[English] 日本語
Yorodumi
- PDB-8ydm: Cryo-EM structure of CaRC-LH complex from Chloroflexus aurantiacus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ydm
TitleCryo-EM structure of CaRC-LH complex from Chloroflexus aurantiacus
Components
  • (Light-harvesting protein B-808/866 ...) x 2
  • (Reaction center protein ...) x 2
  • Cytochrome c-554
  • hypothetical protein chain N
KeywordsPHOTOSYNTHESIS
Function / homology
Function and homology information


organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosystem II / photosynthetic electron transport in photosystem II / : / photosynthesis, light reaction / periplasmic space / electron transfer activity / iron ion binding ...organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosystem II / photosynthetic electron transport in photosystem II / : / photosynthesis, light reaction / periplasmic space / electron transfer activity / iron ion binding / heme binding / metal ion binding / plasma membrane
Similarity search - Function
: / Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Multiheme cytochrome c family profile. ...: / Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Antenna complex, beta subunit, conserved site / Antenna complexes beta subunits signature. / Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Multiheme cytochrome c family profile. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily / Antenna complex alpha/beta subunit / Light-harvesting complex / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, L subunit / Multiheme cytochrome superfamily / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature.
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / PROTOPORPHYRIN IX CONTAINING FE / : / Chem-MQE / Chem-PGV / gamma-Carotene / Light-harvesting protein B-808/866 alpha chain / Reaction center protein M chain / Light-harvesting protein B-808/866 beta chain ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / PROTOPORPHYRIN IX CONTAINING FE / : / Chem-MQE / Chem-PGV / gamma-Carotene / Light-harvesting protein B-808/866 alpha chain / Reaction center protein M chain / Light-harvesting protein B-808/866 beta chain / Reaction center protein L chain / Cytochrome c-554
Similarity search - Component
Biological speciesChloroflexus aurantiacus J-10-fl (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.05 Å
AuthorsGuoqiang, H. / Shishang, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: J Integr Plant Biol / Year: 2025
Title: Cryo-EM structure of a minimal reaction center-light-harvesting complex from the phototrophic bacterium Chloroflexus aurantiacus.
Authors: Guoqiang Huang / Shishang Dong / Lin Ma / Lin Li / Jinxin Ju / Mei-Jiao Wang / Jian-Ping Zhang / Sen-Fang Sui / Xiaochun Qin /
Abstract: Photosynthetic organisms have developed various light-harvesting antenna systems to capture light and transfer energy to reaction centers (RCs). Simultaneous utilization of the integral membrane ...Photosynthetic organisms have developed various light-harvesting antenna systems to capture light and transfer energy to reaction centers (RCs). Simultaneous utilization of the integral membrane light-harvesting antenna (LH complex) and the extrinsic antenna (chlorosomes) makes the phototrophic bacterium Chloroflexus (Cfx.) aurantiacus an ideal model for studying filamentous anoxygenic phototrophs (FAPs). Here, we determined the structure of a minimal RC-LH photocomplex from Cfx. aurantiacus J-10-fl (CaRC-LH) at 3.05-Å resolution. The CaRC-LH binds only to seven LH subunits, which form a crescent-shaped antenna surrounding the movable menaquinone-10 (Q) binding site of CaRC. In this complex with minimal LH units, an extra antenna is required to ensure sufficient light-gathering, providing a clear explanation for the presence of chlorosomes in Cfx. aurantiacus. More importantly, the semicircle of the antenna represents a novel RC-LH assembly pattern. Our structure provides a basis for understanding the existence of chlorosomes in Cfx. aurantiacus and the possible assembly pattern of RC-LH.
History
DepositionFeb 20, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Light-harvesting protein B-808/866 alpha chain
B: Light-harvesting protein B-808/866 beta chain
C: Cytochrome c-554
D: Light-harvesting protein B-808/866 alpha chain
E: Light-harvesting protein B-808/866 beta chain
F: Light-harvesting protein B-808/866 alpha chain
G: Light-harvesting protein B-808/866 beta chain
H: Light-harvesting protein B-808/866 alpha chain
I: Light-harvesting protein B-808/866 beta chain
J: Light-harvesting protein B-808/866 alpha chain
K: Light-harvesting protein B-808/866 beta chain
L: Reaction center protein L chain
M: Reaction center protein M chain
N: hypothetical protein chain N
O: Light-harvesting protein B-808/866 alpha chain
P: Light-harvesting protein B-808/866 beta chain
Q: Light-harvesting protein B-808/866 alpha chain
R: Light-harvesting protein B-808/866 beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,99566
Polymers210,35918
Non-polymers36,63648
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

-
Light-harvesting protein B-808/866 ... , 2 types, 14 molecules ADFHJOQBEGIKPR

#1: Protein
Light-harvesting protein B-808/866 alpha chain / Antenna pigment protein alpha chain / Bacteriochlorophyll a-binding protein


Mass: 6202.317 Da / Num. of mol.: 7 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus J-10-fl (bacteria)
Strain: J-10-fl / References: UniProt: P07503
#2: Protein
Light-harvesting protein B-808/866 beta chain / Antenna pigment protein beta chain / Bacteriochlorophyll a-binding protein


Mass: 6327.378 Da / Num. of mol.: 7 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus J-10-fl (bacteria)
Strain: J-10-fl / References: UniProt: P09927

-
Protein , 2 types, 2 molecules CN

#3: Protein Cytochrome c-554 / Cytochrome c554


Mass: 45625.227 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus J-10-fl (bacteria)
Strain: J-10-fl / References: UniProt: P33325
#6: Protein hypothetical protein chain N


Mass: 6865.124 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus J-10-fl (bacteria)

-
Reaction center protein ... , 2 types, 2 molecules LM

#4: Protein Reaction center protein L chain / Photosynthetic reaction center L subunit


Mass: 35173.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus J-10-fl (bacteria)
Strain: J-10-fl / References: UniProt: P11695
#5: Protein Reaction center protein M chain / Photosynthetic reaction center M subunit


Mass: 34987.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Chloroflexus aurantiacus J-10-fl (bacteria)
Strain: J-10-fl / References: UniProt: P09438

-
Non-polymers , 7 types, 48 molecules

#7: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C55H74MgN4O6
#8: Chemical
ChemComp-U4Z / gamma-Carotene / 2-[(1~{E},3~{E},5~{E},7~{E},9~{E},11~{E},13~{E},15~{E},17~{E},19~{E})-3,7,12,16,20,24-hexamethylpentacosa-1,3,5,7,9,11,13,15,17,19,23-undecaenyl]-1,3,3-trimethyl-cyclohexene


Mass: 536.873 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C40H56
#9: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#10: Chemical ChemComp-PGV / (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE / PHOSPHATIDYLGLYCEROL / 2-VACCENOYL-1-PALMITOYL-SN-GLYCEROL-3-PHOSPHOGLYCEROL


Mass: 749.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#11: Chemical ChemComp-MQE / 2-methyl-3-[(2E,6E,10E,14E,18E,22E,26E,30E,34E,38E)-3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,1 4,18,22,26,30,34,38,42-undecaen-1-yl]naphthalene-1,4-dione / Menaquinone 11


Mass: 921.467 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C66H96O2
#12: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C55H76N4O6
#13: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn

-
Details

Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Cryo-EM structure of CaRC-LH complex from Chloroflexus aurantiacus
Type: COMPLEX / Entity ID: #1-#6 / Source: NATURAL
Source (natural)Organism: Chloroflexus aurantiacus J-10-fl (bacteria)
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281.15 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 / Nominal defocus max: 1500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.05 Å / Num. of particles: 36181 / Symmetry type: POINT
RefinementHighest resolution: 3.05 Å

+
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