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Yorodumi- EMDB-5001: Native, unliganded GroEL, D7 symmetrized, 4.2 A resolution 0.5 cr... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5001 | |||||||||
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Title | Native, unliganded GroEL, D7 symmetrized, 4.2 A resolution 0.5 criterion | |||||||||
Map data | D7 structure of GroEL at 4.2 Angstrom resolution | |||||||||
Sample |
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Keywords | groel / chaperonin / chaperone / backbone trace / eman / single particle | |||||||||
Function / homology | Function and homology information GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat ...GroEL-GroES complex / chaperonin ATPase / virion assembly / chaperone cofactor-dependent protein refolding / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / unfolded protein binding / protein folding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Ludtke SJ / Baker ML / Chen D / Song J / Chuang DT / Chiu W | |||||||||
Citation | Journal: Structure / Year: 2008 Title: De novo backbone trace of GroEL from single particle electron cryomicroscopy. Authors: Steven J Ludtke / Matthew L Baker / Dong-Hua Chen / Jiu-Li Song / David T Chuang / Wah Chiu / Abstract: In this work, we employ single-particle electron cryo-microscopy (cryo-EM) to reconstruct GroEL to approximately 4 A resolution with both D7 and C7 symmetry. Using a newly developed skeletonization ...In this work, we employ single-particle electron cryo-microscopy (cryo-EM) to reconstruct GroEL to approximately 4 A resolution with both D7 and C7 symmetry. Using a newly developed skeletonization algorithm and secondary structure element identification in combination with sequence-based secondary structure prediction, we demonstrate that it is possible to achieve a de novo Calpha trace directly from a cryo-EM reconstruction. The topology of our backbone trace is completely accurate, though subtle alterations illustrate significant differences from existing crystal structures. In the map with C7 symmetry, the seven monomers in each ring are identical; however, the subunits have a subtly different structure in each ring, particularly in the equatorial domain. These differences include an asymmetric salt bridge, density in the nucleotide-binding pocket of only one ring, and small shifts in alpha helix positions. This asymmetric conformation is different from previous asymmetric structures, including GroES-bound GroEL, and may represent a "primed state" in the chaperonin pathway. | |||||||||
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_5001.map.gz | 13.7 MB | EMDB map data format | |
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Header (meta data) | emd-5001-v30.xml emd-5001.xml | 10 KB 10 KB | Display Display | EMDB header |
Images | emd_5001_1.png | 628.1 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5001 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5001 | HTTPS FTP |
-Related structure data
Related structure data | 3cauMC 5002C 3c9vC 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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Related items in Molecule of the Month |
-Map
File | Download / File: emd_5001.map.gz / Format: CCP4 / Size: 29.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | D7 structure of GroEL at 4.2 Angstrom resolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 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 : Native unliganded GroEL, residual ADP
Entire | Name: Native unliganded GroEL, residual ADP |
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Components |
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-Supramolecule #1000: Native unliganded GroEL, residual ADP
Supramolecule | Name: Native unliganded GroEL, residual ADP / type: sample / ID: 1000 / Oligomeric state: Two back to back homo-heptameric rings / Number unique components: 1 |
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Molecular weight | Theoretical: 800 KDa |
-Macromolecule #1: GroEL
Macromolecule | Name: GroEL / type: protein_or_peptide / ID: 1 / Name.synonym: GroEL / Number of copies: 14 / Oligomeric state: 14-mer / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 800 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: ESts CG-712 / Recombinant plasmid: pGroESL |
Sequence | GO: protein folding / InterPro: INTERPRO: IPR012723 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | Details: 20 mM Tris.HCl, pH 7.5, 50 mM MgCl2 |
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Grid | Details: Quantifoil grids with 2 um holes |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 100 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blot for 2 sec |
-Electron microscopy
Microscope | JEOL 3000SFF |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: OTHER / Cs: 1.6 mm / Nominal defocus max: 2.3 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 60000 |
Sample stage | Specimen holder: Top entry / Specimen holder model: OTHER |
Temperature | Min: 4 K / Max: 4 K / Average: 4 K |
Details | low dose on JEOL 3000SFF |
Date | Jan 1, 2005 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 135 / Average electron dose: 36 e/Å2 / Bits/pixel: 14 |
-Image processing
CTF correction | Details: per micrograph |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 20401 |