1EII

NMR STRUCTURE OF HOLO CELLULAR RETINOL-BINDING PROTEIN II


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 30 
  • Conformers Submitted: 25 
  • Selection Criteria: FINAL PENALTY FUNCTION VALUES WITHIN 2 STANDARD DEVIATIONS FROM THE MEAN 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Binding of retinol induces changes in rat cellular retinol-binding protein II conformation and backbone dynamics.

Lu, J.Lin, C.L.Tang, C.Ponder, J.W.Kao, J.L.Cistola, D.P.Li, E.

(2000) J Mol Biol 300: 619-632

  • DOI: 10.1006/jmbi.2000.3883
  • Primary Citation of Related Structures:  
    1EII

  • PubMed Abstract: 
  • The structure and backbone dynamics of rat holo cellular retinol-binding protein II (holo-CRBP II) in solution has been determined by multidimensional NMR. The final structure ensemble was based on 3980 distance and 30 dihedral angle restraints, and was calculated using metric matrix distance geometry with pairwise Gaussian metrization followed by simulated annealing ...

    The structure and backbone dynamics of rat holo cellular retinol-binding protein II (holo-CRBP II) in solution has been determined by multidimensional NMR. The final structure ensemble was based on 3980 distance and 30 dihedral angle restraints, and was calculated using metric matrix distance geometry with pairwise Gaussian metrization followed by simulated annealing. The average RMS deviation of the backbone atoms for the final 25 structures relative to their mean coordinates is 0.85(+/-0.09) A. Comparison of the solution structure of holo-CRBP II with apo-CRBP II indicates that the protein undergoes conformational changes not previously observed in crystalline CRBP II, affecting residues 28-35 of the helix-turn-helix, residues 37-38 of the subsequent linker, as well as the beta-hairpin C-D, E-F and G-H loops. The bound retinol is completely buried inside the binding cavity and oriented as in the crystal structure. The order parameters derived from the (15)N T(1), T(2) and steady-state NOE parameters show that the backbone dynamics of holo-CRBP II is restricted throughout the polypeptide. The T(2) derived apparent backbone exchange rate and amide (1)H exchange rate both indicate that the microsecond to second timescale conformational exchange occurring in the portal region of the apo form has been suppressed in the holo form.


    Related Citations: 
    • The Structure and Dynamics of Rat Apo-Cellular Retinol-Binding Protein II in Solution: Comparison with the X-ray Structure
      Lu, J., Lin, C.L., Tang, C., Ponder, J.W., Kao, J.L., Cistola, D.P., Li, E.
      (1999) J Mol Biol 286: 1179
    • Crystal Structures of Holo and Apo-Cellular Retinol-Binding Protein II
      Winter, N.S., Bratt, J.M., Banaszak, L.J.
      (1993) J Mol Biol 230: 1247
    • Lipid-Binding Proteins: A Family of Fatty Acid and Retinoid Transport Proteins
      Banaszak, L., Winter, N., Xu, Z., Bernlohr, D.A., Cowan, S., Jones, T.A.
      (1994) Adv Protein Chem 45: 89
    • The NMR Solution Structure of Intestinal Fatty Acid-Binding Protein Complexed with Palmitate: Application of a Novel Distance Geometry Algorithm
      Hodsdon, M.E., Ponder, J.W., Cistola, D.P.
      (1996) J Mol Biol 264: 585
    • Ligand Binding Alters the Backbone Mobility of Intestinal Fatty Acid-Binding Protein as Monitored by 15N NMR Relaxation and 1H Exchange
      Hodsdon, M.E., Cistola, D.P.
      (1997) Biochemistry 36: 2278

    Organizational Affiliation

    Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CELLULAR RETINOL-BINDING PROTEIN IIA134Rattus norvegicusMutation(s): 0 
Gene Names: Rbp2Crbpii
UniProt
Find proteins for P06768 (Rattus norvegicus)
Explore P06768 
Go to UniProtKB:  P06768
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06768
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RTL
Query on RTL

Download Ideal Coordinates CCD File 
B [auth A]RETINOL
C20 H30 O
FPIPGXGPPPQFEQ-OVSJKPMPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 30 
  • Conformers Submitted: 25 
  • Selection Criteria: FINAL PENALTY FUNCTION VALUES WITHIN 2 STANDARD DEVIATIONS FROM THE MEAN 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-08-09
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-02-16
    Changes: Data collection, Database references, Derived calculations