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- PDB-8z81: Photosynthetic LH2-LH1 complex from the purple bacterium Halorhod... -

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Basic information

Entry
Database: PDB / ID: 8z81
TitlePhotosynthetic LH2-LH1 complex from the purple bacterium Halorhodospira halophila
Components(Antenna complex, alpha/beta ...) x 6
KeywordsPHOTOSYNTHESIS / LH2-LH1 COMPLEX
Function / homology
Function and homology information


organelle inner membrane / plasma membrane light-harvesting complex / bacteriochlorophyll binding / photosynthesis, light reaction / : / metal ion binding / plasma membrane
Similarity search - Function
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
Similarity search - Domain/homology
BACTERIOCHLOROPHYLL A / SPIRILLOXANTHIN / Chem-PGV / Antenna complex, alpha/beta subunit / Antenna complex, alpha/beta subunit / Antenna complex, alpha/beta subunit / Antenna complex, alpha/beta subunit / Antenna complex, alpha/beta subunit / Antenna complex, alpha/beta subunit
Similarity search - Component
Biological speciesHalorhodospira halophila (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.2 Å
AuthorsTani, K. / Nagashima, K.V.P. / Kanno, R. / Hiwatashi, N. / Kawakami, M. / Nakata, K. / Nagashima, S. / Inoue, K. / Takaichi, S. / Purba, E.R. ...Tani, K. / Nagashima, K.V.P. / Kanno, R. / Hiwatashi, N. / Kawakami, M. / 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.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED)JP21am0101118 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101116 Japan
Japan Society for the Promotion of Science (JSPS)JP16H04174 Japan
Japan Society for the Promotion of Science (JSPS)JP18H05153 Japan
Japan Society for the Promotion of Science (JSPS)20H05086 Japan
Japan Society for the Promotion of Science (JSPS)20H02856 Japan
CitationJournal: Nat Commun / Year: 2025
Title: A distinct double-ring LH1-LH2 photocomplex from an extremophilic phototroph.
Authors: Kazutoshi Tani / Kenji V P Nagashima / Risa Kojima / Masaharu Kondo / Ryo Kanno / Issei Satoh / Mai Kawakami / Naho Hiwatashi / Kazuna Nakata / Sakiko Nagashima / Kazuhito Inoue / Yugo Isawa ...Authors: Kazutoshi Tani / Kenji V P Nagashima / Risa Kojima / Masaharu Kondo / Ryo Kanno / Issei Satoh / Mai Kawakami / Naho Hiwatashi / Kazuna Nakata / Sakiko Nagashima / Kazuhito Inoue / Yugo Isawa / Ryoga Morishita / Shinichi Takaichi / Endang R Purba / Malgorzata Hall / Long-Jiang Yu / Michael T Madigan / Akira Mizoguchi / Bruno M Humbel / Yukihiro Kimura / Yutaka Nagasawa / Takehisa Dewa / Zheng-Yu Wang-Otomo /
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 ...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.
History
DepositionApr 21, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Antenna complex, alpha/beta subunit
B: Antenna complex, alpha/beta subunit
C: Antenna complex, alpha/beta subunit
D: Antenna complex, alpha/beta subunit
E: Antenna complex, alpha/beta subunit
F: Antenna complex, alpha/beta subunit
G: Antenna complex, alpha/beta subunit
H: Antenna complex, alpha/beta subunit
I: Antenna complex, alpha/beta subunit
J: Antenna complex, alpha/beta subunit
K: Antenna complex, alpha/beta subunit
L: Antenna complex, alpha/beta subunit
M: Antenna complex, alpha/beta subunit
N: Antenna complex, alpha/beta subunit
O: Antenna complex, alpha/beta subunit
P: Antenna complex, alpha/beta subunit
Q: Antenna complex, alpha/beta subunit
R: Antenna complex, alpha/beta subunit
S: Antenna complex, alpha/beta subunit
T: Antenna complex, alpha/beta subunit
U: Antenna complex, alpha/beta subunit
V: Antenna complex, alpha/beta subunit
W: Antenna complex, alpha/beta subunit
X: Antenna complex, alpha/beta subunit
Y: Antenna complex, alpha/beta subunit
Z: Antenna complex, alpha/beta subunit
1: Antenna complex, alpha/beta subunit
2: Antenna complex, alpha/beta subunit
3: Antenna complex, alpha/beta subunit
4: Antenna complex, alpha/beta subunit
5: Antenna complex, alpha/beta subunit
6: Antenna complex, alpha/beta subunit
7: Antenna complex, alpha/beta subunit
8: Antenna complex, alpha/beta subunit
9: Antenna complex, alpha/beta subunit
0: Antenna complex, alpha/beta subunit
a: Antenna complex, alpha/beta subunit
b: Antenna complex, alpha/beta subunit
c: Antenna complex, alpha/beta subunit
d: Antenna complex, alpha/beta subunit
e: Antenna complex, alpha/beta subunit
f: Antenna complex, alpha/beta subunit
g: Antenna complex, alpha/beta subunit
h: Antenna complex, alpha/beta subunit
i: Antenna complex, alpha/beta subunit
j: Antenna complex, alpha/beta subunit
k: Antenna complex, alpha/beta subunit
l: Antenna complex, alpha/beta subunit
m: Antenna complex, alpha/beta subunit
n: Antenna complex, alpha/beta subunit
o: Antenna complex, alpha/beta subunit
p: Antenna complex, alpha/beta subunit
q: Antenna complex, alpha/beta subunit
r: Antenna complex, alpha/beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)533,680225
Polymers407,36554
Non-polymers126,315171
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Antenna complex, alpha/beta ... , 6 types, 54 molecules AEIMQUY37BFJNRVZ48CGKOSW159DHL...

#1: Protein
Antenna complex, alpha/beta subunit


Mass: 7275.500 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halophila (bacteria) / Strain: BN9622 / References: UniProt: A1WWW5
#2: Protein
Antenna complex, alpha/beta subunit


Mass: 8068.154 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halophila (bacteria) / Strain: BN9622 / References: UniProt: A1WWW6
#3: Protein
Antenna complex, alpha/beta subunit


Mass: 7664.882 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halophila (bacteria) / Strain: BN9622 / References: UniProt: A1WXF8
#4: Protein
Antenna complex, alpha/beta subunit


Mass: 7893.913 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halophila (bacteria) / Strain: BN9622 / References: UniProt: A1WXF9
#5: Protein
Antenna complex, alpha/beta subunit


Mass: 7658.842 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halophila (bacteria) / Strain: BN9622 / References: UniProt: A1WWW3
#6: Protein
Antenna complex, alpha/beta subunit


Mass: 6701.490 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Halorhodospira halophila (bacteria) / Strain: BN9622 / References: UniProt: A1WWW2

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Sugars , 1 types, 45 molecules

#8: Sugar...
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 45 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 3 types, 126 molecules

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


Mass: 911.504 Da / Num. of mol.: 72 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-CRT / SPIRILLOXANTHIN / RHODOVIOLASCIN


Mass: 596.925 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C42H60O2
#10: 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.: 36 / Source method: obtained synthetically / Formula: C40H77O10P / 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

Component
IDNameTypeEntity IDParent-IDSource
1Photosynthetic LH2-LH1 complex from the purple phototrophic bacterium Halorhodospira halophilaCOMPLEX#1-#60NATURAL
2LH2-LH1 complex of Halorhodospira halophilaCOMPLEX#1-#61NATURAL
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
21Halorhodospira halophila (bacteria)1053BN9622
32Halorhodospira halophila (bacteria)1053BN9622
Buffer solutionpH: 8
SpecimenConc.: 6 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse.
VitrificationInstrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 1100 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
9RELION3.1initial Euler assignment
10RELION3.1final Euler assignment
11RELION3.1classification
12RELION3.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 331335
3D reconstructionResolution: 2.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 126108 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingB value: 70 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
15Y5S

5y5s

15Y5S1PDBexperimental model
21NKZ

1nkz

11NKZ2PDBexperimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00830636
ELECTRON MICROSCOPYf_angle_d3.64142300
ELECTRON MICROSCOPYf_dihedral_angle_d18.73812807
ELECTRON MICROSCOPYf_chiral_restr0.1084302
ELECTRON MICROSCOPYf_plane_restr0.0054743

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