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- PDB-5m9t: Human angiogenin ALS variant H114R -

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Basic information

Entry
Database: PDB / ID: 5m9t
TitleHuman angiogenin ALS variant H114R
ComponentsAngiogenin
KeywordsHYDROLASE / ALS / RNase / angiogenesis
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 / peptide binding / RNA endonuclease activity / stress granule assembly / 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 / chromosome / ribosome binding / growth cone / actin binding / 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 / 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
BORATE ION / Angiogenin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsBradshaw, W.J. / Rehman, S. / Pham, T.T.K. / Thiyagarajan, N. / Lee, R.L. / Subramanian, V. / Acharya, K.R.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust083191 United Kingdom
Wellcome Trust088464 United Kingdom
CitationJournal: Sci Rep / Year: 2017
Title: Structural insights into human angiogenin variants implicated in Parkinson's disease and Amyotrophic Lateral Sclerosis.
Authors: Bradshaw, W.J. / Rehman, S. / Pham, T.T. / Thiyagarajan, N. / Lee, R.L. / Subramanian, V. / Acharya, K.R.
History
DepositionNov 2, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Angiogenin
B: Angiogenin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8094
Polymers28,6392
Non-polymers1712
Water1,20767
1
A: Angiogenin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,4903
Polymers14,3191
Non-polymers1712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Angiogenin


Theoretical massNumber of molelcules
Total (without water)14,3191
Polymers14,3191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.426, 81.426, 85.985
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Angiogenin / Ribonuclease 5 / RNase 5


Mass: 14319.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ANG, RNASE5 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P03950, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-BO4 / BORATE ION


Mass: 78.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BH4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 67 / 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: 2.87 Å3/Da / Density % sol: 57.19 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.01 M Na borate 1.1 M Na citrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.2→70.5 Å / Num. obs: 16435 / % possible obs: 95.8 % / Redundancy: 9.5 % / CC1/2: 0.994 / Net I/σ(I): 12.1
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 1101 / CC1/2: 0.681 / % possible all: 75.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0151refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ANG

1ang


Resolution: 2.2→70.5 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.47 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.222 / ESU R Free: 0.196 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23596 955 5.8 %RANDOM
Rwork0.18238 ---
obs0.18556 15455 95.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 49.751 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20.56 Å2-0 Å2
2--1.12 Å20 Å2
3----3.62 Å2
Refinement stepCycle: 1 / Resolution: 2.2→70.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1962 0 11 67 2040
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0192050
X-RAY DIFFRACTIONr_bond_other_d0.0020.021929
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.9292766
X-RAY DIFFRACTIONr_angle_other_deg0.97634419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9915249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.5922110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.07315356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2761529
X-RAY DIFFRACTIONr_chiral_restr0.1230.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212341
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02544
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.3384.671978
X-RAY DIFFRACTIONr_mcbond_other3.3184.669977
X-RAY DIFFRACTIONr_mcangle_it5.2886.9881221
X-RAY DIFFRACTIONr_mcangle_other5.2896.9921222
X-RAY DIFFRACTIONr_scbond_it3.8515.1951072
X-RAY DIFFRACTIONr_scbond_other3.8385.191069
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2737.5931539
X-RAY DIFFRACTIONr_long_range_B_refined8.87953.4642222
X-RAY DIFFRACTIONr_long_range_B_other8.88753.4372216
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 68 -
Rwork0.293 845 -
obs--74.59 %

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