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Yorodumi- PDB-1gn1: crystal structure of the mouse CCT gamma apical domain (monoclinic) -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gn1 | ||||||
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Title | crystal structure of the mouse CCT gamma apical domain (monoclinic) | ||||||
Components | CCT-GAMMA | ||||||
Keywords | CHAPERONE / CHAPERONIN / ACTIN / TUBULIN | ||||||
Function / homology | Function and homology information Association of TriC/CCT with target proteins during biosynthesis / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / zona pellucida receptor complex / positive regulation of establishment of protein localization to telomere / binding of sperm to zona pellucida / chaperonin-containing T-complex / chaperone-mediated protein folding / positive regulation of telomere maintenance via telomerase / ATP-dependent protein folding chaperone / unfolded protein binding ...Association of TriC/CCT with target proteins during biosynthesis / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / zona pellucida receptor complex / positive regulation of establishment of protein localization to telomere / binding of sperm to zona pellucida / chaperonin-containing T-complex / chaperone-mediated protein folding / positive regulation of telomere maintenance via telomerase / ATP-dependent protein folding chaperone / unfolded protein binding / protein folding / myelin sheath / cell body / microtubule / protein stabilization / ATP hydrolysis activity / ATP binding Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Pappenberger, G. / Wilsher, J.A. / Roe, S.M. / Willison, K.R. / Pearl, L.H. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2002 Title: Crystal Structure of the Cct Gamma Apical Domain:: Implications for Substrate Binding to the Eukaryotic Cytosolic Chaperonin Authors: Pappenberger, G. / Wilsher, J.A. / Roe, S.M. / Counsell, D.J. / Willison, K.R. / Pearl, L.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gn1.cif.gz | 236.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gn1.ent.gz | 187.6 KB | Display | PDB format |
PDBx/mmJSON format | 1gn1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1gn1_validation.pdf.gz | 495.2 KB | Display | wwPDB validaton report |
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Full document | 1gn1_full_validation.pdf.gz | 535.7 KB | Display | |
Data in XML | 1gn1_validation.xml.gz | 46.4 KB | Display | |
Data in CIF | 1gn1_validation.cif.gz | 61.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gn/1gn1 ftp://data.pdbj.org/pub/pdb/validation_reports/gn/1gn1 | HTTPS FTP |
-Related structure data
Related structure data | 1gmlSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Details | THE KNOWN BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATEOF THE MOLECULE IS THE MONOMER . TOGETHER WITH THE SEVENOTHER SUBUNITS OF CCT, IT IS PART OF A DOUBLE TOROIDALQUATERNARY STRUCTURE OF 2X8 SUBUNITS. |
-Components
#1: Protein | Mass: 20644.701 Da / Num. of mol.: 8 / Fragment: APICAL DOMAIN, RESIDUES 209-380 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET11C / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P80318 #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: microbatch / pH: 6.5 Details: CRYSTALS GROWN BY MICROBATCH METHOD (UNDER OIL) USING A 1:1 MIXTURE OF 30MG/ML PROTEIN, 400MM NACL, 20% GLYCEROL, 8MM TRIS PH8.0, 0.4MM EDTA AND 14% PEG 8K, 100MM NA-CACODYLATE PH6.5, 40MM ...Details: CRYSTALS GROWN BY MICROBATCH METHOD (UNDER OIL) USING A 1:1 MIXTURE OF 30MG/ML PROTEIN, 400MM NACL, 20% GLYCEROL, 8MM TRIS PH8.0, 0.4MM EDTA AND 14% PEG 8K, 100MM NA-CACODYLATE PH6.5, 40MM CA(OAC)2, 40% GLYCEROL, pH 6.50 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 14 ℃ / Method: batch method | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.92 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 15, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→30 Å / Num. obs: 32855 / % possible obs: 85.2 % / Redundancy: 2.1 % / Biso Wilson estimate: 100.6 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.8→2.94 Å / Redundancy: 2 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 4.7 / % possible all: 74.1 |
Reflection | *PLUS Lowest resolution: 29 Å / Num. obs: 33738 |
Reflection shell | *PLUS % possible obs: 74.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GML Resolution: 2.8→29.11 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1054377.25 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Stereochemistry target values: MAXIMUM LIKELIHOOD USING AMPLITUDES Details: NO INTERPRETABLE DENSITY WAS FOUND FOR THE LOOPS A250 - A260, B249 - B270, C248 - C272, D248 - D266, E248 - E272, F250 - F262, G249 - G261, H248 - H264 NO INTERPRETABLE DENSITY WAS FOUND FOR ...Details: NO INTERPRETABLE DENSITY WAS FOUND FOR THE LOOPS A250 - A260, B249 - B270, C248 - C272, D248 - D266, E248 - E272, F250 - F262, G249 - G261, H248 - H264 NO INTERPRETABLE DENSITY WAS FOUND FOR SEVERAL SIDECHAINS THESE WERE TRUNCATED AT CB
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 41.4219 Å2 / ksol: 0.288995 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 83.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.8→29.11 Å
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Refine LS restraints |
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Refine LS restraints NCS | Rms dev Biso : 5 Å2 / Weight position: 2000 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.8→2.98 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Rfactor Rfree: 0.287 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.433 |