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- PDB-4aoh: Structural snapshots and functional analysis of human angiogenin ... -

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Basic information

Entry
Database: PDB / ID: 4aoh
TitleStructural snapshots and functional analysis of human angiogenin variants associated with Amyotrophic Lateral Sclerosis (ALS)
ComponentsANGIOGENIN
KeywordsHYDROLASE / ANGIOGENESIS / NEOVASCULARISATION / AMYOTROPIC LATERAL SCLEROSIS / ALS / MOTOR NEURON DISEASE / RIBONUCLEASE INHIBITOR / NUCLEAR LOCALISATION / NUCLEAR LOCALIZATION
Function / homology
Function and homology information


activation of phospholipase A2 activity / angiogenin-PRI complex / diacylglycerol biosynthetic process / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / cell communication / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Adherens junctions interactions / oocyte maturation / homeostatic process ...activation of phospholipase A2 activity / angiogenin-PRI complex / diacylglycerol biosynthetic process / tRNA-derived small RNA (tsRNA or tRNA-related fragment, tRF) biogenesis / tRNA decay / cell communication / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Adherens junctions interactions / oocyte maturation / homeostatic process / rRNA transcription / basement membrane / RNA nuclease activity / positive regulation of phosphorylation / ovarian follicle development / positive regulation of endothelial cell proliferation / activation of protein kinase B activity / actin filament polymerization / RNA endonuclease activity / response to hormone / positive regulation of protein secretion / negative regulation of smooth muscle cell proliferation / peptide binding / placenta development / antimicrobial humoral immune response mediated by antimicrobial peptide / cell migration / actin cytoskeleton / antibacterial humoral response / heparin binding / chromosome / actin binding / growth cone / cytoplasmic vesicle / angiogenesis / endonuclease activity / negative regulation of translation / response to hypoxia / rRNA binding / defense response to Gram-positive bacterium / copper ion binding / innate immune response / signaling receptor binding / neuronal cell body / nucleolus / protein homodimerization activity / DNA binding / extracellular space / extracellular region / nucleus / cytosol
Similarity search - Function
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
D(-)-TARTARIC ACID / L(+)-TARTARIC ACID / Angiogenin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.041 Å
AuthorsThiyagarajan, N. / Ferguson, R. / Subramanian, V. / Acharya, K.R.
CitationJournal: Nat.Commun. / Year: 2012
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
DepositionMar 27, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Nov 28, 2012Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANGIOGENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5403
Polymers14,2401
Non-polymers3002
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.549, 37.505, 37.512
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-2060-

HOH

21A-2123-

HOH

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Components

#1: Protein ANGIOGENIN / RIBONUCLEASE 5 / RNASE 5


Mass: 14240.115 Da / Num. of mol.: 1 / Fragment: RESIDUES 24-147
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODON PLUS-RIPL
References: UniProt: P03950, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.15 Å3/Da / Density % sol: 42.8 % / Description: NONE
Crystal growpH: 7
Details: 20 % PEG 4K, 0.05 M NA/K TARTRATE, 0.1 M NACL, 0.1 M HEPES PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9796
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 17, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ANG

1ang


Resolution: 1.041→42.774 Å / SU ML: 0.07 / σ(F): 1.35 / Phase error: 17.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1879 2463 5.1 %
Rwork0.1689 --
obs0.1698 48524 82.69 %
Solvent computationShrinkage 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 parametersBiso mean: 17.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.0236 Å20 Å20 Å2
2---0.3581 Å20 Å2
3---0.3818 Å2
Refinement stepCycle: LAST / Resolution: 1.041→42.774 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms980 0 20 155 1155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061118
X-RAY DIFFRACTIONf_angle_d1.1361518
X-RAY DIFFRACTIONf_dihedral_angle_d11.001440
X-RAY DIFFRACTIONf_chiral_restr0.077158
X-RAY DIFFRACTIONf_plane_restr0.005207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0407-1.06070.3669540.3266916X-RAY DIFFRACTION31
1.0607-1.08240.2769550.24731447X-RAY DIFFRACTION47
1.0824-1.10590.2124890.20431721X-RAY DIFFRACTION56
1.1059-1.13170.20831260.15922008X-RAY DIFFRACTION66
1.1317-1.160.20381120.14382192X-RAY DIFFRACTION72
1.16-1.19130.14121280.14522383X-RAY DIFFRACTION78
1.1913-1.22640.16911310.14252626X-RAY DIFFRACTION85
1.2264-1.2660.16091530.14232747X-RAY DIFFRACTION90
1.266-1.31120.15941600.13562887X-RAY DIFFRACTION94
1.3112-1.36370.15841560.13142930X-RAY DIFFRACTION95
1.3637-1.42580.15281670.12772946X-RAY DIFFRACTION95
1.4258-1.5010.16481560.13122983X-RAY DIFFRACTION96
1.501-1.5950.16141460.13362960X-RAY DIFFRACTION97
1.595-1.71820.16511800.14353017X-RAY DIFFRACTION97
1.7182-1.89110.17951710.15363017X-RAY DIFFRACTION97
1.8911-2.16470.19811520.16723080X-RAY DIFFRACTION98
2.1647-2.72720.21371770.18323095X-RAY DIFFRACTION97
2.7272-42.81070.1931500.19493106X-RAY DIFFRACTION93

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