[English] 日本語
Yorodumi
- EMDB-31945: Phycocyanin rod structure of cyanobacterial phycobilisome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-31945
TitlePhycocyanin rod structure of cyanobacterial phycobilisome
Map datapostprocess_masked.mrc
Sample
  • Complex: Phycocyanin rod complex of cyanobacterial phyocobilisome
    • Protein or peptide: C-phycocyanin alpha subunit
    • Protein or peptide: C-phycocyanin beta subunit
    • Protein or peptide: Phycobilisome 8.9 kDa linker polypeptide, phycocyanin-associated, rod
    • Protein or peptide: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod
    • Protein or peptide: Phycobilisome rod-core linker polypeptide CpcG2
  • Ligand: PHYCOCYANOBILIN
Function / homology
Function and homology information


phycobilisome / plasma membrane-derived thylakoid membrane / photosynthesis
Similarity search - Function
Phycobilisome linker protein / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycocyanin, alpha subunit / Phycocyanin, beta subunit / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. ...Phycobilisome linker protein / Phycobilisome linker domain / Phycobilisome linker domain superfamily / Phycobilisome Linker polypeptide / Phycobilisome (PBS) linker domain profile. / Phycocyanin, alpha subunit / Phycocyanin, beta subunit / CpcD-like domain / CpcD/allophycocyanin linker domain / CpcD-like domain profile. / CpcD/allophycocyanin linker domain / Phycobilisome, alpha/beta subunit / Phycobilisome, alpha/beta subunit superfamily / Phycobilisome protein / Globin-like superfamily
Similarity search - Domain/homology
C-phycocyanin alpha subunit / C-phycocyanin beta subunit / Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod / Phycobilisome 8.9 kDa linker polypeptide, phycocyanin-associated, rod / Phycobilisome rod-core linker polypeptide CpcG2
Similarity search - Component
Biological speciesThermosynechococcus vulcanus NIES-2134 (bacteria) / Thermosynechococcus elongatus BP-1 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsKawakami K / Hamaguchi T / Hirose Y / Kosumi D / Miyata M / Kamiya N / Yonekura K
Funding support Japan, 3 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)20H05109 Japan
Japan Society for the Promotion of Science (JSPS)20K06528 Japan
Japan Society for the Promotion of Science (JSPS)17H06434 Japan
CitationJournal: Nat Commun / Year: 2022
Title: Core and rod structures of a thermophilic cyanobacterial light-harvesting phycobilisome.
Authors: Keisuke Kawakami / Tasuku Hamaguchi / Yuu Hirose / Daisuke Kosumi / Makoto Miyata / Nobuo Kamiya / Koji Yonekura /
Abstract: Cyanobacteria, glaucophytes, and rhodophytes utilize giant, light-harvesting phycobilisomes (PBSs) for capturing solar energy and conveying it to photosynthetic reaction centers. PBSs are ...Cyanobacteria, glaucophytes, and rhodophytes utilize giant, light-harvesting phycobilisomes (PBSs) for capturing solar energy and conveying it to photosynthetic reaction centers. PBSs are compositionally and structurally diverse, and exceedingly complex, all of which pose a challenge for a comprehensive understanding of their function. To date, three detailed architectures of PBSs by cryo-electron microscopy (cryo-EM) have been described: a hemiellipsoidal type, a block-type from rhodophytes, and a cyanobacterial hemidiscoidal-type. Here, we report cryo-EM structures of a pentacylindrical allophycocyanin core and phycocyanin-containing rod of a thermophilic cyanobacterial hemidiscoidal PBS. The structures define the spatial arrangement of protein subunits and chromophores, crucial for deciphering the energy transfer mechanism. They reveal how the pentacylindrical core is formed, identify key interactions between linker proteins and the bilin chromophores, and indicate pathways for unidirectional energy transfer.
History
DepositionSep 8, 2021-
Header (metadata) releaseJun 15, 2022-
Map releaseJun 15, 2022-
UpdateAug 17, 2022-
Current statusAug 17, 2022Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_31945.png

Downloads & links

-
Map

FileDownload / File: emd_31945.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpostprocess_masked.mrc
Voxel sizeX=Y=Z: 1.86 Å
Density
Contour LevelBy AUTHOR: 0.0286
Minimum - Maximum-0.0954498 - 0.1498202
Average (Standard dev.)0.00049829273 (±0.006029715)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 297.6 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Phycocyanin rod complex of cyanobacterial phyocobilisome

EntireName: Phycocyanin rod complex of cyanobacterial phyocobilisome
Components
  • Complex: Phycocyanin rod complex of cyanobacterial phyocobilisome
    • Protein or peptide: C-phycocyanin alpha subunit
    • Protein or peptide: C-phycocyanin beta subunit
    • Protein or peptide: Phycobilisome 8.9 kDa linker polypeptide, phycocyanin-associated, rod
    • Protein or peptide: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod
    • Protein or peptide: Phycobilisome rod-core linker polypeptide CpcG2
  • Ligand: PHYCOCYANOBILIN

-
Supramolecule #1: Phycocyanin rod complex of cyanobacterial phyocobilisome

SupramoleculeName: Phycocyanin rod complex of cyanobacterial phyocobilisome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Thermosynechococcus vulcanus NIES-2134 (bacteria)

-
Macromolecule #1: C-phycocyanin alpha subunit

MacromoleculeName: C-phycocyanin alpha subunit / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 17.456631 KDa
SequenceString:
MKTPITEAIA AADTQGRFLS NTELQAVDGR FKRAVASMEA ARALTNNAQS LIDGAAQAVY QKFPYTTTMQ GSQYASTPEG KAKCARDIG YYLRMVTYCL VAGGTGPMDE YLIAGLSEIN STFDLSPSWY IEALKYIKAN HGLTGQAAVE ANAYIDYAIN A LS

-
Macromolecule #2: C-phycocyanin beta subunit

MacromoleculeName: C-phycocyanin beta subunit / type: protein_or_peptide / ID: 2 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 18.216652 KDa
SequenceString:
MLDAFAKVVA QADARGEFLT NAQFDALSNL VKEGNKRLDA VNRITSNAST IVANAARALF AEQPQLIQPG G(MEN)AYTN RRM AACLRDMEII LRYVTYAILA GDSSVLDDRC LNGLRETYQA LGTPGSSVAV AIQKMKDAAI AIANDPNGIT PGDCSAL MS EIAGYFDRAA AAVA

-
Macromolecule #3: Phycobilisome 8.9 kDa linker polypeptide, phycocyanin-associated, rod

MacromoleculeName: Phycobilisome 8.9 kDa linker polypeptide, phycocyanin-associated, rod
type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 8.681903 KDa
SequenceString:
MFGQTASGSA ALSPSGARVF RYEVVGLRQN EETDRMEFPI RRSGSTFITV PYNRMNEEMQ RITRMGGKIV SITPVVAS

-
Macromolecule #4: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod

MacromoleculeName: Phycobilisome 32.1 kDa linker polypeptide, phycocyanin-associated, rod
type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 32.158914 KDa
SequenceString: MAITAAASRL GTSAFSDAPP VELRANWSEE DLETVIRAVY RQVLGNDYVM ASERLVSAES LLRNGKITVR EFVRAVAKSE LYKEKFLYG NFQTRVIELN YKHLLGRAPY DESEVIFHLD LYENEGFDAD IDSYIDSPEY TNSFGDWVVP YYRGFNTQPG Q KTVGFNRI ...String:
MAITAAASRL GTSAFSDAPP VELRANWSEE DLETVIRAVY RQVLGNDYVM ASERLVSAES LLRNGKITVR EFVRAVAKSE LYKEKFLYG NFQTRVIELN YKHLLGRAPY DESEVIFHLD LYENEGFDAD IDSYIDSPEY TNSFGDWVVP YYRGFNTQPG Q KTVGFNRI FRLYRGYANS DRAQAEGSMS RLARDLATNR ANTVVPPSNS DTAFAYYTPS ADVPPRACLG GSFGESGRVY RI EVAGIRQ PGYPGVRRSS TAFLVPYEQL SAKMQQLQRT GARIISVNPA

-
Macromolecule #5: Phycobilisome rod-core linker polypeptide CpcG2

MacromoleculeName: Phycobilisome rod-core linker polypeptide CpcG2 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermosynechococcus elongatus BP-1 (bacteria) / Strain: BP-1
Molecular weightTheoretical: 28.817357 KDa
SequenceString: MTIPLLSYAP SSQNQRVAGY EVPNEETPWR YSLEDAVDQS DIDELIWAAY RQVFSEHVVL KSTRQPHLES QLANRAISVR DFIRGLAKS ETFRRLVVET NSNYRLVEIA LKRLLGRAPY NKQEELAWSI RIATDGWQKF VDTLVDSDEY TQNFGDNTVP Y QRRRYKDR ...String:
MTIPLLSYAP SSQNQRVAGY EVPNEETPWR YSLEDAVDQS DIDELIWAAY RQVFSEHVVL KSTRQPHLES QLANRAISVR DFIRGLAKS ETFRRLVVET NSNYRLVEIA LKRLLGRAPY NKQEELAWSI RIATDGWQKF VDTLVDSDEY TQNFGDNTVP Y QRRRYKDR PFNLVTPRYS DYWRDKLENS RYKWGDIRNF LEMARSVKVT PVQFKPVSTA NVQIPDTTRR DRPTVPASIN PT ASFPLR

-
Macromolecule #6: PHYCOCYANOBILIN

MacromoleculeName: PHYCOCYANOBILIN / type: ligand / ID: 6 / Number of copies: 36 / Formula: CYC
Molecular weightTheoretical: 588.694 Da
Chemical component information

ChemComp-CYC:
PHYCOCYANOBILIN

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 6.5
VitrificationCryogen name: NITROGEN

-
Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 150.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm

+
Image processing

Startup modelType of model: OTHER / Details: ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 159537
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
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://pdbjlvh1.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