3WVM

The 0.88 angstrom X-ray structure of the human heart fatty acid-binding protein complexed with stearic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.88 Å
  • R-Value Free: 0.113 
  • R-Value Work: 0.108 
  • R-Value Observed: 0.108 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Water-mediated recognition of simple alkyl chains by heart-type fatty-acid-binding protein.

Matsuoka, S.Sugiyama, S.Matsuoka, D.Hirose, M.Lethu, S.Ano, H.Hara, T.Ichihara, O.Kimura, S.R.Murakami, S.Ishida, H.Mizohata, E.Inoue, T.Murata, M.

(2015) Angew Chem Int Ed Engl 54: 1508-1511

  • DOI: https://doi.org/10.1002/anie.201409830
  • Primary Citation of Related Structures:  
    3WVM, 4TJZ, 4TKB, 4TKH, 4TKJ

  • PubMed Abstract: 

    Long-chain fatty acids (FAs) with low water solubility require fatty-acid-binding proteins (FABPs) to transport them from cytoplasm to the mitochondria for energy production. However, the precise mechanism by which these proteins recognize the various lengths of simple alkyl chains of FAs with similar high affinity remains unknown. To address this question, we employed a newly developed calorimetric method for comprehensively evaluating the affinity of FAs, sub-Angstrom X-ray crystallography to accurately determine their 3D structure, and energy calculations of the coexisting water molecules using the computer program WaterMap. Our results clearly showed that the heart-type FABP (FABP3) preferentially incorporates a U-shaped FA of C10-C18 using a lipid-compatible water cluster, and excludes longer FAs using a chain-length-limiting water cluster. These mechanisms could help us gain a general understanding of how proteins recognize diverse lipids with different chain lengths.


  • Organizational Affiliation

    JST-ERATO and Graduate School of Science, Osaka University, Machikaneyama, Toyonaka, Osaka 560-0043 (Japan); Project Research Centre for Fundamental Science, Osaka University, Machikaneyama, Toyonaka, Osaka 560-0043 (Japan).


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fatty acid-binding protein, heart133Homo sapiensMutation(s): 0 
Gene Names: FABP3
UniProt & NIH Common Fund Data Resources
Find proteins for P05413 (Homo sapiens)
Explore P05413 
Go to UniProtKB:  P05413
PHAROS:  P05413
GTEx:  ENSG00000121769 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05413
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.88 Å
  • R-Value Free: 0.113 
  • R-Value Work: 0.108 
  • R-Value Observed: 0.108 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.557α = 90
b = 69.418β = 90
c = 33.812γ = 90
Software Package:
Software NamePurpose
BSSdata collection
CCP4model building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-01-28
    Type: Initial release
  • Version 1.1: 2022-08-24
    Changes: Database references, Derived calculations
  • Version 1.2: 2024-05-29
    Changes: Data collection