[English] 日本語
Yorodumi
- EMDB-6430: Characterization of red-shifted phycobiliprotein complexes isolat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6430
TitleCharacterization of red-shifted phycobiliprotein complexes isolated from the chlorophyll f-containing cyanobacterium Halomicronema hongdechloris
Map dataReconstruction of red-shifted phycobiliprotein complex
Sample
  • Sample: Red-shifted phycobilisomes from Halomicronema hongdechloris
  • Protein or peptide: APC phycobilisome complex
Keywordsphycobiliprotein / complementary chromatic acclimation / far-red light / small angle neutron scattering / photosynthesis / cyanobacteria
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Allophycocyanin, beta subunit / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
Allophycocyanin subunit alpha-B / Allophycocyanin beta chain
Similarity search - Component
Biological speciesHalomicronema hongdechloris (bacteria)
Methodsingle particle reconstruction / negative staining / Resolution: 26.0 Å
AuthorsLi Y / Lin Y / Garvey C / Birch D / Corkery RW / Loughlin PC / Scheer H / Willows RD / Chen M
CitationJournal: Biochim Biophys Acta / Year: 2016
Title: Characterization of red-shifted phycobilisomes isolated from the chlorophyll f-containing cyanobacterium Halomicronema hongdechloris.
Authors: Yaqiong Li / Yuankui Lin / Christopher J Garvey / Debra Birch / Robert W Corkery / Patrick C Loughlin / Hugo Scheer / Robert D Willows / Min Chen /
Abstract: Phycobilisomes are the main light-harvesting protein complexes in cyanobacteria and some algae. It is commonly accepted that these complexes only absorb green and orange light, complementing ...Phycobilisomes are the main light-harvesting protein complexes in cyanobacteria and some algae. It is commonly accepted that these complexes only absorb green and orange light, complementing chlorophyll absorbance. Here, we present a new phycobilisome derived complex that consists only of allophycocyanin core subunits, having red-shifted absorption peaks of 653 and 712 nm. These red-shifted phycobiliprotein complexes were isolated from the chlorophyll f-containing cyanobacterium, Halomicronema hongdechloris, grown under monochromatic 730 nm-wavelength (far-red) light. The 3D model obtained from single particle analysis reveals a double disk assembly of 120-145 Å with two α/β allophycocyanin trimers fitting into the two separated disks. They are significantly smaller than typical phycobilisomes formed from allophycocyanin subunits and core-membrane linker proteins, which fit well with a reduced distance between thylakoid membranes observed from cells grown under far-red light. Spectral analysis of the dissociated and denatured phycobiliprotein complexes grown under both these light conditions shows that the same bilin chromophore, phycocyanobilin, is exclusively used. Our findings show that red-shifted phycobilisomes are required for assisting efficient far-red light harvesting. Their discovery provides new insights into the molecular mechanisms of light harvesting under extreme conditions for photosynthesis, as well as the strategies involved in flexible chromatic acclimation to diverse light conditions.
History
DepositionAug 20, 2015-
Header (metadata) releaseSep 23, 2015-
Map releaseNov 11, 2015-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.86
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.86
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3jbb
  • Surface level: 0.86
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3jbb
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6430.jpg

Downloads & links

-
Map

FileDownload / File: emd_6430.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of red-shifted phycobiliprotein complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.8 Å/pix.
x 72 pix.
= 273.6 Å		3.8 Å/pix.
x 72 pix.
= 273.6 Å		3.8 Å/pix.
x 72 pix.
= 273.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.8 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.86 / Movie #1: 0.86
Minimum - Maximum-0.16323277 - 1.13121307
Average (Standard dev.)0.0772727 (±0.24691321)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions727272
Spacing727272
CellA=B=C: 273.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.83.83.8
M x/y/z727272
origin x/y/z0.0000.0000.000
length x/y/z273.600273.600273.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS727272
D min/max/mean-0.1631.1310.077

-
Supplemental data

-
Segmentation: Mask volume for reconstruction

AnnotationMask volume for reconstruction
Fileemd_6430_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Red-shifted phycobilisomes from Halomicronema hongdechloris

EntireName: Red-shifted phycobilisomes from Halomicronema hongdechloris
Components
  • Sample: Red-shifted phycobilisomes from Halomicronema hongdechloris
  • Protein or peptide: APC phycobilisome complex

-
Supramolecule #1000: Red-shifted phycobilisomes from Halomicronema hongdechloris

SupramoleculeName: Red-shifted phycobilisomes from Halomicronema hongdechloris
type: sample / ID: 1000 / Oligomeric state: Two APC trimers linked with APC E / Number unique components: 1

-
Macromolecule #1: APC phycobilisome complex

MacromoleculeName: APC phycobilisome complex / type: protein_or_peptide / ID: 1 / Details: Taxonomy ID 1209493 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Halomicronema hongdechloris (bacteria)

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5 / Details: 0.8 M phosphate buffer
StainingType: NEGATIVE / Details: 2% uranyl acetate for 2-3 seconds
GridDetails: 200 mesh gold grid with thin carbon support
VitrificationCryogen name: NONE / Instrument: OTHER

-
Electron microscopy

MicroscopeOTHER
DateJun 8, 2015
Image recordingCategory: CCD / Film or detector model: GENERIC IMAGE PLATES / Number real images: 12
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal magnification: 180000
Sample stageSpecimen holder model: PHILIPS ROTATION HOLDER

+
Image processing

DetailsSemiautomatic selection using e2boxer.py swarm function
CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 26.0 Å / Resolution method: OTHER / Software - Name: EMAN2 / Number images used: 420
Final two d classificationNumber classes: 32
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

4po5


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B
SoftwareName: Chimera
DetailsTwo trimers were fitted to each end of the EM map. 98% of atoms fit within the map at contour level 0.87.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-3jbb:
Characterization of red-shifted phycobiliprotein complexes isolated from the chlorophyll f-containing cyanobacterium Halomicronema hongdechloris

+
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