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- PDB-8wdv: Photosynthetic LH1-RC complex from the purple sulfur bacterium Al... -

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Basic information

Entry
Database: PDB / ID: 8wdv
TitlePhotosynthetic LH1-RC complex from the purple sulfur bacterium Allochromatium vinosum purified by Ca2+-DEAE
Components
  • (Antenna complex alpha/beta ...) x 5
  • (Photosynthetic reaction center ...) x 2
  • (Reaction center protein ...) x 2
KeywordsPHOTOSYNTHESIS / LH1-RC COMPLEX / PURPLE SULFUR BACTERIA
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 / electron transfer activity / iron ion binding / heme 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 / 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, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Multiheme cytochrome c family profile. / Antenna complex, alpha/beta subunit / Light-harvesting protein B beta chain / Antenna complex, beta domain superfamily ...Photosynthetic reaction centre, cytochrome c subunit / Multihaem cytochrome, PRC subunit superfamily / Photosynthetic reaction centre cytochrome C subunit / Antenna complex, alpha subunit / Antenna complex, alpha subunit conserved site / Antenna complexes alpha subunits signature. / Multiheme cytochrome c family profile. / 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 / PRC-barrel domain / Photosynthetic reaction centre, H subunit, N-terminal domain superfamily / Photosynthetic reaction centre, H-chain N-terminal region / 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
BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / SPIRILLOXANTHIN / : / PROTOPORPHYRIN IX CONTAINING FE / MENAQUINONE 8 / Chem-PGV / PALMITIC ACID / Ubiquinone-8 ...BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / SPIRILLOXANTHIN / : / PROTOPORPHYRIN IX CONTAINING FE / MENAQUINONE 8 / Chem-PGV / PALMITIC ACID / Ubiquinone-8 / (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate / 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 / Photosynthetic reaction center H subunit / Photosynthetic reaction center cytochrome c subunit / Reaction center protein L chain / Reaction center protein M chain
Similarity search - Component
Biological speciesAllochromatium vinosum DSM 180 (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.24 Å
AuthorsTani, K. / Kanno, R. / Harada, A. / Kobayashi, A. / Minamino, A. / Nakamura, N. / Ji, X.-C. / Purba, E.R. / Hall, M. / Yu, L.-J. ...Tani, K. / Kanno, R. / Harada, A. / Kobayashi, A. / Minamino, A. / Nakamura, N. / Ji, X.-C. / Purba, E.R. / Hall, M. / Yu, L.-J. / Madigan, M.T. / Mizoguchi, A. / Iwasaki, K. / 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: Commun Biol / Year: 2024
Title: High-resolution structure and biochemical properties of the LH1-RC photocomplex from the model purple sulfur bacterium, Allochromatium vinosum.
Authors: Kazutoshi Tani / Ryo Kanno / Ayaka Harada / Yuki Kobayashi / Akane Minamino / Shinji Takenaka / Natsuki Nakamura / Xuan-Cheng Ji / Endang R Purba / Malgorzata Hall / Long-Jiang Yu / Michael ...Authors: Kazutoshi Tani / Ryo Kanno / Ayaka Harada / Yuki Kobayashi / Akane Minamino / Shinji Takenaka / Natsuki Nakamura / Xuan-Cheng Ji / Endang R Purba / Malgorzata Hall / Long-Jiang Yu / Michael T Madigan / Akira Mizoguchi / Kenji Iwasaki / Bruno M Humbel / Yukihiro Kimura / Zheng-Yu Wang-Otomo /
Abstract: The mesophilic purple sulfur phototrophic bacterium Allochromatium (Alc.) vinosum (bacterial family Chromatiaceae) has been a favored model for studies of bacterial photosynthesis and sulfur ...The mesophilic purple sulfur phototrophic bacterium Allochromatium (Alc.) vinosum (bacterial family Chromatiaceae) has been a favored model for studies of bacterial photosynthesis and sulfur metabolism, and its core light-harvesting (LH1) complex has been a focus of numerous studies of photosynthetic light reactions. However, despite intense efforts, no high-resolution structure and thorough biochemical analysis of the Alc. vinosum LH1 complex have been reported. Here we present cryo-EM structures of the Alc. vinosum LH1 complex associated with reaction center (RC) at 2.24 Å resolution. The overall structure of the Alc. vinosum LH1 resembles that of its moderately thermophilic relative Alc. tepidum in that it contains multiple pigment-binding α- and β-polypeptides. Unexpectedly, however, six Ca ions were identified in the Alc. vinosum LH1 bound to certain α1/β1- or α1/β3-polypeptides through a different Ca-binding motif from that seen in Alc. tepidum and other Chromatiaceae that contain Ca-bound LH1 complexes. Two water molecules were identified as additional Ca-coordinating ligands. Based on these results, we reexamined biochemical and spectroscopic properties of the Alc. vinosum LH1-RC. While modest but distinct effects of Ca were detected in the absorption spectrum of the Alc. vinosum LH1 complex, a marked decrease in thermostability of its LH1-RC complex was observed upon removal of Ca. The presence of Ca in the photocomplex of Alc. vinosum suggests that Ca-binding to LH1 complexes may be a common adaptation in species of Chromatiaceae for conferring spectral and thermal flexibility on this key component of their photosynthetic machinery.
History
DepositionSep 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 20, 2024Group: Data collection / Structure summary
Category: em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
A: Antenna complex alpha/beta subunit
B: 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
I: Antenna complex alpha/beta subunit
J: Antenna complex alpha/beta subunit
K: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)396,514147
Polymers320,21336
Non-polymers76,302111
Water6,377354
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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Photosynthetic reaction center ... , 2 types, 2 molecules CH

#1: Protein Photosynthetic reaction center cytochrome c subunit


Mass: 41512.555 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Allochromatium vinosum DSM 180 (bacteria) / Strain: DSM 180 / References: UniProt: O82947
#4: Protein Photosynthetic reaction center H subunit


Mass: 28231.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Allochromatium vinosum DSM 180 (bacteria) / Strain: DSM 180 / References: UniProt: D3RPF6

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

#2: Protein Reaction center protein L chain


Mass: 31217.410 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Allochromatium vinosum DSM 180 (bacteria) / Strain: DSM 180 / References: UniProt: P51762
#3: Protein Reaction center protein M chain


Mass: 36364.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Allochromatium vinosum DSM 180 (bacteria) / Strain: DSM 180 / References: UniProt: P51763

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Antenna complex alpha/beta ... , 5 types, 32 molecules AIKOQ1579BJNPR24680DFSUWYEGTVXZ3

#5: Protein/peptide
Antenna complex alpha/beta subunit


Mass: 5136.131 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Allochromatium vinosum DSM 180 (bacteria) / Strain: DSM 180 / References: UniProt: D3RP69
#6: Protein/peptide
Antenna complex alpha/beta subunit


Mass: 5269.103 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Allochromatium vinosum DSM 180 (bacteria) / Strain: DSM 180 / References: UniProt: D3RP75
#7: Protein
Antenna complex alpha/beta subunit


Mass: 7244.583 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Allochromatium vinosum DSM 180 (bacteria) / Strain: DSM 180 / References: UniProt: D3RP74
#8: Protein/peptide
Antenna complex alpha/beta subunit


Mass: 5518.472 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Allochromatium vinosum DSM 180 (bacteria) / Strain: DSM 180 / References: UniProt: D3RP68
#9: Protein Antenna complex alpha/beta subunit


Mass: 7392.857 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Allochromatium vinosum DSM 180 (bacteria) / Strain: DSM 180 / References: UniProt: D3RP67

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Sugars , 1 types, 19 molecules

#24: Sugar
ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE


Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C24H46O11 / Comment: detergent*YM

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Non-polymers , 15 types, 446 molecules

#10: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#11: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#12: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#13: Chemical ChemComp-Z41 / (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate


Mass: 568.911 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H68O5
#14: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#15: 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.: 10 / Source method: obtained synthetically / Formula: C40H77O10P / Comment: phospholipid*YM
#16: Chemical...
ChemComp-BCL / BACTERIOCHLOROPHYLL A


Mass: 911.504 Da / Num. of mol.: 36 / Source method: obtained synthetically / Formula: C55H74MgN4O6 / Feature type: SUBJECT OF INVESTIGATION
#17: Chemical ChemComp-BPH / BACTERIOPHEOPHYTIN A


Mass: 889.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C55H76N4O6
#18: 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.: 3 / Source method: obtained synthetically / Formula: C49H74O4
#19: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#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.: 1 / Source method: obtained synthetically / Formula: C51H72O2
#21: Chemical
ChemComp-CRT / SPIRILLOXANTHIN / RHODOVIOLASCIN


Mass: 596.925 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C42H60O2
#22: 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.: 5 / Source method: obtained synthetically / Formula: C81H156O17P2 / Comment: phospholipid*YM
#23: Chemical ChemComp-LDA / LAURYL DIMETHYLAMINE-N-OXIDE


Mass: 229.402 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H31NO / Comment: LDAO, detergent*YM
#25: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / Source method: isolated from a natural source / Formula: H2O

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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: Photosynthetic LH1-RC complex from the purple sulfur phototrophic bacterium Allochromatium vinosum
Type: COMPLEX / Entity ID: #1-#9 / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Allochromatium vinosum DSM 180 (bacteria)
Buffer solutionpH: 7.5
SpecimenConc.: 5.2 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: 2600 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 30.15 sec. / Electron 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: 833998
3D reconstructionResolution: 2.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 219233 / Symmetry type: POINT
Atomic model buildingB value: 63 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient
Atomic model buildingPDB-ID: 7VRJ

7vrj


Accession code: 7VRJ / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00626918
ELECTRON MICROSCOPYf_angle_d2.80737014
ELECTRON MICROSCOPYf_dihedral_angle_d15.62810508
ELECTRON MICROSCOPYf_chiral_restr0.093801
ELECTRON MICROSCOPYf_plane_restr0.0054380

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