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- PDB-4ahk: K54E - Angiogenin mutants and amyotrophic lateral sclerosis - a b... -

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Basic information

Entry
Database: PDB / ID: 4ahk
TitleK54E - Angiogenin mutants and amyotrophic lateral sclerosis - a biochemical and biological analysis
ComponentsANGIOGENIN
KeywordsHYDROLASE / AMYOTROPHIC / LATERAL SCLEROSIS / NEOVASCULARISATION
Function / homology
Function and homology information


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 / positive regulation of endothelial cell proliferation / actin filament polymerization / RNA endonuclease activity / stress granule assembly / peptide binding / positive regulation of protein secretion / placenta development / negative regulation of smooth muscle cell proliferation / antimicrobial humoral immune response mediated by antimicrobial peptide / cytoplasmic stress granule / antibacterial humoral response / cell migration / actin cytoskeleton / heparin binding / ribosome binding / actin binding / chromosome / growth cone / endonuclease activity / angiogenesis / 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
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 / Angiogenin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsThiyagarajan, N. / Ferguson, R. / Saha, S. / Pham, T. / 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
DepositionFeb 6, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 10, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2012Group: Database references
Revision 1.2Dec 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 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANGIOGENIN
B: ANGIOGENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6384
Polymers28,3382
Non-polymers3002
Water2,360131
1
A: ANGIOGENIN


Theoretical massNumber of molelcules
Total (without water)14,1691
Polymers14,1691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ANGIOGENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4693
Polymers14,1691
Non-polymers3002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.396, 37.338, 83.237
Angle α, β, γ (deg.)90.00, 119.92, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2038-

HOH

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Components

#1: Protein ANGIOGENIN / RIBONUCLEASE 5 / RNASE 5


Mass: 14168.971 Da / Num. of mol.: 2 / Mutation: YES
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.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 78 TO GLU
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: 3 Å3/Da / Density % sol: 58.9 % / Description: NONE
Crystal growDetails: 20 % PEG 4K, 0.4 M NA/K TARTRATE, 0.1 M NA CITRATE PH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 23796 / % possible obs: 88.8 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 25.57 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.3
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 2 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.9 / % possible all: 72.9

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Processing

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

1ang


Resolution: 1.97→36.072 Å / SU ML: 0.27 / σ(F): 0.04 / Phase error: 32.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2791 898 4.7 %
Rwork0.2142 --
obs0.2171 19181 80.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.21 Å2 / ksol: 0.402 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-28.9498 Å20 Å213.2422 Å2
2---20.6248 Å20 Å2
3----8.325 Å2
Refinement stepCycle: LAST / Resolution: 1.97→36.072 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1906 0 20 131 2057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061990
X-RAY DIFFRACTIONf_angle_d1.012677
X-RAY DIFFRACTIONf_dihedral_angle_d14.578754
X-RAY DIFFRACTIONf_chiral_restr0.071277
X-RAY DIFFRACTIONf_plane_restr0.005360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9701-2.09360.28351140.22672359X-RAY DIFFRACTION63
2.0936-2.25520.30711410.22232723X-RAY DIFFRACTION73
2.2552-2.48210.28881420.22453033X-RAY DIFFRACTION80
2.4821-2.84110.31521710.22933272X-RAY DIFFRACTION87
2.8411-3.5790.27941860.20413404X-RAY DIFFRACTION90
3.579-36.07770.2441440.20573492X-RAY DIFFRACTION89

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