RCSB PDB - 8Z83: Photosynthetic LH1-RC complex from the purple bacterium Halorhodospira halophila

 8Z83

Photosynthetic LH1-RC complex from the purple bacterium Halorhodospira halophila


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

A Native LH1-RC-HiPIP Supercomplex from an Extremophilic Phototroph.

Tani, K.Kanno, R.Nagashima, K.V.P.Kawakami, M.Hiwatashi, N.Nakata, K.Nagashima, S.Inoue, K.Takaichi, S.Purba, E.R.Hall, M.Yu, L.J.Madigan, M.T.Mizoguchi, A.Humbel, B.M.Kimura, Y.Wang-Otomo, Z.Y.

(2025) Commun Biol 8: 42-42

  • DOI: https://doi.org/10.1038/s42003-024-07421-w
  • Primary Citation of Related Structures:  
    8Z82, 8Z83

  • PubMed Abstract: 

    Halorhodospira (Hlr.) halophila strain BN9622 is an extremely halophilic and alkaliphilic purple phototrophic bacterium and has been widely used as a model for exploring the osmoadaptive and photosynthetic strategies employed by phototrophic extreme halophiles that enable them to thrive in hypersaline environments. Here we present the cryo-EM structures of (1) a unique native Hlr. halophila triple-complex formed from light-harvesting (LH1), the reaction center (RC), and high-potential iron-sulfur protein (HiPIP) at 2.44 Å resolution, and (2) a HiPIP-free LH1-RC complex at 2.64 Å resolution. Differing from the LH1 in the Hlr. halophila LH1-LH2 co-complex where LH1 encircles LH2, the RC-associated LH1 complex consists of 16 (rather than 18) αβ-subunits circularly surrounding the RC. These distinct forms of LH1 indicate that the number of subunits in a Hlr. halophila LH1 complex is flexible and its size is a function of the photocomplex it encircles. Like LH1 in the LH1-LH2 co-complex, the RC-associated LH1 complex also contained two forms of αβ-polypeptides and both dimeric and monomeric molecules of bacteriochlorophyll a. The majority of the isolated Hlr. halophila LH1-RC complexes contained the electron donor HiPIP bound to the surface of the RC cytochrome subunit near the heme-1 group. The bound HiPIP consisted of an N-terminal functional domain and a long C-terminal extension firmly attached to the cytochrome subunit. Despite overall highly negative surface-charge distributions for both the cytochrome subunit and HiPIP, the interface between the two proteins was relatively uncharged and neutral, forming a pathway for electron tunneling. The structure of the Hlr. halophila LH1-RC-HiPIP complex provides insights into the mechanism of light energy acquisition coupled with a long-distance electron donating process toward the charge separation site in a multi-extremophilic phototroph.


  • Organizational Affiliation

    Center for Computational Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, Japan. ktani@ccs.tsukuba.ac.jp.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center cytochrome c subunitA [auth C]362Halorhodospira halophilaMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein L chainB [auth L]276Halorhodospira halophilaMutation(s): 0 
UniProt
Find proteins for A0A2L1K3P0 (Halorhodospira halophila)
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Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2L1K3P0
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Reaction center protein M chainC [auth M]323Halorhodospira halophilaMutation(s): 0 
UniProt
Find proteins for A0A2L1K3T5 (Halorhodospira halophila)
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UniProt GroupA0A2L1K3T5
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosynthetic reaction center H subunitD [auth H]278Halorhodospira halophilaMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Antenna complex, alpha/beta subunit64Halorhodospira halophilaMutation(s): 0 
UniProt
Find proteins for A1WWW5 (Halorhodospira halophila (strain DSM 244 / SL1))
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UniProt GroupA1WWW5
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Antenna complex, alpha/beta subunit75Halorhodospira halophilaMutation(s): 0 
UniProt
Find proteins for A1WWW6 (Halorhodospira halophila (strain DSM 244 / SL1))
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UniProt GroupA1WWW6
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Antenna complex, alpha/beta subunit67Halorhodospira halophilaMutation(s): 0 
UniProt
Find proteins for A1WXF8 (Halorhodospira halophila (strain DSM 244 / SL1))
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UniProt GroupA1WXF8
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Antenna complex, alpha/beta subunit74Halorhodospira halophilaMutation(s): 0 
UniProt
Find proteins for A1WXF9 (Halorhodospira halophila (strain DSM 244 / SL1))
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UniProt GroupA1WXF9
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Small Molecules
Ligands 13 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CDL
Query on CDL

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EB [auth L]
FC [auth F]
GB [auth M]
LB [auth M]
MB [auth M]
CARDIOLIPIN
C81 H156 O17 P2
XVTUQDWPJJBEHJ-KZCWQMDCSA-L
BCL (Subject of Investigation/LOI)
Query on BCL

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AC [auth D]
AD [auth O]
AF [auth 7]
BC [auth D]
BD [auth P]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
BPH
Query on BPH

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IB [auth M],
VA [auth L]
BACTERIOPHEOPHYTIN A
C55 H76 N4 O6
KWOZSBGNAHVCKG-SZQBJALDSA-N
PGV
Query on PGV

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AB [auth L]
BB [auth L]
BF [auth 8]
CD [auth P]
CE [auth Z]
(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
Query on UQ8

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WA [auth L],
YA [auth L],
ZA [auth L]
Ubiquinone-8
C49 H74 O4
ICFIZJQGJAJRSU-SGHXUWJISA-N
MQ8
Query on MQ8

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JB [auth M]MENAQUINONE 8
C51 H72 O2
LXKDFTDVRVLXFY-ACMRXAIVSA-N
HEC
Query on HEC

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KA [auth C],
LA [auth C],
MA [auth C],
NA [auth C]
HEME C
C34 H34 Fe N4 O4
HXQIYSLZKNYNMH-LJNAALQVSA-N
CRT
Query on CRT

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CF [auth 8]
DE [auth Z]
GD [auth R]
IC [auth G]
KB [auth M]
SPIRILLOXANTHIN
C42 H60 O2
VAZQBTJCYODOSV-RISZBRKMSA-N
Z41
Query on Z41

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PA [auth C](2S)-3-hydroxypropane-1,2-diyl dihexadecanoate
C35 H68 O5
JEJLGIQLPYYGEE-XIFFEERXSA-N
LMT
Query on LMT

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AE [auth Y]
ED [auth Q]
FF [auth 9]
GC [auth F]
RA [auth C]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
PLM
Query on PLM

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QA [auth C]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
FE
Query on FE

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

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OA [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP21am0101118
Japan Agency for Medical Research and Development (AMED)JapanJP21am0101116
Japan Society for the Promotion of Science (JSPS)JapanJP16H04174
Japan Society for the Promotion of Science (JSPS)JapanJP18H05153
Japan Society for the Promotion of Science (JSPS)Japan20H05086
Japan Society for the Promotion of Science (JSPS)Japan20H02856

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release