLDAFAKVVS QADTKGEFLS SAQLDALSNV VKDGSKRLDA VNRMTSNAST IVANAARSLF EEQPQLIQP GG(MEN)AYTNRRM AACLRDMEII LRYVTYATLA GDSSVLDDRC LNGLRETYQA L GVPGGSVA AGVAKMKDAA IAIVNDPNGI TKGDCSALVS EIASYFDRAA AAVA

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration6.7 mg/mL
BufferpH: 7
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR / Details: The grid was washed by acetone prior to use.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 291 K / Instrument: FEI VITROBOT MARK IV / Details: Blotting time was 5 seconds (blot force 15).
DetailsThis sample was mono-disperse.

-
Electron microscopy

MicroscopeTFS TALOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 120000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 2 / Number real images: 2036 / Average exposure time: 49.2 sec. / Average electron dose: 50.0 e/Å2

-
Image processing

Particle selectionNumber selected: 129653
CTF correctionSoftware - Name: Gctf
Startup modelType of model: OTHER
Details: An ab initio model was generated using RELION3's own implementation of Stochastic Gradient Descent (SGD) algorithm and low-pass filtered to 60 A for use as an initial model for 3D classification.
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 2 / Avg.num./class: 11821 / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D4 (2x4 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.71 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 10402
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