+Open data
-Basic information
Entry | Database: PDB / ID: 5bn8 | ||||||
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Title | Crystal structure of nucleotide-free human Hsp70 NBD. | ||||||
Components | Heat shock 70 kDa protein 1A | ||||||
Keywords | HYDROLASE / ATP hydrolysis activity | ||||||
Function / homology | Function and homology information positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / death receptor agonist activity / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / C3HC4-type RING finger domain binding / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity ...positive regulation of endoribonuclease activity / denatured protein binding / cellular heat acclimation / death receptor agonist activity / negative regulation of inclusion body assembly / Viral RNP Complexes in the Host Cell Nucleus / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / C3HC4-type RING finger domain binding / positive regulation of microtubule nucleation / ATP-dependent protein disaggregase activity / misfolded protein binding / regulation of mitotic spindle assembly / negative regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway / positive regulation of tumor necrosis factor-mediated signaling pathway / transcription regulator inhibitor activity / aggresome / lysosomal transport / cellular response to steroid hormone stimulus / mRNA catabolic process / regulation of protein ubiquitination / chaperone cofactor-dependent protein refolding / HSF1-dependent transactivation / response to unfolded protein / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / chaperone-mediated protein complex assembly / Regulation of HSF1-mediated heat shock response / Attenuation phase / cellular response to unfolded protein / negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway / ATP metabolic process / inclusion body / negative regulation of protein ubiquitination / protein folding chaperone / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / centriole / positive regulation of RNA splicing / positive regulation of erythrocyte differentiation / negative regulation of transforming growth factor beta receptor signaling pathway / positive regulation of interleukin-8 production / AUF1 (hnRNP D0) binds and destabilizes mRNA / G protein-coupled receptor binding / ATP-dependent protein folding chaperone / PKR-mediated signaling / negative regulation of cell growth / histone deacetylase binding / transcription corepressor activity / disordered domain specific binding / unfolded protein binding / virus receptor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of NF-kappaB transcription factor activity / cellular response to oxidative stress / cellular response to heat / protein refolding / vesicle / ficolin-1-rich granule lumen / blood microparticle / receptor ligand activity / protein stabilization / nuclear speck / cadherin binding / ribonucleoprotein complex / negative regulation of cell population proliferation / focal adhesion / signaling receptor binding / centrosome / ubiquitin protein ligase binding / Neutrophil degranulation / positive regulation of gene expression / negative regulation of apoptotic process / perinuclear region of cytoplasm / enzyme binding / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / ATP hydrolysis activity / protein-containing complex / mitochondrion / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å | ||||||
Authors | Narayanan, D. / Engh, R.A. | ||||||
Funding support | Norway, 1items
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Citation | Journal: To Be Published Title: Nucleotide binding to variants of the HSP70-NBD. Authors: Narayanan, D. / Pflug, A. / Christopeit, T. / Kyomuhendo, P. / Engh, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5bn8.cif.gz | 196.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5bn8.ent.gz | 155.6 KB | Display | PDB format |
PDBx/mmJSON format | 5bn8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5bn8_validation.pdf.gz | 436 KB | Display | wwPDB validaton report |
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Full document | 5bn8_full_validation.pdf.gz | 439.1 KB | Display | |
Data in XML | 5bn8_validation.xml.gz | 22.4 KB | Display | |
Data in CIF | 5bn8_validation.cif.gz | 35.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/5bn8 ftp://data.pdbj.org/pub/pdb/validation_reports/bn/5bn8 | HTTPS FTP |
-Related structure data
Related structure data | 5bn9C 5bplC 5bpmC 5bpnC 3atvS 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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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 42758.355 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA1A, HSPA1, HSX70 / Plasmid: pET28b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0DMV8 |
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-Non-polymers , 6 types, 586 molecules
#2: Chemical | ChemComp-EPE / | ||||||||
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#3: Chemical | #4: Chemical | ChemComp-PO4 / #5: Chemical | ChemComp-CL / | #6: Chemical | ChemComp-NA / | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.39 Å3/Da / Density % sol: 48.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 25 % PEG-3350 W/V, 0.1 M HEPES / PH range: 7.0 - 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 23, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.34→38.35 Å / Num. obs: 93866 / % possible obs: 97.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.03823 / Net I/σ(I): 17.85 |
Reflection shell | Resolution: 1.34→1.39 Å / Redundancy: 3 % / Rmerge(I) obs: 0.4752 / Mean I/σ(I) obs: 2.48 / % possible all: 81.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ATV Resolution: 1.34→38.35 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.945 / SU ML: 0.034 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: 22.46 Å2
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Refinement step | Cycle: LAST / Resolution: 1.34→38.35 Å
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