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- PDB-8iun: Cryo-EM structure of the CRT-LESS RC-LH core complex from roseifl... -

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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 chain
  • 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, alpha subunit conserved site / Antenna complexes alpha subunits signature. / 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, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / 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, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water00
1


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

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Components

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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 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

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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)

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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)

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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

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Non-polymers , 12 types, 112 molecules

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


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


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


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


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


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


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


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

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Details

Has ligand of interestY

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Experimental details

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Experiment

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

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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

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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 FIELD / 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)

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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

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