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- PDB-3c9v: C7 Symmetrized Structure of Unliganded GroEL at 4.7 Angstrom Reso... -
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Basic information
Entry | Database: PDB / ID: 3c9v | ||||||
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Title | C7 Symmetrized Structure of Unliganded GroEL at 4.7 Angstrom Resolution from CryoEM | ||||||
![]() | 60 kDa chaperonin | ||||||
![]() | CHAPERONE / GroEL / ATP-binding / Cell cycle / Cell division / Nucleotide-binding / Phosphoprotein | ||||||
Function / homology | ![]() GroEL-GroES complex / chaperonin ATPase / mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / virion assembly / chaperone cofactor-dependent protein refolding / positive regulation of interferon-alpha production / isomerase activity / ATP-dependent protein folding chaperone / response to radiation ...GroEL-GroES complex / chaperonin ATPase / mitochondrial unfolded protein response / protein import into mitochondrial intermembrane space / virion assembly / chaperone cofactor-dependent protein refolding / positive regulation of interferon-alpha production / isomerase activity / ATP-dependent protein folding chaperone / response to radiation / positive regulation of interleukin-6 production / positive regulation of type II interferon production / unfolded protein binding / protein folding / positive regulation of T cell activation / protein-folding chaperone binding / response to heat / protein refolding / magnesium ion binding / ATP hydrolysis activity / ATP binding / identical protein binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.7 Å | ||||||
![]() | Ludtke, S.J. / Baker, M.L. / Chen, D.H. / Song, J.L. / Chuang, D. / Chiu, W. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 192.3 KB | Display | ![]() |
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PDB format | ![]() | 128.5 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 847.2 KB | Display | ![]() |
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Full document | ![]() | 846.8 KB | Display | |
Data in XML | ![]() | 78.8 KB | Display | |
Data in CIF | ![]() | 123.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5002MC ![]() 5001C ![]() 3cauC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 55463.387 Da / Num. of mol.: 14 / Fragment: residues 2-527 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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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 |
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Sample preparation
Component | Name: GroEL / Type: COMPLEX / Details: 14-mer. Two back to back homo-heptameric rings. |
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Buffer solution | Name: 20 mM Tris.HCl, pH 7.5, 50 mM MgCl2 / pH: 7.5 / Details: 20 mM Tris.HCl, pH 7.5, 50 mM MgCl2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Details: ETHANE. Vitrobot, blot for 2 sec. |
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Electron microscopy imaging
Microscopy | Model: JEOL 3200FS / Date: Jan 1, 2005 |
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Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 2300 nm / Nominal defocus min: 900 nm / Cs: 1.6 mm |
Specimen holder | Temperature: 4 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 36 e/Å2 / Film or detector model: KODAK SO-163 FILM |
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Processing
CTF correction | Details: per micrograph | ||||||||||||
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Symmetry | Point symmetry: C7 (7 fold cyclic) | ||||||||||||
3D reconstruction | Method: EMAN, single particle / Resolution: 4.7 Å / Num. of particles: 20401 / Nominal pixel size: 1.06 Å / Details: C7 symmetry, This entry contains CA atom only / Symmetry type: POINT | ||||||||||||
Refinement step | Cycle: LAST
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