6VIT

The Crystal Structure of Apo Domain-Swapped dimer Q108K:T51D:I32C Variant of HCRBPII with an Engineered Disulfide Bond


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.239 

wwPDB Validation   3D Report Full Report

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This is version 1.2 of the entry. See complete history


Literature

Human Cellular Retinol Binding Protein II Forms a Domain-Swapped Trimer Representing a Novel Fold and a New Template for Protein Engineering.

Ghanbarpour, A.Santos, E.M.Pinger, C.Assar, Z.Hossaini Nasr, S.Vasileiou, C.Spence, D.Borhan, B.Geiger, J.H.

(2020) Chembiochem 21: 3192-3196

  • DOI: https://doi.org/10.1002/cbic.202000405
  • Primary Citation of Related Structures:  
    6VIS, 6VIT, 6WNF, 6WNJ, 6WP0, 6WP1, 6WP2

  • PubMed Abstract: 

    Domain-swapping is a mechanism for evolving new protein structure from extant scaffolds, and has been an efficient protein-engineering strategy for tailoring functional diversity. However, domain swapping can only be exploited if it can be controlled, especially in cases where various folds can coexist. Herein, we describe the structure of a domain-swapped trimer of the iLBP family member hCRBPII, and suggest a mechanism for domain-swapped trimerization. It is further shown that domain-swapped trimerization can be favored by strategic installation of a disulfide bond, thus demonstrating a strategy for fold control. We further show the domain-swapped trimer to be a useful protein design template by installing a high-affinity metal binding site through the introduction of a single mutation, taking advantage of its threefold symmetry. Together, these studies show how nature can promote oligomerization, stabilize a specific oligomer, and generate new function with minimal changes to the protein sequence.


  • Organizational Affiliation

    Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Retinol-binding protein 2
A, B
133Homo sapiensMutation(s): 3 
Gene Names: RBP2CRBP2
UniProt & NIH Common Fund Data Resources
Find proteins for P50120 (Homo sapiens)
Explore P50120 
Go to UniProtKB:  P50120
PHAROS:  P50120
GTEx:  ENSG00000114113 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50120
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.239 
  • Space Group: P 63
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 133.283α = 90
b = 133.283β = 90
c = 51.16γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM101353

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release
  • Version 1.1: 2021-05-05
    Changes: Database references
  • Version 1.2: 2023-10-11
    Changes: Data collection, Database references, Refinement description