4GIX

Crystal structure of human GLTP bound with 12:0 disulfatide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.187 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structural insights into lipid-dependent reversible dimerization of human GLTP.

Samygina, V.R.Ochoa-Lizarralde, B.Popov, A.N.Cabo-Bilbao, A.Goni-de-Cerio, F.Molotkovsky, J.G.Patel, D.J.Brown, R.E.Malinina, L.

(2013) Acta Crystallogr D Biol Crystallogr 69: 603-616

  • DOI: https://doi.org/10.1107/S0907444913000024
  • Primary Citation of Related Structures:  
    4GH0, 4GHP, 4GHS, 4GIX, 4GJQ, 4GVT, 4GXD, 4GXG, 4H2Z

  • PubMed Abstract: 

    Human glycolipid transfer protein (hsGLTP) forms the prototypical GLTP fold and is characterized by a broad transfer selectivity for glycosphingolipids (GSLs). The GLTP mutation D48V near the `portal entrance' of the glycolipid binding site has recently been shown to enhance selectivity for sulfatides (SFs) containing a long acyl chain. Here, nine novel crystal structures of hsGLTP and the SF-selective mutant complexed with short-acyl-chain monoSF and diSF in different crystal forms are reported in order to elucidate the potential functional roles of lipid-mediated homodimerization. In all crystal forms, the hsGLTP-SF complexes displayed homodimeric structures supported by similarly organized intermolecular interactions. The dimerization interface always involved the lipid sphingosine chain, the protein C-terminus (C-end) and α-helices 6 and 2, but the D48V mutant displayed a `locked' dimer conformation compared with the hinge-like flexibility of wild-type dimers. Differences in contact angles, areas and residues at the dimer interfaces in the `flexible' and `locked' dimers revealed a potentially important role of the dimeric structure in the C-end conformation of hsGLTP and in the precise positioning of the key residue of the glycolipid recognition centre, His140. ΔY207 and ΔC-end deletion mutants, in which the C-end is shifted or truncated, showed an almost complete loss of transfer activity. The new structural insights suggest that ligand-dependent reversible dimerization plays a role in the function of human GLTP.


  • Organizational Affiliation

    Structural Biology Unit, CIC bioGUNE, Technology Park of Bizkaia, 48160 Derio, Spain.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glycolipid transfer protein209Homo sapiensMutation(s): 0 
Gene Names: GLTP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZD2 (Homo sapiens)
Explore Q9NZD2 
Go to UniProtKB:  Q9NZD2
PHAROS:  Q9NZD2
GTEx:  ENSG00000139433 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NZD2
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0SG
Query on 0SG

Download Ideal Coordinates CCD File 
B [auth A]N-{(2S,3R,4E)-1-[(3,6-di-O-sulfo-beta-D-galactopyranosyl)oxy]-3-hydroxyoctadec-4-en-2-yl}dodecanamide
C36 H69 N O14 S2
JBJSVLZKWGLXMO-AZNTWQPMSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.768α = 90
b = 50.163β = 118.82
c = 65.85γ = 90
Software Package:
Software NamePurpose
MAR345dtbdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data 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: 2013-04-10
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description