4ZH6

Crystal Structure of the Domain-Swapped Dimer Y60L mutant of Human Cellular Retinol Binding Protein II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5497 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Domain-Swapped Dimers of Intracellular Lipid-Binding Proteins: Evidence for Ordered Folding Intermediates.

Assar, Z.Nossoni, Z.Wang, W.Santos, E.M.Kramer, K.McCornack, C.Vasileiou, C.Borhan, B.Geiger, J.H.

(2016) Structure 24: 1590-1598

  • DOI: 10.1016/j.str.2016.05.022
  • Primary Citation of Related Structures:  
  • Also Cited By: 5U6G

  • PubMed Abstract: 
  • Human Cellular Retinol Binding Protein II (hCRBPII), a member of the intracellular lipid-binding protein family, is a monomeric protein responsible for the intracellular transport of retinol and retinal. Herein we report that hCRBPII forms an extensi ...

    Human Cellular Retinol Binding Protein II (hCRBPII), a member of the intracellular lipid-binding protein family, is a monomeric protein responsible for the intracellular transport of retinol and retinal. Herein we report that hCRBPII forms an extensive domain-swapped dimer during bacterial expression. The domain-swapped region encompasses almost half of the protein. The dimer represents a novel structural architecture with the mouths of the two binding cavities facing each other, producing a new binding cavity that spans the length of the protein complex. Although wild-type hCRBPII forms the dimer, the propensity for dimerization can be substantially increased via mutation at Tyr60. The monomeric form of the wild-type protein represents the thermodynamically more stable species, making the domain-swapped dimer a kinetically trapped entity. Hypothetically, the wild-type protein has evolved to minimize dimerization of the folding intermediate through a critical hydrogen bond (Tyr60-Glu72) that disfavors the dimeric form.


    Related Citations: 
    • Structures of holo wild-type human cellular retinol-binding protein II (hCRBPII) bound to retinol and retinal.
      Nossoni, Z.,Assar, Z.,Yapici, I.,Nosrati, M.,Wang, W.,Berbasova, T.,Vasileiou, C.,Borhan, B.,Geiger, J.
      (2014) Acta Crystallogr.,Sect.D 70: 3226
    • Tuning the electronic absorption of protein-embedded all-trans-retinal.
      Wang, W.,Nossoni, Z.,Berbasova, T.,Watson, C.T.,Yapici, I.,Lee, K.S.,Vasileiou, C.,Geiger, J.H.,Borhan, B.
      (2012) Science 338: 1340


    Organizational Affiliation

    Department of Chemistry, Michigan State University, East Lansing, MI 48824, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Retinol-binding protein 2
A
133Homo sapiensMutation(s): 1 
Gene Names: RBP2 (CRBP2)
Find proteins for P50120 (Homo sapiens)
Go to Gene View: RBP2
Go to UniProtKB:  P50120
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5497 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.187 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.776α = 90.00
b = 60.424β = 90.00
c = 63.603γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM101353

Revision History 

  • Version 1.0: 2016-06-08
    Type: Initial release
  • Version 1.1: 2017-09-06
    Type: Author supporting evidence, Database references, Derived calculations
  • Version 1.2: 2017-11-01
    Type: Author supporting evidence, Refinement description