7PNJ

Human Angiogenin quardruple mutant-S28AT36AS37AS87A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural and Biochemical Characterization of the Human Angiogenin-Proliferating Cell Nuclear Antigen Interaction.

Papaioannou, O.S.E.Tsika, A.C.Rovoli, M.Papadopoulos, G.E.Kontopidis, G.Spyroulias, G.A.Leonidas, D.D.

(2023) Biochemistry 62: 1706-1715

  • DOI: https://doi.org/10.1021/acs.biochem.3c00158
  • Primary Citation of Related Structures:  
    7PNJ, 7PNP, 7PNR

  • PubMed Abstract: 

    The molecular details of the interaction between human angiogenin (hAng) and proliferating cell nuclear antigen (PCNA) have been investigated by isothermal titration calorimetry (ITC), mutagenesis, and NMR spectroscopy. The two proteins were shown to interact directly through immunoprecipitation studies of hAng with PCNA in vitro , and their interaction was quantified by ITC, obtaining information on stoichiometry, enthalpy, entropy, and binding kinetics of the association. The hAng-PCNA association is strong, with a K d value of 126 nM. The interaction surface was mapped by NMR spectroscopy, indicating participating residues. A structural model for the PCNA-hAng complex was constructed by docking and molecular dynamics simulations based on NMR data. The model was validated by mutating the hAng residues Arg5 and Arg101, which seem critical for the complex formation, to glutamate. ITC experiments showed that the angiogenin variants R5E and R5ER101E displayed 6.5 and 7.8 times higher K d values, respectively, than that of the native protein, indicating the correctness of the model. The hAng S28AT36AS37A and hAng S28AT36AS37AS87A variants were also tested as positive controls, further supporting the validity of the model. The crystal structures of the hAng variants S28AT36AS37A and S28AT36AS37AS87A showed that the mutations did not cause any significant conformational change. This study presents evidence for the structural mode of the hAng-PCNA interaction, revealing valuable information about the angiogenin and PCNA biological roles in the cytoplasm.


  • Organizational Affiliation

    Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500Larissa, Greece.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Angiogenin121Homo sapiensMutation(s): 4 
Gene Names: ANGRNASE5
EC: 3.1.27
UniProt & NIH Common Fund Data Resources
Find proteins for P03950 (Homo sapiens)
Explore P03950 
Go to UniProtKB:  P03950
PHAROS:  P03950
GTEx:  ENSG00000214274 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03950
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CIT
Query on CIT

Download Ideal Coordinates CCD File 
B [auth A]CITRIC ACID
C6 H8 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.250 
  • R-Value Observed: 0.252 
  • Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.568α = 90
b = 55.052β = 90
c = 68.66γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-29
    Type: Initial release
  • Version 1.1: 2023-05-31
    Changes: Database references
  • Version 1.2: 2023-06-14
    Changes: Database references
  • Version 1.3: 2024-02-07
    Changes: Data collection, Refinement description