8K5O

Cryo-EM structure of the RC-LH core comples from Halorhodospira halochloris


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.2 of the entry. See complete history


Literature

Structural insights into the unusual core photocomplex from a triply extremophilic purple bacterium, Halorhodospira halochloris.

Qi, C.H.Wang, G.L.Wang, F.F.Wang, J.Wang, X.P.Zou, M.J.Ma, F.Madigan, M.T.Kimura, Y.Wang-Otomo, Z.Y.Yu, L.J.

(2024) J Integr Plant Biol 66: 2262-2272

  • DOI: https://doi.org/10.1111/jipb.13628
  • Primary Citation of Related Structures:  
    8K5O

  • PubMed 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 (LH1-RC) core complex of this bacterium displays an LH1-Q y 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 y 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.


  • Organizational Affiliation

    Key Laboratory of Photobiology, Photosynthesis Research Center, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center cytochrome c subunitA [auth C]372Halorhodospira halochlorisMutation(s): 0 
UniProt
Find proteins for A0A0X8X829 (Halorhodospira halochloris)
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UniProt GroupA0A0X8X829
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chainB [auth L]279Halorhodospira halochlorisMutation(s): 0 
UniProt
Find proteins for A0A0X8XAH6 (Halorhodospira halochloris)
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UniProt GroupA0A0X8XAH6
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chainC [auth M]320Halorhodospira halochlorisMutation(s): 0 
UniProt
Find proteins for A0A0X8X847 (Halorhodospira halochloris)
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UniProt GroupA0A0X8X847
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center H subunitD [auth H]274Halorhodospira halochlorisMutation(s): 0 
UniProt
Find proteins for A0A0X8X838 (Halorhodospira halochloris)
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UniProt GroupA0A0X8X838
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Antenna complex alpha/beta subunit domain-containing proteinE [auth 4]105Halorhodospira halochlorisMutation(s): 0 
UniProt
Find proteins for A0A110B4Z6 (Halorhodospira halochloris)
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UniProt GroupA0A110B4Z6
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Light-harvesting LHIF [auth 3]65Halorhodospira halochlorisMutation(s): 0 
UniProt
Find proteins for A0A120MZP7 (Halorhodospira halochloris)
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UniProt GroupA0A120MZP7
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Antenna complex alpha/beta subunit domain-containing protein65Halorhodospira halochlorisMutation(s): 0 
UniProt
Find proteins for A0A0X8XBE4 (Halorhodospira halochloris)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Beta subunit of light-harvesting 186Halorhodospira halochlorisMutation(s): 0 
UniProt
Find proteins for A0A0X8X9B2 (Halorhodospira halochloris)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Gamma subunit of light-harvesting 129Halorhodospira halochlorisMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
reaction center small polypeptideCB [auth 2]31Halorhodospira halochlorisMutation(s): 0 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
reactin center small polypeptideDB [auth 9]33Halorhodospira halochlorisMutation(s): 0 
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Small Molecules
Ligands 14 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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EC [auth M],
FC [auth M],
MC [auth H]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
A1LZQ (Subject of Investigation/LOI)
Query on A1LZQ

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DE [auth l]
DG [auth N]
FF [auth 1]
GH [auth W]
ID [auth Z]
Trans-Geranyl 8-vinyl-bacteriochlorophyll B
C55 H70 Mg N4 O6
FQBSMLYJYBYPGF-CZXYOYAHSA-M
A1LZM (Subject of Investigation/LOI)
Query on A1LZM

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BF [auth z]
CE [auth l]
CF [auth z]
CG [auth N]
CH [auth V]
Trans-Geranyl Bacteriochlorophyll B
C55 H70 Mg N4 O6
CEXNNVAXOSZTBM-NEIICFFNSA-M
A1LZP (Subject of Investigation/LOI)
Query on A1LZP

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OB [auth L],
ZB [auth M]
Trans-Geranyl Bacteriopheophytin B
C55 H72 N4 O6
GITBURVOIOOMIM-KBVICSHCSA-N
PGV
Query on PGV

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AF [auth s]
BE [auth k]
BH [auth R]
CC [auth M]
CD [auth v]
(1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE
C40 H77 O10 P
ADYWCMPUNIVOEA-GPJPVTGXSA-N
UQ8 (Subject of Investigation/LOI)
Query on UQ8

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PB [auth L]Ubiquinone-8
C49 H74 O4
ICFIZJQGJAJRSU-SGHXUWJISA-N
LHG
Query on LHG

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JB [auth C]1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
MQ8 (Subject of Investigation/LOI)
Query on MQ8

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AC [auth M],
BC [auth M]
MENAQUINONE 8
C51 H72 O2
LXKDFTDVRVLXFY-ACMRXAIVSA-N
PEF
Query on PEF

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BG [auth K]DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE
C37 H74 N O8 P
SLKDGVPOSSLUAI-PGUFJCEWSA-N
HEC (Subject of Investigation/LOI)
Query on HEC

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EB [auth C],
FB [auth C],
GB [auth C],
HB [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
LYC (Subject of Investigation/LOI)
Query on LYC

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SC [auth 3]LYCOPENE
C40 H56
OAIJSZIZWZSQBC-GYZMGTAESA-N
BGL
Query on BGL

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VG [auth S],
WH [auth h]
2-O-octyl-beta-D-glucopyranose
C14 H28 O6
BVHPDIWLWHHJPD-RKQHYHRCSA-N
FE (Subject of Investigation/LOI)
Query on FE

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WB [auth M]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
UNL
Query on UNL

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AD [auth v]
AE [auth k]
AG [auth K]
AH [auth R]
AI [auth g]
Unknown ligand
VTLYFUHAOXGGBS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.42 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Ministry of Science and Technology (MoST, China)China2022YFC3401800

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-22
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-11-20
    Changes: Data collection