8Z81

Photosynthetic LH2-LH1 complex from the purple bacterium Halorhodospira halophila


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

A distinct double-ring LH1-LH2 photocomplex from an extremophilic phototroph.

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

(2025) Nat Commun 16: 1410-1410

  • DOI: https://doi.org/10.1038/s41467-024-55811-9
  • Primary Citation of Related Structures:  
    8Z81

  • PubMed Abstract: 

    Halorhodospira (Hlr.) halophila strain BN9622 is an extremely halophilic and alkaliphilic phototrophic purple sulfur bacterium isolated from a hypersaline lake in the Libyan Desert whose total salinity exceeded 35% at pH 10.7. Here we present a cryo-EM structure of the native LH1-LH2 co-complex from strain BN9622 at 2.22 Å resolution. Surprisingly, the LH1-LH2 co-complex consists of a double-ring cylindrical structure with the larger LH1 ring encircling a smaller LH2 ring. The Hlr. halophila LH1 contains 18 αβ-subunits and additional bacteriochlorophyll a (BChl a) molecules that absorb maximally at 797 nm. The LH2 ring is composed of 9 αβ-subunits, and the BChl a molecules in the co-complex form extensive intra- and inter-complex networks to allow near 100% efficiency of energy transfer to its surrounding LH1. The additional LH1-B797 BChls a are located in such a manner that they facilitate exciton transfer from monomeric BChls in LH2 to the dimeric BChls in LH1. The structural features of the strain BN9622 LH1-LH2 co-complex may have evolved to allow a minimal LH2 complex to maximize excitation transfer to the core complex and effectively harvest light in the physiologically demanding ecological niche of this purple bacterium.


  • Organizational Affiliation

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


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antenna complex, alpha/beta subunit64Halorhodospira halophilaMutation(s): 0 
UniProt
Find proteins for A1WWW5 (Halorhodospira halophila (strain DSM 244 / SL1))
Explore A1WWW5 
Go to UniProtKB:  A1WWW5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1WWW5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Antenna complex, alpha/beta subunit75Halorhodospira halophilaMutation(s): 0 
UniProt
Find proteins for A1WWW6 (Halorhodospira halophila (strain DSM 244 / SL1))
Explore A1WWW6 
Go to UniProtKB:  A1WWW6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1WWW6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Antenna complex, alpha/beta subunit67Halorhodospira halophilaMutation(s): 0 
UniProt
Find proteins for A1WXF8 (Halorhodospira halophila (strain DSM 244 / SL1))
Explore A1WXF8 
Go to UniProtKB:  A1WXF8
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UniProt GroupA1WXF8
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Antenna complex, alpha/beta subunit74Halorhodospira halophilaMutation(s): 0 
UniProt
Find proteins for A1WXF9 (Halorhodospira halophila (strain DSM 244 / SL1))
Explore A1WXF9 
Go to UniProtKB:  A1WXF9
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UniProt GroupA1WXF9
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Antenna complex, alpha/beta subunit71Halorhodospira halophilaMutation(s): 0 
UniProt
Find proteins for A1WWW3 (Halorhodospira halophila (strain DSM 244 / SL1))
Explore A1WWW3 
Go to UniProtKB:  A1WWW3
Entity Groups  
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UniProt GroupA1WWW3
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Antenna complex, alpha/beta subunit59Halorhodospira halophilaMutation(s): 0 
UniProt
Find proteins for A1WWW2 (Halorhodospira halophila (strain DSM 244 / SL1))
Explore A1WWW2 
Go to UniProtKB:  A1WWW2
Entity Groups  
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UniProt GroupA1WWW2
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BCL (Subject of Investigation/LOI)
Query on BCL

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AC [auth I]
AE [auth 1]
AF [auth 9]
BD [auth R]
BE [auth 1]
BACTERIOCHLOROPHYLL A
C55 H74 Mg N4 O6
DSJXIQQMORJERS-AGGZHOMASA-M
PGV
Query on PGV

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AH [auth m]
CD [auth R]
EC [auth J]
EG [auth g]
FE [auth 2]
(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
CRT
Query on CRT

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AD [auth R]
CC [auth J]
DH [auth o]
EB [auth B]
GG [auth h]
SPIRILLOXANTHIN
C42 H60 O2
VAZQBTJCYODOSV-RISZBRKMSA-N
LMT
Query on LMT

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AG [auth f]
BC [auth I]
BF [auth 9]
BH [auth n]
CE [auth 1]
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CXM
Query on CXM
AB [auth q]
KA [auth a]
MA [auth c]
OA [auth e]
QA [auth g]
L-PEPTIDE LINKINGC6 H11 N O4 SMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.20 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: 2025-02-19
    Type: Initial release