3UI4

0.8 A resolution crystal structure of human Parvulin 14

• PDB DOI: https://doi.org/10.2210/pdb3UI4/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-11-04 Released: 2011-12-07 
• Deposition Author(s): Mueller, J.W., Link, N.M., Matena, A., Hoppstock, L., Rueppel, A., Bayer, P., Blankenfeldt, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.80 Å
• R-Value Free: 0.098 
• R-Value Work: 0.095 
• R-Value Observed: 0.095 

Literature

Crystallographic proof for an extended hydrogen-bonding network in small prolyl isomerases.

Mueller, J.W., Link, N.M., Matena, A., Hoppstock, L., Ruppel, A., Bayer, P., Blankenfeldt, W.

(2011) J Am Chem Soc 133: 20096-20099

• PubMed: 22081960 
• DOI: https://doi.org/10.1021/ja2086195
• Primary Citation of Related Structures:  
  3UI4, 3UI5


• PubMed Abstract: 
  

  Parvulins compose a family of small peptidyl-prolyl isomerases (PPIases) involved in protein folding and protein quality control. A number of amino acids in the catalytic cavity are highly conserved, but their precise role within the catalytic mechanism is unknown. The 0.8 Å crystal structure of the prolyl isomerase domain of parvulin Par14 shows the electron density of hydrogen atoms between the D74, H42, H123, and T118 side chains. This threonine residue has previously not been associated with catalysis, but a corresponding T152A mutant of Pin1 shows a dramatic reduction of catalytic activity without compromising protein stability. The observed catalytic tetrad is strikingly conserved in Pin1- and parvulin-type proteins and hence constitutes a common feature of small peptidyl prolyl isomerases.

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Organizational Affiliation: 

Institute for Structural and Medicinal Biochemistry, Center for Medical Biotechnology (ZMB), University of Duisburg-Essen, 45117 Essen, Germany.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 11.62 kDa 
• Atom Count: 1,169 
• Modelled Residue Count: 101 
• Deposited Residue Count: 101 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 4	A	101	Homo sapiens	Mutation(s): 0  Gene Names: PIN4, Q9Y237 EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y237 (Homo sapiens) Explore Q9Y237  Go to UniProtKB:  Q9Y237
PHAROS:  Q9Y237 GTEx:  ENSG00000102309

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	B [auth A], C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.80 Å
• R-Value Free: 0.098 
• R-Value Work: 0.095 
• R-Value Observed: 0.095 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.043	α = 90
b = 46.966	β = 90
c = 51.826	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-12-07 
Deposition Author(s): Mueller, J.W., Link, N.M., Matena, A., Hoppstock, L., Rueppel, A., Bayer, P., Blankenfeldt, W.

Revision History  

• Version 1.0: 2011-12-07
  Type: Initial release
  
• Version 1.1: 2012-12-05
  Changes: Structure summary
• Version 1.2: 2013-01-09
  Changes: Database references
• Version 1.3: 2024-02-28
  Changes: Data collection, Database references, Derived calculations