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Yorodumi- PDB-2byu: Negative stain EM reconstruction of M.tuberculosis Acr1(Hsp 16.3)... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2byu | ||||||
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Title | Negative stain EM reconstruction of M.tuberculosis Acr1(Hsp 16.3) fitted with wheat sHSP dimer | ||||||
Components | HEAT SHOCK PROTEIN 16.9BHeat shock response | ||||||
Keywords | CHAPERONE / SMALL HEAT SHOCK PROTEIN / ALPHA-CRYSTALLIN | ||||||
Function / homology | Function and homology information response to salt stress / response to hydrogen peroxide / protein homooligomerization / protein self-association / unfolded protein binding / protein complex oligomerization / protein folding / response to heat / cytoplasm Similarity search - Function | ||||||
Biological species | TRITICUM AESTIVUM (bread wheat) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 16.5 Å | ||||||
Authors | Kennaway, C.K. / Benesch, J.L.P. / Gohlke, U. / Wang, L. / Robinson, C.V. / Orlova, E.V. / Saibil, H.R. / Keep, N.H. | ||||||
Citation | Journal: J Biol Chem / Year: 2005 Title: Dodecameric structure of the small heat shock protein Acr1 from Mycobacterium tuberculosis. Authors: Christopher K Kennaway / Justin L P Benesch / Ulrich Gohlke / Luchun Wang / Carol V Robinson / Elena V Orlova / Helen R Saibil / Nicholas H Keep / Abstract: Small heat shock proteins are a ubiquitous and diverse family of stress proteins that have in common an alpha-crystallin domain. Mycobacterium tuberculosis has two small heat shock proteins, Acr1 ...Small heat shock proteins are a ubiquitous and diverse family of stress proteins that have in common an alpha-crystallin domain. Mycobacterium tuberculosis has two small heat shock proteins, Acr1 (alpha-crystallin-related protein 1, or Hsp16.3/16-kDa antigen) and Acr2 (HrpA), both of which are highly expressed under different stress conditions. Small heat shock proteins form large oligomeric assemblies and are commonly polydisperse. Nanoelectrospray mass spectrometry showed that Acr2 formed a range of oligomers composed of dimers and tetramers, whereas Acr1 was a dodecamer. Electron microscopy of Acr2 showed a variety of particle sizes. Using three-dimensional analysis of negative stain electron microscope images, we have shown that Acr1 forms a tetrahedral assembly with 12 polypeptide chains. The atomic structure of a related alpha-crystallin domain dimer was docked into the density to build a molecular structure of the dodecameric Acr1 complex. Along with the differential regulation of these two proteins, the differences in their quaternary structures demonstrated here supports their distinct functional roles. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 2byu.cif.gz | 235.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2byu.ent.gz | 198.4 KB | Display | PDB format |
PDBx/mmJSON format | 2byu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/by/2byu ftp://data.pdbj.org/pub/pdb/validation_reports/by/2byu | HTTPS FTP |
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-Related structure data
Related structure data | 1149MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 12376.149 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Details: THE PROTEIN MODEL WAS OBTAINED FROM PDB ENTRY 1GME / Source: (natural) TRITICUM AESTIVUM (bread wheat) / References: UniProt: Q41560 Sequence details | COOORDINAT | |
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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 |
-Sample preparation
Component | Name: HSP 16.3 / Type: COMPLEX |
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Buffer solution | Name: 20MM TRIS / pH: 7 / Details: 20MM TRIS |
Specimen | Conc.: 0.01 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: CARBON COATED 400 MESH COPPER GRID / Grid material: COPPER / Grid mesh size: 400 divisions/in. |
-Electron microscopy imaging
Microscopy | Model: FEI TECNAI 12 / Date: Mar 28, 2004 |
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Electron gun | Electron source: TUNGSTEN HAIRPIN / Accelerating voltage: 120 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 42000 X / Nominal defocus max: 600 nm / Nominal defocus min: 390 nm / Cs: 2 mm |
Specimen holder | Temperature: 293 K |
Image recording | Electron dose: 10 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 18 |
Radiation wavelength | Relative weight: 1 |
-Processing
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
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3D reconstruction | Resolution: 16.5 Å / Num. of particles: 6123 / Nominal pixel size: 3.33 Å / Actual pixel size: 3.33 Å Details: DIMER ALPHA CRYSTALLIN DOMAIN OF 1GME (43-137 AND 146-151) FITTED INTO DENSITY USING URO. RESOLUTION WAS DETERMINED BY 0.5 FOURIER SHELL CORRELATION. Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: OTHER / Space: RECIPROCAL / Target criteria: Cross-correlation coefficient Details: METHOD--QUALITY OF THE FIT R-FACTOR= 0.516, CROSS- CORRELATION COEFFICIENT 81.5% | ||||||||||||
Atomic model building | PDB-ID: 1GME | ||||||||||||
Refinement | Highest resolution: 16.5 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 16.5 Å
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