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Yorodumi- PDB-5lcb: In situ atomic-resolution structure of the baseplate antenna comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lcb | |||||||||||||||
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Title | In situ atomic-resolution structure of the baseplate antenna complex in Chlorobaculum tepidum obtained combining solid-state NMR spectroscopy, cryo electron microscopy and polarization spectroscopy | |||||||||||||||
Components | Bacteriochlorophyll c-binding protein | |||||||||||||||
Keywords | bacteriochlorophyll binding protein / photosynthesis / light-harvesting protein / binds bacteriochlorophyll a / oligomeric complex | |||||||||||||||
Function / homology | chlorosome envelope / Bacteriochlorophyll c-binding protein / Bacteriochlorophyll c-binding superfamily / Bacteriochlorophyll C binding protein / bacteriochlorophyll binding / photosynthesis / metal ion binding / BACTERIOCHLOROPHYLL A / Bacteriochlorophyll c-binding protein Function and homology information | |||||||||||||||
Biological species | Chlorobium tepidum (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / SOLID-STATE NMR / single particle reconstruction / torsion angle dynamics / cryo EM / Resolution: 26.5 Å | |||||||||||||||
Authors | Nielsen, J.T. / Kulminskaya, N.V. / Bjerring, M. / Linnanto, J.M. / Ratsep, M. / Pedersen, M. / Lambrev, P.H. / Dorogi, M. / Garab, G. / Thomsen, K. ...Nielsen, J.T. / Kulminskaya, N.V. / Bjerring, M. / Linnanto, J.M. / Ratsep, M. / Pedersen, M. / Lambrev, P.H. / Dorogi, M. / Garab, G. / Thomsen, K. / Jegerschold, C. / Frigaard, N.U. / Lindahl, M. / Nielsen, N.C. | |||||||||||||||
Funding support | Denmark, Estonia, Hungary, 4items
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Citation | Journal: Nat Commun / Year: 2016 Title: In situ high-resolution structure of the baseplate antenna complex in Chlorobaculum tepidum. Authors: Jakob Toudahl Nielsen / Natalia V Kulminskaya / Morten Bjerring / Juha M Linnanto / Margus Rätsep / Marie Østergaard Pedersen / Petar H Lambrev / Márta Dorogi / Győző Garab / Karen ...Authors: Jakob Toudahl Nielsen / Natalia V Kulminskaya / Morten Bjerring / Juha M Linnanto / Margus Rätsep / Marie Østergaard Pedersen / Petar H Lambrev / Márta Dorogi / Győző Garab / Karen Thomsen / Caroline Jegerschöld / Niels-Ulrik Frigaard / Martin Lindahl / Niels Chr Nielsen / Abstract: Photosynthetic antenna systems enable organisms harvesting light and transfer the energy to the photosynthetic reaction centre, where the conversion to chemical energy takes place. One of the most ...Photosynthetic antenna systems enable organisms harvesting light and transfer the energy to the photosynthetic reaction centre, where the conversion to chemical energy takes place. One of the most complex antenna systems, the chlorosome, found in the photosynthetic green sulfur bacterium Chlorobaculum (Cba.) tepidum contains a baseplate, which is a scaffolding super-structure, formed by the protein CsmA and bacteriochlorophyll a. Here we present the first high-resolution structure of the CsmA baseplate using intact fully functional, light-harvesting organelles from Cba. tepidum, following a hybrid approach combining five complementary methods: solid-state NMR spectroscopy, cryo-electron microscopy, isotropic and anisotropic circular dichroism and linear dichroism. The structure calculation was facilitated through development of new software, GASyCS for efficient geometry optimization of highly symmetric oligomeric structures. We show that the baseplate is composed of rods of repeated dimers of the strongly amphipathic CsmA with pigments sandwiched within the dimer at the hydrophobic side of the helix. #1: Journal: Angew Chem Int Ed Engl / Year: 2012 Title: In situ solid-state NMR spectroscopy of protein in heterogeneous membranes: the baseplate antenna complex of Chlorobaculum tepidum. Authors: Natalia V Kulminskaya / Marie Ø Pedersen / Morten Bjerring / Jarl Underhaug / Mette Miller / Niels-Ulrik Frigaard / Jakob T Nielsen / Niels Chr Nielsen / Abstract: A clever combination: an in situ solid-state NMR analysis of CsmA proteins in the heterogeneous environment of the photoreceptor of Chlorobaculum tepidum is reported. Using different combinations of ...A clever combination: an in situ solid-state NMR analysis of CsmA proteins in the heterogeneous environment of the photoreceptor of Chlorobaculum tepidum is reported. Using different combinations of 2D and 3D solid-state NMR spectra, 90 % of the CsmA resonances are assigned and provide on the basis of chemical shift data information about the structure and conformation of CsmA in the CsmA-bacteriochlorophyll a complex. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5lcb.cif.gz | 291.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lcb.ent.gz | 249.4 KB | Display | PDB format |
PDBx/mmJSON format | 5lcb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/5lcb ftp://data.pdbj.org/pub/pdb/validation_reports/lc/5lcb | HTTPS FTP |
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-Related structure data
Related structure data | 4033MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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NMR ensembles |
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-Components
#1: Protein | Mass: 6160.034 Da / Num. of mol.: 14 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chlorobium tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS) (bacteria) Gene: csmA, CT1942 / Production host: Chlorobaculum tepidum (bacteria) / References: UniProt: P0A314 #2: Chemical | ChemComp-BCL / |
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-Experimental details
-Experiment
Experiment |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
NMR experiment |
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-Sample preparation
Component | Name: Carotenosome organelle consisting of csma proteins and bchla antenna molecules. Type: ORGANELLE OR CELLULAR COMPONENT Details: Cryo-EM data of the ice-embedded isolated carotenosomes reveals molecular complex structure. Captured images clearly show supramolecular organization of the protein rows, originating from ...Details: Cryo-EM data of the ice-embedded isolated carotenosomes reveals molecular complex structure. Captured images clearly show supramolecular organization of the protein rows, originating from the BChl a - CsmA baseplate Entity ID: #1 / Source: NATURAL | ||||||||||||||||||||||||
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Source (natural) | Organism: Chlorobaculum tepidum (bacteria) / Organelle: carotenosome | ||||||||||||||||||||||||
Buffer solution | pH: 8 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/4 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 K | ||||||||||||||||||||||||
Details | Type: solid Contents: 10.0 % [U-13C; U-15N] CsmA, 10.0 % [U-13C; U-15N] BACTERIOCHLOROPHYLL A, 35.0 % [U-13C] Carotenoids, 35.0 % [U-13C] Lipids, 10.0 % n.a. Magnesium ion, solid state, lyophylized Details: Stoichiometric amounts of CsmA, BChl a, and Mg2+. Excess of carotenoids and lipids. Label: U15N13C / Solvent system: solid state, lyophylized | ||||||||||||||||||||||||
Sample |
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Sample conditions | Details: solid state / Ionic strength: 0.0 M / Label: U / pH: 7.0 Not defined / Pressure: 1 atm / Temperature: 280 K |
-Data collection
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company | ||||||||||||||||||
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Microscopy | Model: FEI TITAN KRIOS | ||||||||||||||||||
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM | ||||||||||||||||||
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated defocus min: 1700 nm / Calibrated defocus max: 4000 nm | ||||||||||||||||||
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER | ||||||||||||||||||
Image recording | Electron dose: 8 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Num. of real images: 270 | ||||||||||||||||||
NMR spectrometer |
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-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING ONLY | |||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1790 | |||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 26.5 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 1790 / Algorithm: BACK PROJECTION / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 5 | |||||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: target function and agreement with back-calculated cd spectra | |||||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 80 / Conformers submitted total number: 1 |