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Yorodumi- EMDB-4033: In situ atomic-resolution structure of the baseplate antenna comp... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4033 | |||||||||||||||
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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 | |||||||||||||||
Map data | 3D reconstruction of the carotenosome CsmA-Bchl a baseplate obtained by cryo electron microscopy | |||||||||||||||
Sample |
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Keywords | photosynthesis / light-harvesting protein / binds bacteriochlorophyll a / oligomeric complex / bacteriochlorophyll binding protein | |||||||||||||||
Function / homology | chlorosome envelope / Bacteriochlorophyll c-binding protein / Bacteriochlorophyll c-binding superfamily / Bacteriochlorophyll C binding protein / bacteriochlorophyll binding / photosynthesis / metal ion binding / Bacteriochlorophyll c-binding protein Function and homology information | |||||||||||||||
Biological species | Chlorobaculum tepidum (bacteria) / Chlorobium tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS) (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 26.5 Å | |||||||||||||||
Authors | Nielsen JT / Kulminskaya NV | |||||||||||||||
Funding support | Denmark, Estonia, Hungary, 4 items
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Citation | 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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4033.map.gz | 10.9 MB | EMDB map data format | |
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Header (meta data) | emd-4033-v30.xml emd-4033.xml | 14.5 KB 14.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4033_fsc.xml | 10.6 KB | Display | FSC data file |
Images | emd_4033.png | 102.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4033 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4033 | HTTPS FTP |
-Validation report
Summary document | emd_4033_validation.pdf.gz | 430.6 KB | Display | EMDB validaton report |
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Full document | emd_4033_full_validation.pdf.gz | 430.2 KB | Display | |
Data in XML | emd_4033_validation.xml.gz | 11.4 KB | Display | |
Data in CIF | emd_4033_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4033 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4033 | HTTPS FTP |
-Related structure data
Related structure data | 5lcbMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_4033.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | 3D reconstruction of the carotenosome CsmA-Bchl a baseplate obtained by cryo electron microscopy | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Carotenosome organelle consisting of csma proteins and bchla ante...
Entire | Name: Carotenosome organelle consisting of csma proteins and bchla antenna molecules. |
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Components |
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-Supramolecule #1: Carotenosome organelle consisting of csma proteins and bchla ante...
Supramolecule | Name: Carotenosome organelle consisting of csma proteins and bchla antenna molecules. type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 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 |
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Source (natural) | Organism: Chlorobaculum tepidum (bacteria) / Organelle: carotenosome |
-Macromolecule #1: Bacteriochlorophyll c-binding protein
Macromolecule | Name: Bacteriochlorophyll c-binding protein / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO |
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Source (natural) | Organism: Chlorobium tepidum (strain ATCC 49652 / DSM 12025 / NBRC 103806 / TLS) (bacteria) |
Molecular weight | Theoretical: 6.160034 KDa |
Recombinant expression | Organism: Chlorobaculum tepidum (bacteria) |
Sequence | String: MSGGGVFTDI LAAAGRIFEV MVEGHWETVG MLFDSLGKGT MRINRNAYGS MGGGSLRGS UniProtKB: Bacteriochlorophyll c-binding protein |
-Macromolecule #2: BACTERIOCHLOROPHYLL A
Macromolecule | Name: BACTERIOCHLOROPHYLL A / type: ligand / ID: 2 / Number of copies: 14 / Formula: BCL |
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Molecular weight | Theoretical: 911.504 Da |
Chemical component information | ChemComp-BCL: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R2/4 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK II |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 270 / Average electron dose: 8.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated defocus max: 4.0 µm / Calibrated defocus min: 1.7 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |