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- PDB-8k5o: Cryo-EM structure of the RC-LH core comples from Halorhodospira h... -

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Basic information

Entry
Database: PDB / ID: 8k5o
TitleCryo-EM structure of the RC-LH core comples from Halorhodospira halochloris
Components
  • (Antenna complex alpha/beta subunit domain-containing ...) x 2
  • (Photosynthetic reaction center ...) x 2
  • (Reaction center protein ...) x 2
  • Beta subunit of light-harvesting 1
  • Gamma subunit of light-harvesting 1
  • Light-harvesting LHI
  • reactin center small polypeptide
  • reaction center small polypeptide
KeywordsPHOTOSYNTHESIS / RC-LH complex / HALORHODOSPIRA HALOCHLORIS
Function / homology
Function and homology information


organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / : / endomembrane system / electron transfer activity / iron ion binding ...organelle inner membrane / plasma membrane-derived chromatophore membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthetic electron transport in photosystem II / photosynthesis, light reaction / : / endomembrane system / electron transfer activity / iron ion binding / heme binding / metal ion binding / membrane / 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. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain ...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. / 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, H subunit / Bacterial photosynthetic reaction centre, H-chain, C-terminal / Photosynthetic reaction centre, M subunit / Photosynthetic reaction centre, H subunit, N-terminal / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / PRC-barrel domain / PRC-barrel domain / Photosynthetic reaction centre, L subunit / PRC-barrel-like superfamily / Multiheme cytochrome superfamily / : / Photosynthetic reaction centre, L/M / Photosystem II protein D1/D2 superfamily / Photosynthetic reaction centre protein / Photosynthetic reaction center proteins signature. / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
: / : / : / CARDIOLIPIN / : / HEME C / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / LYCOPENE / MENAQUINONE 8 / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE ...: / : / : / CARDIOLIPIN / : / HEME C / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE / LYCOPENE / MENAQUINONE 8 / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / Chem-PGV / Unknown ligand / Ubiquinone-8 / Photosynthetic reaction center cytochrome c subunit / Photosynthetic reaction center H subunit / Reaction center protein M chain / Uncharacterized protein / Reaction center protein L chain / Antenna complex alpha/beta subunit domain-containing protein / Antenna complex alpha/beta subunit domain-containing protein / Light-harvesting LHI
Similarity search - Component
Biological speciesHalorhodospira halochloris (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.42 Å
AuthorsWang, G.-L. / Qi, C.-H. / Yu, L.-J.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2022YFC3401800 China
CitationJournal: J Integr Plant Biol / Year: 2024
Title: Structural insights into the unusual core photocomplex from a triply extremophilic purple bacterium, Halorhodospira halochloris.
Authors: Chen-Hui Qi / Guang-Lei Wang / Fang-Fang Wang / Jie Wang / Xiang-Ping Wang / Mei-Juan Zou / Fei Ma / Michael T Madigan / Yukihiro Kimura / Zheng-Yu Wang-Otomo / Long-Jiang Yu /
Abstract: Halorhodospira (Hlr.) halochloris is a triply extremophilic phototrophic purple sulfur bacterium, as it is thermophilic, alkaliphilic, and extremely halophilic. The light-harvesting-reaction center ...Halorhodospira (Hlr.) halochloris is a triply extremophilic phototrophic purple sulfur bacterium, as it is thermophilic, alkaliphilic, and extremely halophilic. The light-harvesting-reaction center (LH1-RC) core complex of this bacterium displays an LH1-Q transition at 1,016 nm, which is the lowest-energy wavelength absorption among all known phototrophs. Here we report the cryo-EM structure of the LH1-RC at 2.42 Å resolution. The LH1 complex forms a tricyclic ring structure composed of 16 αβγ-polypeptides and one αβ-heterodimer around the RC. From the cryo-EM density map, two previously unrecognized integral membrane proteins, referred to as protein G and protein Q, were identified. Both of these proteins are single transmembrane-spanning helices located between the LH1 ring and the RC L-subunit and are absent from the LH1-RC complexes of all other purple bacteria of which the structures have been determined so far. Besides bacteriochlorophyll b molecules (B1020) located on the periplasmic side of the Hlr. halochloris membrane, there are also two arrays of bacteriochlorophyll b molecules (B800 and B820) located on the cytoplasmic side. Only a single copy of a carotenoid (lycopene) was resolved in the Hlr. halochloris LH1-α3β3 and this was positioned within the complex. The potential quinone channel should be the space between the LH1-α3β3 that accommodates the single lycopene but does not contain a γ-polypeptide, B800 and B820. Our results provide a structural explanation for the unusual Q red shift and carotenoid absorption in the Hlr. halochloris spectrum and reveal new insights into photosynthetic mechanisms employed by a species that thrives under the harshest conditions of any phototrophic microorganism known.
History
DepositionJul 22, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: citation / citation_author ...citation / citation_author / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _citation.country / _citation.journal_volume ..._citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.2Nov 20, 2024Group: Data collection / Category: em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Photosynthetic reaction center cytochrome c subunit
L: Reaction center protein L chain
M: Reaction center protein M chain
H: Photosynthetic reaction center H subunit
4: Antenna complex alpha/beta subunit domain-containing protein
3: Light-harvesting LHI
w: Antenna complex alpha/beta subunit domain-containing protein
x: Beta subunit of light-harvesting 1
v: Gamma subunit of light-harvesting 1
Y: Antenna complex alpha/beta subunit domain-containing protein
Z: Beta subunit of light-harvesting 1
X: Gamma subunit of light-harvesting 1
b: Antenna complex alpha/beta subunit domain-containing protein
c: Beta subunit of light-harvesting 1
a: Gamma subunit of light-harvesting 1
k: Antenna complex alpha/beta subunit domain-containing protein
l: Beta subunit of light-harvesting 1
j: Gamma subunit of light-harvesting 1
n: Antenna complex alpha/beta subunit domain-containing protein
o: Beta subunit of light-harvesting 1
m: Gamma subunit of light-harvesting 1
t: Antenna complex alpha/beta subunit domain-containing protein
u: Beta subunit of light-harvesting 1
s: Gamma subunit of light-harvesting 1
z: Antenna complex alpha/beta subunit domain-containing protein
1: Beta subunit of light-harvesting 1
y: Gamma subunit of light-harvesting 1
6: Antenna complex alpha/beta subunit domain-containing protein
7: Beta subunit of light-harvesting 1
5: Gamma subunit of light-harvesting 1
F: Antenna complex alpha/beta subunit domain-containing protein
G: Beta subunit of light-harvesting 1
8: Gamma subunit of light-harvesting 1
K: Antenna complex alpha/beta subunit domain-containing protein
N: Beta subunit of light-harvesting 1
I: Gamma subunit of light-harvesting 1
P: Antenna complex alpha/beta subunit domain-containing protein
Q: Beta subunit of light-harvesting 1
O: Gamma subunit of light-harvesting 1
S: Antenna complex alpha/beta subunit domain-containing protein
T: Beta subunit of light-harvesting 1
R: Gamma subunit of light-harvesting 1
V: Antenna complex alpha/beta subunit domain-containing protein
W: Beta subunit of light-harvesting 1
U: Gamma subunit of light-harvesting 1
e: Antenna complex alpha/beta subunit domain-containing protein
f: Beta subunit of light-harvesting 1
d: Gamma subunit of light-harvesting 1
h: Antenna complex alpha/beta subunit domain-containing protein
i: Beta subunit of light-harvesting 1
g: Gamma subunit of light-harvesting 1
q: Antenna complex alpha/beta subunit domain-containing protein
r: Beta subunit of light-harvesting 1
p: Gamma subunit of light-harvesting 1
2: reaction center small polypeptide
9: reactin center small polypeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)659,378251
Polymers493,17356
Non-polymers166,204195
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Photosynthetic reaction center ... , 2 types, 2 molecules CH

#1: Protein Photosynthetic reaction center cytochrome c subunit


Mass: 41612.859 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halochloris (bacteria) / References: UniProt: A0A0X8X829
#4: Protein Photosynthetic reaction center H subunit


Mass: 31293.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halochloris (bacteria) / References: UniProt: A0A0X8X838

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

#2: Protein Reaction center protein L chain


Mass: 31115.025 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halochloris (bacteria) / References: UniProt: A0A0X8XAH6
#3: Protein Reaction center protein M chain


Mass: 36221.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halochloris (bacteria) / References: UniProt: A0A0X8X847

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Antenna complex alpha/beta subunit domain-containing ... , 2 types, 17 molecules 4wYbkntz6FKPSVehq

#5: Protein Antenna complex alpha/beta subunit domain-containing protein


Mass: 12053.332 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halochloris (bacteria) / References: UniProt: A0A110B4Z6
#7: Protein
Antenna complex alpha/beta subunit domain-containing protein


Mass: 7696.815 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halochloris (bacteria) / References: UniProt: A0A0X8XBE4

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Protein , 2 types, 17 molecules 3xZclou17GNQTWfir

#6: Protein Light-harvesting LHI


Mass: 7562.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halochloris (bacteria) / References: UniProt: A0A120MZP7
#8: Protein
Beta subunit of light-harvesting 1


Mass: 9555.675 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halochloris (bacteria) / References: UniProt: A0A0X8X9B2

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Protein/peptide , 3 types, 18 molecules vXajmsy58IORUdgp29

#9: Protein/peptide
Gamma subunit of light-harvesting 1


Mass: 3123.757 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halochloris (bacteria)
#10: Protein/peptide reaction center small polypeptide


Mass: 3531.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halochloris (bacteria)
#11: Protein/peptide reactin center small polypeptide


Mass: 3762.490 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halochloris (bacteria)

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Sugars , 1 types, 2 molecules

#25: 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.: 2 / Source method: obtained synthetically / Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-D-Glcp2octylIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 13 types, 193 molecules

#12: Chemical
ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H34FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#13: 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.: 50 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#14: Chemical ChemComp-LHG / 1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE


Mass: 722.970 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H75O10P / Comment: phospholipid*YM
#15: Chemical...
ChemComp-A1LZM / Trans-Geranyl Bacteriochlorophyll B


Mass: 907.472 Da / Num. of mol.: 54 / Source method: obtained synthetically / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#16: Chemical ChemComp-A1LZP / Trans-Geranyl Bacteriopheophytin B


Mass: 885.183 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H72N4O6 / Feature type: SUBJECT OF INVESTIGATION
#17: Chemical ChemComp-UQ8 / Ubiquinone-8 / 2,3-dimethoxy-5-methyl-6-[(6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-octamethyldotriaconta-2,6,10,14,18,22,26,30-oc taen-1-yl]cyclohexa-2,5-diene-1,4-dione


Mass: 727.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C49H74O4 / Feature type: SUBJECT OF INVESTIGATION
#18: Chemical...
ChemComp-UNL / UNKNOWN LIGAND


Mass: 909.488 Da / Num. of mol.: 57 / Source method: obtained synthetically
#19: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#20: Chemical ChemComp-MQ8 / MENAQUINONE 8 / 2-METHYL-3-(3,7,11,15,19,23,27,31-OCTAMETHYL-DOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL)-[1,4]NAPTHOQUINONE


Mass: 717.116 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C51H72O2 / Feature type: SUBJECT OF INVESTIGATION
#21: 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.: 3 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#22: Chemical ChemComp-LYC / LYCOPENE


Mass: 536.873 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H56 / Feature type: SUBJECT OF INVESTIGATION
#23: Chemical
ChemComp-A1LZQ / Trans-Geranyl 8-vinyl-bacteriochlorophyll B


Mass: 907.472 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C55H70MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#24: Chemical ChemComp-PEF / DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE / 3-[AMINOETHYLPHOSPHORYL]-[1,2-DI-PALMITOYL]-SN-GLYCEROL


Mass: 691.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H74NO8P / Comment: phospholipid*YM

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Details

Has ligand of interestY
Has protein modificationY

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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: RC-LH core complex / Type: COMPLEX / Entity ID: #1, #3-#11 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Halorhodospira halochloris (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: 60.8 e/Å2 / Film or detector model: GATAN K2 BASE (4k 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: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 353518 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00940019
ELECTRON MICROSCOPYf_angle_d3.27254754
ELECTRON MICROSCOPYf_dihedral_angle_d19.0759079
ELECTRON MICROSCOPYf_chiral_restr0.0545020
ELECTRON MICROSCOPYf_plane_restr0.0066461

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