Crystal Structure of Human Glycolipid Transfer Protein complexed with 3-O-sulfo-galactosylceramide containing nervonoyl acyl chain (24:1)

Experimental Data Snapshot

  • Resolution: 1.10 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 

Starting Model: experimental
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Enhanced selectivity for sulfatide by engineered human glycolipid transfer protein.

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

(2011) Structure 19: 1644-1654

  • DOI: https://doi.org/10.1016/j.str.2011.09.011
  • Primary Citation of Related Structures:  
    3RIC, 3RWV, 3RZN, 3S0I, 3S0K

  • PubMed Abstract: 

    Human glycolipid transfer protein (GLTP) fold represents a novel structural motif for lipid binding/transfer and reversible membrane translocation. GLTPs transfer glycosphingolipids (GSLs) that are key regulators of cell growth, division, surface adhesion, and neurodevelopment. Herein, we report structure-guided engineering of the lipid binding features of GLTP. New crystal structures of wild-type GLTP and two mutants (D48V and A47D‖D48V), each containing bound N-nervonoyl-sulfatide, reveal the molecular basis for selective anchoring of sulfatide (3-O-sulfo-galactosylceramide) by D48V-GLTP. Directed point mutations of "portal entrance" residues, A47 and D48, reversibly regulate sphingosine access to the hydrophobic pocket via a mechanism that could involve homodimerization. "Door-opening" conformational changes by phenylalanines within the hydrophobic pocket are revealed during lipid encapsulation by new crystal structures of bona fide apo-GLTP and GLTP complexed with N-oleoyl-glucosylceramide. The development of "engineered GLTPs" with enhanced specificity for select GSLs provides a potential new therapeutic approach for targeting GSL-mediated pathologies.

  • Organizational Affiliation

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

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
GTEx:  ENSG00000139433 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NZD2
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on CIS

Download Ideal Coordinates CCD File 
C48 H91 N O11 S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.10 Å
  • R-Value Free: 0.157 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.891α = 90
b = 50.06β = 118.52
c = 65.404γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
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: 2012-02-08
    Type: Initial release
  • Version 1.1: 2017-10-25
    Changes: Author supporting evidence
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description