5NU6 | pdb_00005nu6

Structure of non-fluorescent human amniotic fluid RBP4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free: 
    0.197 (Depositor), 0.221 (DCC) 
  • R-Value Work: 
    0.169 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Human plasma retinol-binding protein (RBP4) is also a fatty acid-binding protein.

Perduca, M.Nicolis, S.Mannucci, B.Galliano, M.Monaco, H.L.

(2018) Biochim Biophys Acta 1863: 458-466

  • DOI: https://doi.org/10.1016/j.bbalip.2018.01.010
  • Primary Citation Related Structures: 
    5NTY, 5NU2, 5NU6, 5NU7, 5NU8, 5NU9, 5NUA, 5NUB

  • PubMed Abstract: 

    RBP4 (plasma retinol-binding protein) is the 21 kDa transporter of all-trans retinol that circulates in plasma as a moderately tight 1:1 molar complex of the vitamin with the protein. RBP4 is primarily synthesized in the liver but is also produced by adipose tissue and circulates bound to a larger protein, transthyretin, TTR, that serves to increase its molecular mass and thus avoid its elimination by glomerular filtration. This paper reports the high resolution three-dimensional structures of human RBP4 naturally lacking bound retinol purified from plasma, urine and amniotic fluid. In all these crystals we found a fatty acid molecule bound in the hydrophobic ligand-binding site, a result confirmed by mass spectrometry measurements. In addition we also report the 1.5 Å resolution structures of human holo-RBP4 and of the protein saturated with palmitic and lauric acid and discuss the interaction of the fatty acids and retinol with the protein.


  • Organizational Affiliation
    • Biocrystallography Laboratory, Department of Biotechnology, University of Verona, Ca Vignal 1, strada Le Grazie 15, 37134 Verona, Italy.

Macromolecule Content 

  • Total Structure Weight: 21.31 kDa 
  • Atom Count: 1,517 
  • Modeled Residue Count: 175 
  • Deposited Residue Count: 182 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Retinol-binding protein 4182Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P02753 (Homo sapiens)
Explore P02753 
Go to UniProtKB:  P02753
PHAROS:  P02753
GTEx:  ENSG00000138207 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02753
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.68 Å
  • R-Value Free:  0.197 (Depositor), 0.221 (DCC) 
  • R-Value Work:  0.169 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.58α = 90
b = 102.58β = 90
c = 73.282γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Structure summary