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- PDB-1a4y: RIBONUCLEASE INHIBITOR-ANGIOGENIN COMPLEX -

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Basic information

Entry
Database: PDB / ID: 1a4y
TitleRIBONUCLEASE INHIBITOR-ANGIOGENIN COMPLEX
Components
  • ANGIOGENIN
  • RIBONUCLEASE INHIBITOR
KeywordsCOMPLEX (INHIBITOR/NUCLEASE) / COMPLEX (INHIBITOR-NUCLEASE) / COMPLEX (RI-ANG) / HYDROLASE MOLECULAR RECOGNITION / EPITOPE MAPPING / LEUCINE-RICH REPEATS / COMPLEX (INHIBITOR-NUCLEASE) complex
Function / homology
Function and homology information


tRNA stabilization / ribonuclease inhibitor activity / 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 / regulation of Arp2/3 complex-mediated actin nucleation / signaling / cell communication ...tRNA stabilization / ribonuclease inhibitor activity / 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 / regulation of Arp2/3 complex-mediated actin nucleation / signaling / cell communication / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / Adherens junctions interactions / oocyte maturation / homeostatic process / hematopoietic stem cell proliferation / mRNA catabolic process / rRNA transcription / basement membrane / positive regulation of phosphorylation / endocytic vesicle / RNA nuclease activity / regulation of angiogenesis / ovarian follicle development / response to hormone / positive regulation of endothelial cell proliferation / actin filament polymerization / stress granule assembly / peptide binding / RNA endonuclease activity / 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 / lamellipodium / 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 exosome / extracellular region / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Ribonuclease inhibitor, leucine rich repeat cap / Capping Ribonuclease inhibitor Leucine Rich Repeat / : / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / P-30 Protein ...Ribonuclease inhibitor, leucine rich repeat cap / Capping Ribonuclease inhibitor Leucine Rich Repeat / : / Leucine-rich repeat, cysteine-containing subtype / Leucine-rich repeat - CC (cysteine-containing) subfamily / Leucine rich repeat, ribonuclease inhibitor type / Leucine Rich repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / P-30 Protein / Ribonuclease A-like domain / Alpha-Beta Horseshoe / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Angiogenin / Ribonuclease inhibitor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPapageorgiou, A.C. / Acharya, K.R.
CitationJournal: EMBO J. / Year: 1997
Title: Molecular recognition of human angiogenin by placental ribonuclease inhibitor--an X-ray crystallographic study at 2.0 A resolution.
Authors: Papageorgiou, A.C. / Shapiro, R. / Acharya, K.R.
History
DepositionFeb 8, 1998Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Refinement description / Category: database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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: RIBONUCLEASE INHIBITOR
B: ANGIOGENIN
D: RIBONUCLEASE INHIBITOR
E: ANGIOGENIN


Theoretical massNumber of molelcules
Total (without water)128,1124
Polymers128,1124
Non-polymers00
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8860 Å2
ΔGint-11 kcal/mol
Surface area41150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.553, 105.605, 93.516
Angle α, β, γ (deg.)90.00, 107.09, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.63908, 0.58117, 0.50381), (0.59165, -0.04709, 0.80482), (0.49145, 0.81242, -0.31375)
Vector: 10.75084, -16.24662, 11.34353)
DetailsTHERE ARE TWO COMPLEXES IN THE ASYMMETRIC UNIT (CHAINS A, B, C AND D, E, F). CHAINS A AND D CORRESPOND TO THE INHIBITOR, CHAINS B AND E CORRESPOND TO ANGIOGENIN, AND CHAINS C AND F CORRESPOND TO THE WATER MOLECULES ASSOCIATED WITH THE RESPECTIVE COMPLEX.

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Components

#1: Protein RIBONUCLEASE INHIBITOR


Mass: 49887.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: PLACENTA / Plasmid: PANG2 / Species (production host): Escherichia coli
Production host: Escherichia coli str. K12 substr. W3110 (bacteria)
Strain (production host): W3110 / References: UniProt: P13489
#2: Protein ANGIOGENIN


Mass: 14169.036 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: PLACENTA / Plasmid: PANG2 / Species (production host): Escherichia coli
Production host: Escherichia coli str. K12 substr. W3110 (bacteria)
Strain (production host): W3110
References: UniProt: P03950, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 49.82 %
Description: THE POSITION OF ANGIOGENIN WAS LOCATED BY EXAMINATION OF THE ELECTRON DENSITY MAP
Crystal growpH: 4.2
Details: THE COMPLEX WAS CRYSTALLIZED FROM 10% PEG4000, 20MM SODIUM CITRATE (PH 4.2), 0.1 AMMONIUM SULPHATE AND 25 MM DTT.
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 16 ℃ / Method: vapor diffusion, hanging drop / pH: 7.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115.6 mg/mlinhibitor1drop
25.0 mg/mlprotein1drop
30.2 Mdithiothreitol1drop
510 %PEG40001reservoir
620 mMsodium citrate1reservoirpH4.2
70.1 Mammonium sulfate1reservoir
825 mMdithiothreitol1reservoir
4glycerol1drop0.0063ml

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Data collection

DiffractionMean temperature: 289 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 / Wavelength: 0.87, 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.871
21.54181
ReflectionResolution: 2→40 Å / Num. obs: 72355 / % possible obs: 86.9 % / Observed criterion σ(I): 0 / Redundancy: 2.2 % / Biso Wilson estimate: 40.4 Å2 / Rmerge(I) obs: 0.094 / Net I/σ(I): 4.5
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 1.6 / % possible all: 65.4
Reflection
*PLUS
Num. measured all: 158593
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 65.4 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
XDSdata scaling
SCALAdata scaling
X-PLOR3.8model building
X-PLOR3.8refinement
XDSdata reduction
CCP4(SCALA)data scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BNH (PIG RIBONUCLEASE INHIBITOR)

1bnh
PDB Unreleased entry


Resolution: 2→20 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.286 -5 %RANDOM
Rwork0.193 ---
obs0.193 72308 86.9 %-
Displacement parametersBiso mean: 42 Å2
Refine analyzeLuzzati sigma a free: 0.36 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8806 0 0 123 8929
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.61.5
X-RAY DIFFRACTIONx_mcangle_it4.22
X-RAY DIFFRACTIONx_scbond_it5.32
X-RAY DIFFRACTIONx_scangle_it8.32.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPHCSDX.PRO
X-RAY DIFFRACTION2TOPH19.PEP
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 42 Å2

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