[English] 日本語
Yorodumi
- PDB-8imi: A1-A2, A3-A4, B'1-B'2, C'1-C'2 cylinder in cyanobacterial phycobi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8imi
TitleA1-A2, A3-A4, B'1-B'2, C'1-C'2 cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster A)
Components
  • ApcA2
  • ApcB2
  • ApcB3
  • ApcC2
  • ApcE
KeywordsPHOTOSYNTHESIS / Complex
Function / homologyPHYCOCYANOBILIN
Function and homology information
Biological speciesAnthocerotibacter panamensis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsWang, C.H. / Yang, C.H. / Wu, H.Y. / Jiang, H.W. / Ho, M.C. / Ho, M.Y.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
National Science Council (NSC, Taiwan) Taiwan
CitationJournal: Nat Commun / Year: 2023
Title: A structure of the relict phycobilisome from a thylakoid-free cyanobacterium.
Authors: Han-Wei Jiang / Hsiang-Yi Wu / Chun-Hsiung Wang / Cheng-Han Yang / Jui-Tse Ko / Han-Chen Ho / Ming-Daw Tsai / Donald A Bryant / Fay-Wei Li / Meng-Chiao Ho / Ming-Yang Ho /
Abstract: Phycobilisomes (PBS) are antenna megacomplexes that transfer energy to photosystems II and I in thylakoids. PBS likely evolved from a basic, inefficient form into the predominant hemidiscoidal shape ...Phycobilisomes (PBS) are antenna megacomplexes that transfer energy to photosystems II and I in thylakoids. PBS likely evolved from a basic, inefficient form into the predominant hemidiscoidal shape with radiating peripheral rods. However, it has been challenging to test this hypothesis because ancestral species are generally inaccessible. Here we use spectroscopy and cryo-electron microscopy to reveal a structure of a "paddle-shaped" PBS from a thylakoid-free cyanobacterium that likely retains ancestral traits. This PBS lacks rods and specialized ApcD and ApcF subunits, indicating relict characteristics. Other features include linkers connecting two chains of five phycocyanin hexamers (CpcN) and two core subdomains (ApcH), resulting in a paddle-shaped configuration. Energy transfer calculations demonstrate that chains are less efficient than rods. These features may nevertheless have increased light absorption by elongating PBS before multilayered thylakoids with hemidiscoidal PBS evolved. Our results provide insights into the evolution and diversification of light-harvesting strategies before the origin of thylakoids.
History
DepositionMar 7, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 25, 2023Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation / citation_author
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.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
0: ApcE
A: ApcA2
B: ApcA2
C: ApcA2
D: ApcA2
E: ApcA2
G: ApcB3
H: ApcB2
I: ApcB2
J: ApcB2
K: ApcB2
L: ApcB2
M: ApcC2
N: ApcA2
O: ApcA2
P: ApcA2
Q: ApcA2
R: ApcA2
S: ApcA2
T: ApcB2
U: ApcB2
V: ApcB2
W: ApcB2
X: ApcB2
Y: ApcB2
Z: ApcC2
a: ApcA2
b: ApcA2
c: ApcA2
d: ApcA2
e: ApcA2
f: ApcA2
g: ApcB2
h: ApcB2
i: ApcB2
j: ApcB2
k: ApcB2
l: ApcB2
m: ApcC2
n: ApcA2
o: ApcA2
p: ApcA2
q: ApcA2
r: ApcA2
s: ApcA2
t: ApcB2
u: ApcB2
v: ApcB2
w: ApcB2
x: ApcB2
y: ApcB2
z: ApcC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,009,986100
Polymers981,72852
Non-polymers28,25748
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 5 types, 52 molecules 0ABCDENOPQRSabcdefnopqrsGHIJKL...

#1: Protein ApcE


Mass: 127950.656 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Anthocerotibacter panamensis (bacteria)
#2: Protein ...
ApcA2


Mass: 17470.910 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Source: (natural) Anthocerotibacter panamensis (bacteria)
#3: Protein ApcB3


Mass: 17673.301 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Anthocerotibacter panamensis (bacteria)
#4: Protein ...
ApcB2


Mass: 17524.729 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Source: (natural) Anthocerotibacter panamensis (bacteria)
#5: Protein
ApcC2


Mass: 7801.207 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Anthocerotibacter panamensis (bacteria)

-
Non-polymers , 1 types, 48 molecules

#6: Chemical...
ChemComp-CYC / PHYCOCYANOBILIN


Mass: 588.694 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: C33H40N4O6 / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: A1-A2, A3-A4, B'1-B'2, C'1-C'2 cylinder in cyanobacterial phycobilisome from Anthocerotibacter panamensis (Cluster A)
Type: COMPLEX / Entity ID: #1-#5 / Source: NATURAL
Source (natural)Organism: Anthocerotibacter panamensis (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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 / Nominal magnification: 81000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1109579 / Symmetry type: POINT

+
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