1H8X

Domain-swapped Dimer of a Human Pancreatic Ribonuclease Variant

• PDB DOI: https://doi.org/10.2210/pdb1H8X/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2001-02-16 Released: 2002-02-14 
• Deposition Author(s): Canals, A., Pous, J., Guasch, A., Benito, A., Ribo, M., Vilanova, M., Coll, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.243 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 

Literature

The Structure of an Engineered Domain-Swapped Ribonuclease Dimer and its Implications for the Evolution of Proteins Toward Oligomerization

Canals, A., Pous, J., Guasch, A., Benito, A., Ribo, M., Vilanova, M., Coll, M.

(2001) Structure 9: 967

• PubMed: 11591351 
• DOI: https://doi.org/10.1016/s0969-2126(01)00659-1
• Primary Citation of Related Structures:  
  1H8X


• PubMed Abstract: 
  

  Domain swapping has been proposed as a mechanism that explains the evolution from monomeric to oligomeric proteins. Bovine and human pancreatic ribonucleases are monomers with no biological properties other than their RNA cleavage ability. In contrast, the closely related bovine seminal ribonuclease is a natural domain-swapped dimer that has special biological properties, such as cytotoxicity to tumour cells. Several recombinant ribonuclease variants are domain-swapped dimers, but a structure of this kind has not yet been reported for the human enzyme.

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Organizational Affiliation: 

Laboratori d'Enginyeria de Proteïnes, Facultat de Ciències, Universitat de Girona, Campus de Montilivi, Girona E-17071, Spain.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 28.91 kDa 
• Atom Count: 2,327 
• Modelled Residue Count: 252 
• Deposited Residue Count: 256 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBONUCLEASE 1	A, B	128	Homo sapiens	Mutation(s): 6  Gene Names: PM8 EC: 3.1.27.5
UniProt & NIH Common Fund Data Resources
Find proteins for P07998 (Homo sapiens) Explore P07998  Go to UniProtKB:  P07998
PHAROS:  P07998 GTEx:  ENSG00000129538

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.243 
• R-Value Work: 0.196 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.61	α = 90
b = 61.43	β = 90
c = 75.14	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-02-14 
Deposition Author(s): Canals, A., Pous, J., Guasch, A., Benito, A., Ribo, M., Vilanova, M., Coll, M.

Revision History  

• Version 1.0: 2002-02-14
  Type: Initial release
  
• Version 1.1: 2011-05-07
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-13
  Changes: Data collection, Database references, Refinement description