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Yorodumi- PDB-6p2u: Structure of Mortalin-NBD with N6-propargyladenosine-5'-diphosphate -
+Open data
-Basic information
Entry | Database: PDB / ID: 6p2u | |||||||||
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Title | Structure of Mortalin-NBD with N6-propargyladenosine-5'-diphosphate | |||||||||
Components | Stress-70 protein, mitochondrial | |||||||||
Keywords | CHAPERONE / inhibitor / complex / ATPase | |||||||||
Function / homology | Function and homology information negative regulation of hemopoiesis / MIB complex / negative regulation of hematopoietic stem cell differentiation / negative regulation of erythrocyte differentiation / SAM complex / TIM23 mitochondrial import inner membrane translocase complex / inner mitochondrial membrane organization / Cristae formation / Mitochondrial protein import / iron-sulfur cluster assembly ...negative regulation of hemopoiesis / MIB complex / negative regulation of hematopoietic stem cell differentiation / negative regulation of erythrocyte differentiation / SAM complex / TIM23 mitochondrial import inner membrane translocase complex / inner mitochondrial membrane organization / Cristae formation / Mitochondrial protein import / iron-sulfur cluster assembly / mitochondrial nucleoid / chaperone cofactor-dependent protein refolding / Regulation of HSF1-mediated heat shock response / protein folding chaperone / Mitochondrial protein degradation / heat shock protein binding / protein export from nucleus / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / erythrocyte differentiation / ATP-dependent protein folding chaperone / intracellular protein transport / regulation of erythrocyte differentiation / unfolded protein binding / protein refolding / mitochondrial inner membrane / mitochondrial matrix / focal adhesion / ubiquitin protein ligase binding / nucleolus / negative regulation of apoptotic process / ATP hydrolysis activity / mitochondrion / RNA binding / extracellular exosome / ATP binding / nucleus / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Moseng, M.A. / Page, R.C. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Febs Lett. / Year: 2019 Title: 2- and N6-functionalized adenosine-5'-diphosphate analogs for the inhibition of mortalin. Authors: Moseng, M.A. / Nix, J.C. / Page, R.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6p2u.cif.gz | 95.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6p2u.ent.gz | 67.1 KB | Display | PDB format |
PDBx/mmJSON format | 6p2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6p2u_validation.pdf.gz | 723.4 KB | Display | wwPDB validaton report |
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Full document | 6p2u_full_validation.pdf.gz | 726.3 KB | Display | |
Data in XML | 6p2u_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 6p2u_validation.cif.gz | 27.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/6p2u ftp://data.pdbj.org/pub/pdb/validation_reports/p2/6p2u | HTTPS FTP |
-Related structure data
Related structure data | 4kboS S: Starting model for refinement |
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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
#1: Protein | Mass: 41416.062 Da / Num. of mol.: 1 / Fragment: NBD (UNP residues 52-431) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HSPA9, GRP75, HSPA9B, mt-HSP70 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta2 / References: UniProt: P38646 |
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#2: Chemical | ChemComp-NO7 / |
#3: Chemical | ChemComp-PO4 / |
#4: Chemical | ChemComp-MG / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.21 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 30% w/v PEG8000, 100 mM sodium acetate, 200 mM lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å |
Detector | Type: RDI CMOS_8M / Detector: CMOS / Date: Aug 30, 2015 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00003 Å / Relative weight: 1 |
Reflection | Resolution: 2→47.04 Å / Num. obs: 29169 / % possible obs: 99.27 % / Redundancy: 6.9 % / Biso Wilson estimate: 21.71 Å2 / CC1/2: 0.994 / Net I/σ(I): 10.62 |
Reflection shell | Resolution: 2→2.071 Å / Num. unique obs: 2845 / CC1/2: 0.586 / % possible all: 98.44 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4KBO Resolution: 2→47.04 Å / Cross valid method: FREE R-VALUE
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Refinement step | Cycle: LAST / Resolution: 2→47.04 Å
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LS refinement shell | Resolution: 2→2.07 Å
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