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 

wwPDB Validation 3D Report Full Report


This is version 1.0 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.

(2014) Angew.Chem.Int.Ed.Engl. --: --

  • DOI: 10.1002/anie.201409830
  • Primary Citation of Related Structures:  

  • 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 variou ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fatty acid-binding protein, heart
A
133Homo sapiensMutation(s): 0 
Gene Names: FABP3 (FABP11, MDGI)
Find proteins for P05413 (Homo sapiens)
Go to Gene View: FABP3
Go to UniProtKB:  P05413
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
STE
Query on STE

Download SDF File 
Download CCD File 
A
STEARIC ACID
C18 H36 O2
QIQXTHQIDYTFRH-UHFFFAOYSA-N
 Ligand Interaction
P6G
Query on P6G

Download SDF File 
Download CCD File 
A
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.88 Å
  • R-Value Free: 0.113 
  • R-Value Work: 0.108 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.557α = 90.00
b = 69.418β = 90.00
c = 33.812γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
CCP4model building
BSSdata collection
CCP4phasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-28
    Type: Initial release