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Yorodumi- PDB-7vrj: STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF Allochromatiu... -
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-Basic information
Entry | Database: PDB / ID: 7vrj | |||||||||||||||||||||
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Title | STRUCTURE OF PHOTOSYNTHETIC LH1-RC SUPER-COMPLEX OF Allochromatium tepidum | |||||||||||||||||||||
Components |
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Keywords | PHOTOSYNTHESIS / LH1-RC COMPLEX / PURPLE BACTERIA | |||||||||||||||||||||
Function / homology | Function and homology information BACTERIOCHLOROPHYLL A / BACTERIOPHEOPHYTIN A / CARDIOLIPIN / SPIRILLOXANTHIN / DIACYL GLYCEROL / : / HEME C / MENAQUINONE 8 / Chem-PGV / PALMITIC ACID / Ubiquinone-8 Similarity search - Component | |||||||||||||||||||||
Biological species | Allochromatium tepidum (bacteria) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.81 Å | |||||||||||||||||||||
Authors | Tani, K. / Kobayashi, K. / Hosogi, N. / Ji, X.-C. / Nagashima, S. / Nagashima, K.V.P. / Tsukatani, Y. / Kanno, R. / Hall, M. / Yu, L.-J. ...Tani, K. / Kobayashi, K. / Hosogi, N. / Ji, X.-C. / Nagashima, S. / Nagashima, K.V.P. / Tsukatani, Y. / Kanno, R. / Hall, M. / Yu, L.-J. / Ishikawa, I. / Okura, Y. / Madigan, M.T. / Mizoguchi, A. / Humbel, B.M. / Kimura, Y. / Wang-Otomo, Z.-Y. | |||||||||||||||||||||
Funding support | Japan, 6items
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Citation | Journal: J Biol Chem / Year: 2022 Title: A Ca-binding motif underlies the unusual properties of certain photosynthetic bacterial core light-harvesting complexes. Authors: Kazutoshi Tani / Kazumi Kobayashi / Naoki Hosogi / Xuan-Cheng Ji / Sakiko Nagashima / Kenji V P Nagashima / Airi Izumida / Kazuhito Inoue / Yusuke Tsukatani / Ryo Kanno / Malgorzata Hall / ...Authors: Kazutoshi Tani / Kazumi Kobayashi / Naoki Hosogi / Xuan-Cheng Ji / Sakiko Nagashima / Kenji V P Nagashima / Airi Izumida / Kazuhito Inoue / Yusuke Tsukatani / Ryo Kanno / Malgorzata Hall / Long-Jiang Yu / Isamu Ishikawa / Yoshihiro Okura / Michael T Madigan / Akira Mizoguchi / Bruno M Humbel / Yukihiro Kimura / Zheng-Yu Wang-Otomo / Abstract: The mildly thermophilic purple phototrophic bacterium Allochromatium tepidum provides a unique model for investigating various intermediate phenotypes observed between those of thermophilic and ...The mildly thermophilic purple phototrophic bacterium Allochromatium tepidum provides a unique model for investigating various intermediate phenotypes observed between those of thermophilic and mesophilic counterparts. The core light-harvesting (LH1) complex from A. tepidum exhibits an absorption maximum at 890 nm and mildly enhanced thermostability, both of which are Ca-dependent. However, it is unknown what structural determinants might contribute to these properties. Here, we present a cryo-EM structure of the reaction center-associated LH1 complex at 2.81 Å resolution, in which we identify multiple pigment-binding α- and β-polypeptides within an LH1 ring. Of the 16 α-polypeptides, we show that six (α1) bind Ca along with β1- or β3-polypeptides to form the Ca-binding sites. This structure differs from that of fully Ca-bound LH1 from Thermochromatium tepidum, enabling determination of the minimum structural requirements for Ca-binding. We also identified three amino acids (Trp44, Asp47, and Ile49) in the C-terminal region of the A. tepidum α1-polypeptide that ligate each Ca ion, forming a Ca-binding WxxDxI motif that is conserved in all Ca-bound LH1 α-polypeptides from other species with reported structures. The partial Ca-bound structure further explains the unusual phenotypic properties observed for this bacterium in terms of its Ca-requirements for thermostability, spectroscopy, and phototrophic growth, and supports the hypothesis that A. tepidum may represent a "transitional" species between mesophilic and thermophilic purple sulfur bacteria. The characteristic arrangement of multiple αβ-polypeptides also suggests a mechanism of molecular recognition in the expression and/or assembly of the LH1 complex that could be regulated through interactions with reaction center subunits. | |||||||||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7vrj.cif.gz | 567.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7vrj.ent.gz | 511.9 KB | Display | PDB format |
PDBx/mmJSON format | 7vrj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/7vrj ftp://data.pdbj.org/pub/pdb/validation_reports/vr/7vrj | HTTPS FTP |
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-Related structure data
Related structure data | 32100MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Photosynthetic reaction center ... , 4 types, 4 molecules CLMH
#1: Protein | Mass: 43659.016 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Allochromatium tepidum (bacteria) |
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#2: Protein | Mass: 31098.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Allochromatium tepidum (bacteria) |
#3: Protein | Mass: 36292.117 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Allochromatium tepidum (bacteria) |
#4: Protein | Mass: 28196.340 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Allochromatium tepidum (bacteria) |
-Light-harvesting protein LH1 ... , 5 types, 32 molecules AIKOQ1579BJNPR24680DFSUWYEGTVXZ3
#5: Protein/peptide | Mass: 5136.131 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Allochromatium tepidum (bacteria) #6: Protein/peptide | Mass: 5269.103 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Allochromatium tepidum (bacteria) #7: Protein | Mass: 7330.739 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Allochromatium tepidum (bacteria) #8: Protein/peptide | Mass: 5504.446 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Allochromatium tepidum (bacteria) #9: Protein | | Mass: 7323.753 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Allochromatium tepidum (bacteria) |
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-Sugars , 1 types, 18 molecules
#22: Sugar | ChemComp-LMT / |
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-Non-polymers , 15 types, 144 molecules
#10: Chemical | ChemComp-HEC / #11: Chemical | ChemComp-MG / | #12: Chemical | ChemComp-DGA / | #13: Chemical | ChemComp-PLM / | #14: Chemical | ChemComp-PGV / ( #15: Chemical | ChemComp-BCL / #16: Chemical | #17: Chemical | #18: Chemical | ChemComp-CDL / #19: Chemical | ChemComp-FE / | #20: Chemical | #21: Chemical | ChemComp-CRT / #23: Chemical | ChemComp-CA / #24: Chemical | #25: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Photosynthetic LH1-RC complex from the purple phototrophic bacterium Allochromatium tepidum Type: COMPLEX / Entity ID: #1-#9 / Source: NATURAL |
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Molecular weight | Units: MEGADALTONS / Experimental value: NO |
Source (natural) | Organism: Allochromatium tepidum (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse. |
Vitrification | Instrument: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K |
-Electron microscopy imaging
Microscopy | Model: JEOL CRYO ARM 300 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Alignment procedure: BASIC |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: JEOL |
Image recording | Average exposure time: 1.5 sec. / Electron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | ||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 309706 | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 156992 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 62 / Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Correlation coefficient | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 5Y5S | ||||||||||||||||||||||||||||||||||||
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