Crystal structure of hPin1 WW domain (5-23) fused with maltose-binding protein

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 

wwPDB Validation   3D Report Full Report

This is version 2.1 of the entry. See complete history


Structural studies of the N-terminal fragments of the WW domain: Insights into co-translational folding of a beta-sheet protein

Hanazono, Y.Takeda, K.Miki, K.

(2016) Sci Rep 6: 34654-34654

  • DOI: https://doi.org/10.1038/srep34654
  • Primary Citation of Related Structures:  
    5B3W, 5B3X, 5B3Y, 5B3Z, 5BMY

  • PubMed Abstract: 

    Nascent proteins fold co-translationally because the folding speed and folding pathways are limited by the rate of ribosome biosynthesis in the living cell. In addition, though full-length proteins can fold all their residues during the folding process, nascent proteins initially fold only with the N-terminal residues. However, the transient structure and the co-translational folding pathway are not well understood. Here we report the atomic structures of a series of N-terminal fragments of the WW domain with increasing amino acid length. Unexpectedly, the structures indicate that the intermediate-length fragments take helical conformations even though the full-length protein has no helical regions. The circular dichroism spectra and theoretical calculations also support the crystallographic results. This suggests that the short-range interactions are more decisive in the structure formation than the long-range interactions for short nascent proteins. In the course of the peptide extension, the helical structure change to the structure mediated by the long-range interactions at a particular polypeptide length. Our results will provide unique information for elucidating the nature of co-translational folding.

  • Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1,Maltose-binding periplasmic protein390Homo sapiensEscherichia coli K-12
This entity is chimeric
Mutation(s): 1 
Gene Names: PIN1malE
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for Q13526 (Homo sapiens)
Explore Q13526 
Go to UniProtKB:  Q13526
PHAROS:  Q13526
GTEx:  ENSG00000127445 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0AEX9Q13526
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.165 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.296α = 90
b = 57.637β = 90
c = 124.056γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-26
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Data collection, Derived calculations
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary