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- PDB-3ldl: Crystal structure of human GRP78 (70kDa heat shock protein 5 / BI... -
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Basic information
Entry | Database: PDB / ID: 3ldl | ||||||
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Title | Crystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in complex with ATP | ||||||
![]() | 78 kDa glucose-regulated protein | ||||||
![]() | CHAPERONE / GRP78 / HSP70 / HSC70 / HEAT SHOCK / PROTEIN FOLDING / ATP-BINDING / ADENOSINE / NUCLEOSIDE / NUCLEOTIDE-BINDING / STRESS RESPONSE / SMALL MOLECULE INHIBITOR / SELECTIVITY / Endoplasmic reticulum / Phosphoprotein | ||||||
Function / homology | ![]() regulation of ATF6-mediated unfolded protein response / regulation of PERK-mediated unfolded protein response / regulation of protein folding in endoplasmic reticulum / cerebellum structural organization / ATF6 (ATF6-alpha) activates chaperones / ATF6B (ATF6-beta) activates chaperones / maintenance of protein localization in endoplasmic reticulum / IRE1alpha activates chaperones / ATF6 (ATF6-alpha) activates chaperone genes / regulation of IRE1-mediated unfolded protein response ...regulation of ATF6-mediated unfolded protein response / regulation of PERK-mediated unfolded protein response / regulation of protein folding in endoplasmic reticulum / cerebellum structural organization / ATF6 (ATF6-alpha) activates chaperones / ATF6B (ATF6-beta) activates chaperones / maintenance of protein localization in endoplasmic reticulum / IRE1alpha activates chaperones / ATF6 (ATF6-alpha) activates chaperone genes / regulation of IRE1-mediated unfolded protein response / endoplasmic reticulum chaperone complex / negative regulation of IRE1-mediated unfolded protein response / PERK regulates gene expression / cerebellar Purkinje cell layer development / protein folding in endoplasmic reticulum / misfolded protein binding / post-translational protein targeting to membrane, translocation / protein serine/threonine kinase inhibitor activity / ER overload response / negative regulation of PERK-mediated unfolded protein response / endoplasmic reticulum-Golgi intermediate compartment / non-chaperonin molecular chaperone ATPase / : / Regulation of HSF1-mediated heat shock response / negative regulation of protein-containing complex assembly / cellular response to glucose starvation / endoplasmic reticulum unfolded protein response / ERAD pathway / heat shock protein binding / substantia nigra development / protein folding chaperone / response to endoplasmic reticulum stress / cellular response to interleukin-4 / positive regulation of protein ubiquitination / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / negative regulation of transforming growth factor beta receptor signaling pathway / ATP-dependent protein folding chaperone / unfolded protein binding / melanosome / Platelet degranulation / ribosome binding / protein-folding chaperone binding / midbody / protein refolding / positive regulation of cell migration / cadherin binding / protein domain specific binding / endoplasmic reticulum lumen / chromatin extrusion motor activity / ATP-dependent H2AZ histone chaperone activity / ATP-dependent H3-H4 histone complex chaperone activity / cohesin loader activity / DNA clamp loader activity / intracellular membrane-bounded organelle / focal adhesion / ubiquitin protein ligase binding / calcium ion binding / endoplasmic reticulum membrane / negative regulation of apoptotic process / enzyme binding / cell surface / endoplasmic reticulum / positive regulation of transcription by RNA polymerase II / protein-containing complex / ATP hydrolysis activity / mitochondrion / extracellular exosome / ATP binding / nucleus / membrane / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dokurno, P. / Surgenor, A.E. / Shaw, T. / Macias, A.T. / Massey, A.J. / Williamson, D.S. | ||||||
![]() | ![]() Title: Adenosine-Derived Inhibitors of 78 kDa Glucose Regulated Protein (Grp78) ATPase: Insights into Isoform Selectivity. Authors: Macias, A.T. / Williamson, D.S. / Allen, N. / Borgognoni, J. / Clay, A. / Daniels, Z. / Dokurno, P. / Drysdale, M.J. / Francis, G.L. / Graham, C.J. / Howes, R. / Matassova, N. / Murray, J.B. ...Authors: Macias, A.T. / Williamson, D.S. / Allen, N. / Borgognoni, J. / Clay, A. / Daniels, Z. / Dokurno, P. / Drysdale, M.J. / Francis, G.L. / Graham, C.J. / Howes, R. / Matassova, N. / Murray, J.B. / Parsons, R. / Shaw, T. / Surgenor, A.E. / Terry, L. / Wang, Y. / Wood, M. / Massey, A.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 171.1 KB | Display | ![]() |
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PDB format | ![]() | 132.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1007.6 KB | Display | ![]() |
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Full document | ![]() | 1021.9 KB | Display | |
Data in XML | ![]() | 34.8 KB | Display | |
Data in CIF | ![]() | 50.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3ldnC ![]() 3ldoC ![]() 3ldpC ![]() 3ldqC ![]() 3m3zC ![]() 3fzfS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 42299.852 Da / Num. of mol.: 2 / Fragment: ATPase domain (residues 26-407) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-MG / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.93 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1M Tris buffer, 25% Peg3350, 0.1M Na,K tartrate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 20, 2007 / Details: mirrors |
Radiation | Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.973 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. all: 30393 / Num. obs: 30393 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 2 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 2.8 / Num. unique all: 2879 / % possible all: 87.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: pdb entry 3FZF Resolution: 2.3→15 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.9 / SU B: 8.914 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.678 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.3→2.358 Å / Total num. of bins used: 20
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