[English] 日本語
Yorodumi- PDB-3ldn: Crystal structure of human GRP78 (70kDa heat shock protein 5 / BI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ldn | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of human GRP78 (70kDa heat shock protein 5 / BIP) ATPase domain in apo form | ||||||
Components | 78 kDa glucose-regulated protein | ||||||
Keywords | 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 | Function and homology information 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 / cerebellar Purkinje cell layer development / ATF6 (ATF6-alpha) activates chaperone genes ...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 / cerebellar Purkinje cell layer development / ATF6 (ATF6-alpha) activates chaperone genes / regulation of IRE1-mediated unfolded protein response / negative regulation of IRE1-mediated unfolded protein response / endoplasmic reticulum chaperone complex / PERK regulates gene expression / protein folding in endoplasmic reticulum / misfolded protein binding / post-translational protein targeting to membrane, translocation / ER overload response / non-chaperonin molecular chaperone ATPase / endoplasmic reticulum-Golgi intermediate compartment / chaperone cofactor-dependent protein refolding / Regulation of HSF1-mediated heat shock response / cellular response to interleukin-4 / negative regulation of protein-containing complex assembly / cellular response to glucose starvation / ERAD pathway / endoplasmic reticulum unfolded protein response / protein folding chaperone / heat shock protein binding / substantia nigra development / response to endoplasmic reticulum stress / negative regulation of transforming growth factor beta receptor signaling pathway / positive regulation of protein ubiquitination / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / 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 / 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 / ATP hydrolysis activity / protein-containing complex / mitochondrion / extracellular exosome / ATP binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Dokurno, P. / Surgenor, A.E. / Shaw, T. / Macias, A.T. / Massey, A.J. / Williamson, D.S. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2011 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3ldn.cif.gz | 166.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3ldn.ent.gz | 130.5 KB | Display | PDB format |
PDBx/mmJSON format | 3ldn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3ldn_validation.pdf.gz | 435.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 3ldn_full_validation.pdf.gz | 445 KB | Display | |
Data in XML | 3ldn_validation.xml.gz | 32.7 KB | Display | |
Data in CIF | 3ldn_validation.cif.gz | 47.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ld/3ldn ftp://data.pdbj.org/pub/pdb/validation_reports/ld/3ldn | HTTPS FTP |
-Related structure data
Related structure data | 3ldlC 3ldoC 3ldpC 3ldqC 3m3zC 3fzfS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-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.) Homo sapiens (human) / Gene: HSPA5, GRP78 / Plasmid: pGEX-4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P11021 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.01 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9537 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2007 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 36490 / Num. obs: 36490 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3327 / % possible all: 88.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: pdb entry 3FZF Resolution: 2.2→15 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.896 / SU B: 7.476 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.385 / ESU R Free: 0.272 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 30.869 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→15 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.256 Å / Total num. of bins used: 20
|