3CWK

Crystal Structure of the R132K:Y134F:R111L:T54V:L121E Mutant of Cellular Retinoic Acid Binding Protein Type II in Complex with All-trans-Retinoic Acid at 1.57 Angstroms Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.125 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural analysis of site-directed mutants of cellular retinoic acid-binding protein II addresses the relationship between structural integrity and ligand binding.

Vaezeslami, S.Jia, X.Vasileiou, C.Borhan, B.Geiger, J.H.

(2008) Acta Crystallogr D Biol Crystallogr 64: 1228-1239

  • DOI: 10.1107/S0907444908032216
  • Primary Citation of Related Structures:  
    3D95, 3D96, 3CWK

  • PubMed Abstract: 
  • The structural integrity of cellular retinoic acid-binding protein II (CRABPII) has been investigated using the crystal structures of CRABPII mutants. The overall fold was well maintained by these CRABPII mutants, each of which carried multiple diffe ...

    The structural integrity of cellular retinoic acid-binding protein II (CRABPII) has been investigated using the crystal structures of CRABPII mutants. The overall fold was well maintained by these CRABPII mutants, each of which carried multiple different mutations. A water-mediated network is found to be present across the large binding cavity, extending from Arg111 deep inside the cavity to the alpha2 helix at its entrance. This chain of interactions acts as a ;pillar' that maintains the integrity of the protein. The disruption of the water network upon loss of Arg111 leads to decreased structural integrity of the protein. A water-mediated network can be re-established by introducing the hydrophilic Glu121 inside the cavity, which results in a rigid protein with the alpha2 helix adopting an altered conformation compared with wild-type CRABPII.


    Related Citations: 
    • Determining Crystal Structures of Proteins and Protein Complexes by X-Ray Crystallography: X-Ray Crystallographic Studies of the Mutants of Cellular Retinoic Acid Binding Protein Type II Toward Designing a Mimic of Rhodopsin
      Vaezeslami, S.
      () Thesis --: --

    Organizational Affiliation

    Rigaku Americas Corporation, 9009 New Trails Drive, The Woodlands, TX 77381, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cellular retinoic acid-binding protein 2A137N/AMutation(s): 5 
Gene Names: CRABP2
Find proteins for P29373 (Homo sapiens)
Explore P29373 
Go to UniProtKB:  P29373
NIH Common Fund Data Resources
PHAROS  P29373
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
REA
Query on REA

Download CCD File 
A
RETINOIC ACID
C20 H28 O2
SHGAZHPCJJPHSC-YCNIQYBTSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
REAKd :  250   nM  PDBBind
REAKd:  250   nM  Binding MOAD
REAKd:  200   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.120 
  • R-Value Observed: 0.125 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.787α = 90
b = 44.86β = 90
c = 77.865γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-09
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description