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- PDB-4ahn: R121H - Angiogenin mutants and amyotrophic lateral sclerosis - a ... -

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Basic information

Entry
Database: PDB / ID: 4ahn
TitleR121H - Angiogenin mutants and amyotrophic lateral sclerosis - a biochemical and biological analysis
ComponentsANGIOGENIN
KeywordsHYDROLASE / ANG / ALS 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 / positive regulation of phosphorylation / endocytic vesicle / RNA nuclease activity / ovarian follicle development / response to hormone / positive regulation of endothelial cell proliferation / actin filament polymerization / RNA endonuclease activity / stress granule assembly / peptide binding / placenta development / positive regulation of protein secretion / negative regulation of smooth muscle cell proliferation / cytoplasmic stress granule / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / cell migration / heparin binding / actin cytoskeleton / 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 / extracellular space / DNA binding / extracellular region / nucleus / cytoplasm / 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
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.977 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1852
Polymers14,1501
Non-polymers351
Water00
1
A: ANGIOGENIN
hetero molecules

A: ANGIOGENIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,3714
Polymers28,3002
Non-polymers712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area1280 Å2
ΔGint-20.4 kcal/mol
Surface area13040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.697, 116.696, 37.394
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein ANGIOGENIN / RIBONUCLEASE 5 / RNASE 5


Mass: 14149.989 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET22B(PLUS) / 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 145 TO HIS
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: 3.3 Å3/Da / Density % sol: 62 % / Description: NONE
Crystal growDetails: 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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Sep 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.97→50 Å / Num. obs: 3976 / % possible obs: 92.6 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 42.03 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 10.1
Reflection shellResolution: 2.97→3.11 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.9 / % possible all: 76.9

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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: 2.977→27.735 Å / SU ML: 0.41 / σ(F): 0.14 / Phase error: 27.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2835 155 4.4 %
Rwork0.2055 --
obs0.209 3558 89.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 28.738 Å2 / ksol: 0.341 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.7777 Å20 Å20 Å2
2--13.4032 Å20 Å2
3----12.6255 Å2
Refinement stepCycle: LAST / Resolution: 2.977→27.735 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms968 0 1 0 969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009997
X-RAY DIFFRACTIONf_angle_d1.3271339
X-RAY DIFFRACTIONf_dihedral_angle_d17.282378
X-RAY DIFFRACTIONf_chiral_restr0.087138
X-RAY DIFFRACTIONf_plane_restr0.007178
LS refinement shellResolution: 2.9766→27.7357 Å
RfactorNum. reflection% reflection
Rfree0.2835 155 -
Rwork0.2055 3403 -
obs--90 %

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