+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3163 | |||||||||
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Title | Single-particle reconstruction of negatively stained SufBCD | |||||||||
Map data | Reconstruction of SufBCD. The particle images were low-pass filtered before refinement. The FSC that was calculated using eotest shows higher values than 0.5 every frequencies. | |||||||||
Sample |
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Keywords | Iron-sulfur cluster / ABC-ATPase / Suf machinery / ABC-transporter | |||||||||
Biological species | Escherichia coli K-12 (bacteria) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 30.0 Å | |||||||||
Authors | Hirabayashi K / Yuda E / Tanaka N / Katayama S / Iwasaki K / Matsumoto T / Kurisu G / Outten FW / Fukuyama K / Takahashi Y / Wada K | |||||||||
Citation | Journal: J Biol Chem / Year: 2015 Title: Functional Dynamics Revealed by the Structure of the SufBCD Complex, a Novel ATP-binding Cassette (ABC) Protein That Serves as a Scaffold for Iron-Sulfur Cluster Biogenesis. Authors: Kei Hirabayashi / Eiki Yuda / Naoyuki Tanaka / Sumie Katayama / Kenji Iwasaki / Takashi Matsumoto / Genji Kurisu / F Wayne Outten / Keiichi Fukuyama / Yasuhiro Takahashi / Kei Wada / Abstract: ATP-binding cassette (ABC)-type ATPases are chemomechanical engines involved in diverse biological pathways. Recent genomic information reveals that ABC ATPase domains/subunits act not only in ABC ...ATP-binding cassette (ABC)-type ATPases are chemomechanical engines involved in diverse biological pathways. Recent genomic information reveals that ABC ATPase domains/subunits act not only in ABC transporters and structural maintenance of chromosome proteins, but also in iron-sulfur (Fe-S) cluster biogenesis. A novel type of ABC protein, the SufBCD complex, functions in the biosynthesis of nascent Fe-S clusters in almost all Eubacteria and Archaea, as well as eukaryotic chloroplasts. In this study, we determined the first crystal structure of the Escherichia coli SufBCD complex, which exhibits the common architecture of ABC proteins: two ABC ATPase components (SufC) with function-specific components (SufB-SufD protomers). Biochemical and physiological analyses based on this structure provided critical insights into Fe-S cluster assembly and revealed a dynamic conformational change driven by ABC ATPase activity. We propose a molecular mechanism for the biogenesis of the Fe-S cluster in the SufBCD 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_3163.map.gz | 425.1 KB | EMDB map data format | |
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Header (meta data) | emd-3163-v30.xml emd-3163.xml | 9.4 KB 9.4 KB | Display Display | EMDB header |
Images | EMD-3163.png | 108.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3163 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3163 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3163.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of SufBCD. The particle images were low-pass filtered before refinement. The FSC that was calculated using eotest shows higher values than 0.5 every frequencies. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.2 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 : SufBCD
Entire | Name: SufBCD |
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Components |
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-Supramolecule #1000: SufBCD
Supramolecule | Name: SufBCD / type: sample / ID: 1000 / Details: The sample was monodisperse. Oligomeric state: One of a couple of the SufC subunits binds to the SufB protomer of the heterodimeric complex of SufB and SufD. The other SufC subunit binds to the SufD protomer. Number unique components: 3 |
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Molecular weight | Experimental: 160 KDa / Theoretical: 156.7 KDa Method: Size-exclusion chromatography and Dynamic light scattering |
-Macromolecule #1: SufBCD
Macromolecule | Name: SufBCD / type: protein_or_peptide / ID: 1 Details: Carbon coated grid. Negatively staining with uranyl acetate. Oligomeric state: Heterotetramer / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli K-12 (bacteria) / Location in cell: Cytosol |
Molecular weight | Experimental: 160 KDa / Theoretical: 156.7 KDa |
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Staining | Type: NEGATIVE / Details: 2% Uranyl acetate |
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Grid | Details: Carbon coated grid. |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | HITACHI H-9500SD |
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Electron beam | Acceleration voltage: 200 kV / Electron source: LAB6 |
Electron optics | Calibrated magnification: 109091 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.8 mm / Nominal magnification: 80000 |
Sample stage | Specimen holder: Room temperature / Specimen holder model: OTHER |
Temperature | Average: 293 K |
Date | Jan 21, 2009 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F224 (2k x 2k) / Digitization - Sampling interval: 24 µm |
-Image processing
CTF correction | Details: No correction |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: OTHER / Software - Name: EMAN1 Details: Particles images were lowpass-filtered at 30A before refinement. Therefore, FSC shows higher values than 0.5 in every frequency ranges.So, we think that, in our case, FSC is not appropriate ...Details: Particles images were lowpass-filtered at 30A before refinement. Therefore, FSC shows higher values than 0.5 in every frequency ranges.So, we think that, in our case, FSC is not appropriate to use resolution determination. We used eotest of EMAN. We do not know if this corresponds to FCS type "even/odd maps were refined agains the same model (semi-independedt) or not. Number images used: 7146 |