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- PDB-4aoh: Structural snapshots and functional analysis of human angiogenin ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4aoh | ||||||
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Title | Structural snapshots and functional analysis of human angiogenin variants associated with Amyotrophic Lateral Sclerosis (ALS) | ||||||
![]() | ANGIOGENIN | ||||||
![]() | HYDROLASE / ANGIOGENESIS / NEOVASCULARISATION / AMYOTROPIC LATERAL SCLEROSIS / ALS / MOTOR NEURON DISEASE / RIBONUCLEASE INHIBITOR / NUCLEAR LOCALISATION / NUCLEAR LOCALIZATION | ||||||
Function / homology | ![]() angiogenin-PRI complex / negative regulation of translation in response to stress / tRNA-specific ribonuclease activity / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / signaling / cell communication / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Adherens junctions interactions / oocyte maturation ...angiogenin-PRI complex / negative regulation of translation in response to stress / tRNA-specific ribonuclease activity / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / signaling / cell communication / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Adherens junctions interactions / oocyte maturation / homeostatic process / hematopoietic stem cell proliferation / rRNA transcription / basement membrane / endocytic vesicle / RNA nuclease activity / positive regulation of phosphorylation / ovarian follicle development / response to hormone / stress granule assembly / positive regulation of endothelial cell proliferation / actin filament polymerization / RNA endonuclease activity / peptide binding / positive regulation of protein secretion / placenta development / negative regulation of smooth muscle cell proliferation / cytoplasmic stress granule / cell migration / antimicrobial humoral immune response mediated by antimicrobial peptide / actin cytoskeleton / antibacterial humoral response / heparin binding / ribosome binding / chromosome / actin binding / growth cone / angiogenesis / endonuclease activity / response to hypoxia / defense response to Gram-positive bacterium / rRNA binding / receptor ligand activity / copper ion binding / signaling receptor binding / innate immune response / neuronal cell body / negative regulation of apoptotic process / nucleolus / signal transduction / protein homodimerization activity / DNA binding / extracellular space / extracellular region / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Thiyagarajan, N. / Ferguson, R. / Subramanian, V. / Acharya, K.R. | ||||||
![]() | ![]() Title: Structural and Molecular Insights Into the Mechanism of Action of Human Angiogenin-Als Variants in Neurons Authors: Thiyagarajan, N. / Ferguson, R. / Subramanian, V. / Acharya, K.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 74.3 KB | Display | ![]() |
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PDB format | ![]() | 55.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.1 KB | Display | ![]() |
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Full document | ![]() | 445.8 KB | Display | |
Data in XML | ![]() | 9.1 KB | Display | |
Data in CIF | ![]() | 12.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ahdC ![]() 4aheC ![]() 4ahfC ![]() 4ahgC ![]() 4ahhC ![]() 4ahiC ![]() 4ahjC ![]() 4ahkC ![]() 4ahlC ![]() 4ahmC ![]() 4ahnC ![]() 1angS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Assembly
Deposited unit | ![]()
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1 |
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 14240.115 Da / Num. of mol.: 1 / Fragment: RESIDUES 24-147 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P03950, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters |
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#2: Chemical | ChemComp-TAR / |
#3: Chemical | ChemComp-TLA / |
#4: Water | ChemComp-HOH / |
Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.8 % / Description: NONE |
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Crystal grow | pH: 7 Details: 20 % PEG 4K, 0.05 M NA/K TARTRATE, 0.1 M NACL, 0.1 M HEPES PH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 17, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9796 Å / Relative weight: 1 |
Reflection | Resolution: 1.04→50 Å / Num. obs: 58714 / % possible obs: 82.7 % / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Biso Wilson estimate: 11.92 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 34.1 |
Reflection shell | Resolution: 1.04→1.08 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.9 / % possible all: 37.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1ANG Resolution: 1.041→42.774 Å / SU ML: 0.07 / σ(F): 1.35 / Phase error: 17.24 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.47 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.701 Å2 / ksol: 0.396 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.9 Å2
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Refinement step | Cycle: LAST / Resolution: 1.041→42.774 Å
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Refine LS restraints |
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LS refinement shell |
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