[English] 日本語
Yorodumi
- PDB-8iun: Cryo-EM structure of the CRT-LESS RC-LH core complex from roseifl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8iun
TitleCryo-EM structure of the CRT-LESS RC-LH core complex from roseiflexus castenholzii
Components
  • (reaction center small ...) x 2
  • Alpha subunit of light-harvesting 1
  • Antenna complex alpha/beta subunit
  • Cytochrome subunit of photosynthetic reaction center
  • Reaction center protein L chainPhotosynthetic reaction centre
  • reaction center unknown polypeptide
KeywordsPHOTOSYNTHESIS / CRT-LESS RC-LH CORE COMPLEX / ROSEIFLEXUS CASTENHOLZII
Function / homology
Function and homology information


organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / chlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / electron transfer activity / iron ion binding / heme binding ...organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / chlorophyll binding / photosynthesis, light reaction / electron transporter, transferring electrons within the cyclic electron transport pathway of photosynthesis activity / electron transfer activity / iron ion binding / heme binding / membrane / 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 domain superfamily / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Light-harvesting protein B beta chain / Antenna complex, alpha/beta subunit / Light-harvesting complex / Antenna complex alpha/beta subunit ...Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Antenna complex, beta domain superfamily / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Light-harvesting protein B beta chain / Antenna complex, alpha/beta subunit / Light-harvesting complex / Antenna complex alpha/beta 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 / CARDIOLIPIN / HEME C / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / : / Chem-MQE / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Chem-PGV / gamma-Carotene ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / HEME C / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / : / Chem-MQE / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Chem-PGV / gamma-Carotene / Unknown ligand / Antenna complex alpha/beta subunit / Cytochrome subunit of photosynthetic reaction center / Reaction center protein L chain / Alpha subunit of light-harvesting 1
Similarity search - Component
Biological speciesRoseiflexus castenholzii (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.85 Å
AuthorsWang, G.-L. / Qi, C.-H. / Yu, L.-J.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA0909600 China
Ministry of Science and Technology (MoST, China)2022YFC3401800 China
Ministry of Science and Technology (MoST, China)2019YFA0904600 China
CitationJournal: J Biol Chem / Year: 2023
Title: New insights on the photocomplex of Roseiflexus castenholzii revealed from comparisons of native and carotenoid-depleted complexes.
Authors: Chen-Hui Qi / Guang-Lei Wang / Fang-Fang Wang / Yueyong Xin / Mei-Juan Zou / Michael T Madigan / Zheng-Yu Wang-Otomo / Fei Ma / Long-Jiang Yu /
Abstract: In wild-type phototrophic organisms, carotenoids (Crts) are primarily packed into specific pigment-protein complexes along with (Bacterio)chlorophylls and play important roles in the photosynthesis. ...In wild-type phototrophic organisms, carotenoids (Crts) are primarily packed into specific pigment-protein complexes along with (Bacterio)chlorophylls and play important roles in the photosynthesis. Diphenylamine (DPA) inhibits carotenogenesis but not phototrophic growth of anoxygenic phototrophs and eliminates virtually all Crts from photocomplexes. To investigate the effect of Crts on assembly of the reaction center-light-harvesting (RC-LH) complex from the filamentous anoxygenic phototroph Roseiflexus (Rfl.) castenholzii, we generated carotenoidless (Crt-less) RC-LH complexes by growing cells in the presence of DPA. Here, we present cryo-EM structures of the Rfl. castenholzii native and Crt-less RC-LH complexes with resolutions of 2.86 Å and 2.85 Å, respectively. From the high-quality map obtained, several important but previously unresolved details in the Rfl. castenholzii RC-LH structure were determined unambiguously including the assignment and likely function of three small polypeptides, and the content and spatial arrangement of Crts with bacteriochlorophyll molecules. The overall structures of Crt-containing and Crt-less complexes are similar. However, structural comparisons showed that only five Crts remain in complexes from DPA-treated cells and that the subunit X (TMx) flanked on the N-terminal helix of the Cyt-subunit is missing. Based on these results, the function of Crts in the assembly of the Rfl. castenholzii RC-LH complex and the molecular mechanism of quinone exchange is discussed. These structural details provide a fresh look at the photosynthetic apparatus of an evolutionary ancient phototroph as well as new insights into the importance of Crts for proper assembly and functioning of the RC-LH complex.
History
DepositionMar 24, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
W: Antenna complex alpha/beta subunit
U: Antenna complex alpha/beta subunit
S: Antenna complex alpha/beta subunit
Q: Antenna complex alpha/beta subunit
O: Antenna complex alpha/beta subunit
K: Antenna complex alpha/beta subunit
I: Antenna complex alpha/beta subunit
G: Antenna complex alpha/beta subunit
E: Antenna complex alpha/beta subunit
B: Antenna complex alpha/beta subunit
0: Antenna complex alpha/beta subunit
8: Antenna complex alpha/beta subunit
6: Antenna complex alpha/beta subunit
4: Antenna complex alpha/beta subunit
2: Antenna complex alpha/beta subunit
M: Reaction center protein L chain
L: Reaction center protein L chain
H: Alpha subunit of light-harvesting 1
J: Alpha subunit of light-harvesting 1
N: Alpha subunit of light-harvesting 1
P: Alpha subunit of light-harvesting 1
R: Alpha subunit of light-harvesting 1
T: Alpha subunit of light-harvesting 1
V: Alpha subunit of light-harvesting 1
1: Alpha subunit of light-harvesting 1
3: Alpha subunit of light-harvesting 1
5: Alpha subunit of light-harvesting 1
7: Alpha subunit of light-harvesting 1
9: Alpha subunit of light-harvesting 1
A: Alpha subunit of light-harvesting 1
D: Alpha subunit of light-harvesting 1
F: Alpha subunit of light-harvesting 1
Y: reaction center small polypeptide
h: reaction center small polypeptide
C: Cytochrome subunit of photosynthetic reaction center
Z: reaction center unknown polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)452,414164
Polymers357,85636
Non-polymers94,557128
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 3 types, 18 molecules WUSQOKIGEB08642MLC

#1: Protein
Antenna complex alpha/beta subunit


Mass: 6432.513 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Roseiflexus castenholzii (bacteria) / References: UniProt: A7NQE9
#2: Protein Reaction center protein L chain / Photosynthetic reaction centre / Photosynthetic reaction center L subunit


Mass: 71707.398 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Roseiflexus castenholzii (bacteria) / References: UniProt: Q83XD0
#6: Protein Cytochrome subunit of photosynthetic reaction center /


Mass: 34923.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Roseiflexus castenholzii (bacteria) / References: UniProt: Q83XC9

-
Protein/peptide , 2 types, 16 molecules HJNPRTV13579ADFZ

#3: Protein/peptide
Alpha subunit of light-harvesting 1


Mass: 4724.656 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Source: (natural) Roseiflexus castenholzii (bacteria) / References: UniProt: Q83XD1
#7: Protein/peptide reaction center unknown polypeptide


Mass: 740.804 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Roseiflexus castenholzii (bacteria)

-
Reaction center small ... , 2 types, 2 molecules Yh

#4: Protein/peptide reaction center small polypeptide


Mass: 4493.262 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Roseiflexus castenholzii (bacteria)
#5: Protein reaction center small polypeptide


Mass: 6927.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Roseiflexus castenholzii (bacteria)

-
Sugars , 2 types, 16 molecules

#14: Sugar
ChemComp-BGL / 2-O-octyl-beta-D-glucopyranose / 2-O-octyl-beta-D-glucose / 2-O-octyl-D-glucose / 2-O-octyl-glucose


Type: D-saccharide, beta linking / Mass: 292.369 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-D-Glcp2octylIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#16: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

-
Non-polymers , 12 types, 112 molecules

#8: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A / Bacteriochlorophyll


Mass: 911.504 Da / Num. of mol.: 48 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#9: 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 / Phosphatidylglycerol


Mass: 749.007 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#10: 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.: 5 / Source method: obtained synthetically / Formula: C40H56
#11: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A / Pheophytin


Mass: 889.215 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C55H76N4O6 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#13: 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 / Feature type: SUBJECT OF INVESTIGATION
#15: Chemical
ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL / Phosphatidylethanolamine


Mass: 691.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C37H74NO8P / Comment: phospholipid*YM
#17: Chemical
ChemComp-UNL / UNKNOWN LIGAND


Mass: 691.959 Da / Num. of mol.: 20 / Source method: obtained synthetically
#18: Chemical ChemComp-CDL / CARDIOLIPIN / DIPHOSPHATIDYL GLYCEROL / BIS-(1,2-DIACYL-SN-GLYCERO-3-PHOSPHO)-1',3'-SN-GLYCEROL / Cardiolipin


Mass: 1464.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#19: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / Phosphatidylglycerol


Mass: 722.970 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H75O10P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#20: Chemical
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#21: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: CRT-LESS RC-LH CORE COMPLEX / Type: COMPLEX / Entity ID: #1-#7 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Roseiflexus castenholzii (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2300 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 56 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.19.2_4158: / Category: model refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 373675 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01525281
ELECTRON MICROSCOPYf_angle_d2.07534928
ELECTRON MICROSCOPYf_dihedral_angle_d19.87810168
ELECTRON MICROSCOPYf_chiral_restr0.253540
ELECTRON MICROSCOPYf_plane_restr0.0173759

+
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