4QYP

The Crystal Structures of holo-wt human Cellular Retinol Binding protein II (hCRBPII) bound to Retinal


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

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: 3226-3232

  • DOI: 10.1107/S1399004714023839
  • Primary Citation of Related Structures:  
  • Also Cited By: 5DG4, 4ZR2, 4ZH9, 4ZH6, 4ZGU, 4ZCB

  • PubMed Abstract: 
  • Cellular retinol-binding proteins (CRBPs) I and II, which are members of the intracellular lipid-binding protein (iLBP) family, are retinoid chaperones that are responsible for the intracellular transport and delivery of both retinol and retinal. Alt ...

    Cellular retinol-binding proteins (CRBPs) I and II, which are members of the intracellular lipid-binding protein (iLBP) family, are retinoid chaperones that are responsible for the intracellular transport and delivery of both retinol and retinal. Although structures of retinol-bound CRBPI and CRBPII are known, no structure of a retinal-bound CRBP has been reported. In addition, the retinol-bound human CRBPII (hCRBPII) structure shows partial occupancy of a noncanonical conformation of retinol in the binding pocket. Here, the structure of retinal-bound hCRBPII and the structure of retinol-bound hCRBPII with retinol fully occupying the binding pocket are reported. It is further shown that the retinoid derivative seen in both the zebrafish CRBP and the hCRBPII structures is likely to be the product of flux-dependent and wavelength-dependent X-ray damage during data collection. The structures of retinoid-bound CRBPs are compared and contrasted, and rationales for the differences in binding affinities for retinal and retinol are provided.


    Organizational Affiliation

    Department of Chemistry, Michigan State University, East Lansing, MI 48864, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Retinol-binding protein 2
A, B, C, D
133Homo sapiensMutation(s): 0 
Gene Names: RBP2 (CRBP2)
Find proteins for P50120 (Homo sapiens)
Go to Gene View: RBP2
Go to UniProtKB:  P50120
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
B, C, D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
RET
Query on RET

Download SDF File 
Download CCD File 
A, B, C
RETINAL
C20 H28 O
NCYCYZXNIZJOKI-OVSJKPMPSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.202 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 36.440α = 107.75
b = 54.892β = 97.66
c = 68.716γ = 103.08
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-10
    Type: Initial release
  • Version 1.1: 2015-01-28
    Type: Database references