4RTE | pdb_00004rte

The X-ray structure of bovine pancreatic ribonuclease incubated in the presence of an excess of cisplatin (1:10 ratio)

• PDB DOI: https://doi.org/10.2210/pdb4RTE/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2014-11-14 Released: 2015-03-25 
• Deposition Author(s): Russo Krauss, I., Merlino, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.224 (Depositor), 0.228 (DCC) 
• R-Value Work: 
  0.167 (Depositor), 0.176 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Platinated oligomers of bovine pancreatic ribonuclease: Structure and stability.

Picone, D., Donnarumma, F., Ferraro, G., Russo Krauss, I., Fagagnini, A., Gotte, G., Merlino, A.

(2015) J Inorg Biochem 146: 37-43

• PubMed: 25756333 
• DOI: https://doi.org/10.1016/j.jinorgbio.2015.02.011
• Primary Citation Related Structures: 
  4RTE


• PubMed Abstract: 
  

  The reaction between cis-diamminedichloroplatinum(II) (CDDP), cisplatin, a common anticancer drug, and bovine pancreatic ribonuclease (RNase A), induces extensive protein aggregation, leading to the formation of one dimer, one trimer and higher oligomers whose yields depend on cisplatin/protein ratio. Structural and functional properties of the purified platinated species, together with their spontaneous dissociation and thermally induced denaturation, have been characterized. Platinated species preserve a significant, although reduced, ribonuclease activity. The high resistance of the dimers against dissociation and the different thermal unfolding profiles suggest a quaternary structure different from those of the well-known swapped dimers of RNase A.

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Organizational Affiliation: 
• Department of Chemical Sciences, University of Naples Federico II, Via Cintia, I-80126 Naples, Italy. Electronic address: [e-mail].
Department of Chemical Sciences, University of Naples Federico II, Via Cintia, I-80126 Naples, Italy.
Department of Chemical Sciences, University of Naples Federico II, Via Cintia, I-80126 Naples, Italy; Institute of Biostructures and Bioimages, CNR, Via Mezzocannone 16, I-80134 Naples, Italy.
Department of Life and Reproduction Sciences, Biological Chemistry Section, University of Verona, Strada Le Grazie 8, I-37134 Verona, Italy.
Department of Chemical Sciences, University of Naples Federico II, Via Cintia, I-80126 Naples, Italy; Institute of Biostructures and Bioimages, CNR, Via Mezzocannone 16, I-80134 Naples, Italy. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 15.01 kDa 
• Atom Count: 1,140 
• Modeled Residue Count: 124 
• Deposited Residue Count: 124 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribonuclease pancreatic	A	124	Bos taurus	Mutation(s): 0  Gene Names: RNASE1, RNS1 EC: 3.1.27.5 (PDB Primary Data), 4.6.1.18 (UniProt)
UniProt
Find proteins for P61823 (Bos taurus) Explore P61823  Go to UniProtKB:  P61823

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CPT	B [auth A], C [auth A], D [auth A], E [auth A]	Cisplatin Cl2 H6 N2 Pt LXZZYRPGZAFOLE-UHFFFAOYSA-L
CL	F [auth A], G [auth A], H [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.224 (Depositor), 0.228 (DCC) 
• R-Value Work:  0.167 (Depositor), 0.176 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.77	α = 90
b = 63.77	β = 90
c = 63.575	γ = 120

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-03-25 
Deposition Author(s): Russo Krauss, I., Merlino, A.

Revision History  

• Version 1.0: 2015-03-25
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-06
  Changes: Structure summary