2EUK | pdb_00002euk

Crystal Structure of Human Glycolipid Transfer Protein complexed with 24:1 Galactosylceramide

• PDB DOI: https://doi.org/10.2210/pdb2EUK/pdb

• Classification: LIPID TRANSPORT
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-10-28 Released: 2006-11-14 
• Deposition Author(s): Malinina, L., Malakhova, M.L., Kanack, A.T., Abagyan, R., Brown, R.E., Patel, D.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.230 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.178 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Starting Model: experimental

Literature

The liganding of glycolipid transfer protein is controlled by glycolipid acyl structure.

Malinina, L., Malakhova, M.L., Kanack, A.T., Lu, M., Abagyan, R., Brown, R.E., Patel, D.J.

(2006) PLoS Biol 4: e362-e362

• PubMed: 17105344 
• DOI: https://doi.org/10.1371/journal.pbio.0040362
• Primary Citation Related Structures: 
  2EUK, 2EUM, 2EVD, 2EVL, 2EVS, 2EVT


• PubMed Abstract: 
  

  Glycosphingolipids (GSLs) play major roles in cellular growth and development. Mammalian glycolipid transfer proteins (GLTPs) are potential regulators of cell processes mediated by GSLs and display a unique architecture among lipid binding/transfer proteins. The GLTP fold represents a novel membrane targeting/interaction domain among peripheral proteins. Here we report crystal structures of human GLTP bound to GSLs of diverse acyl chain length, unsaturation, and sugar composition. Structural comparisons show a highly conserved anchoring of galactosyl- and lactosyl-amide headgroups by the GLTP recognition center. By contrast, acyl chain chemical structure and occupancy of the hydrophobic tunnel dictate partitioning between sphingosine-in and newly-observed sphingosine-out ligand-binding modes. The structural insights, combined with computed interaction propensity distributions, suggest a concerted sequence of events mediated by GLTP conformational changes during GSL transfer to and/or from membranes, as well as during GSL presentation and/or transfer to other proteins.

---

Organizational Affiliation: 
• Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 24.84 kDa 
• Atom Count: 1,892 
• Modeled Residue Count: 204 
• Deposited Residue Count: 209 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycolipid transfer protein	A	209	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZD2 (Homo sapiens) Explore Q9NZD2  Go to UniProtKB:  Q9NZD2
PHAROS:  Q9NZD2 GTEx:  ENSG00000139433

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NER	D [auth A]	(15E)-TETRACOS-15-ENOIC ACID C24 H46 O2 GWHCXVQVJPWHRF-KTKRTIGZSA-N
SPH	C [auth A]	SPHINGOSINE C18 H37 N O2 WWUZIQQURGPMPG-MSOLQXFVSA-N
GAL	B [auth A]	beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N
OCT	E [auth A]	N-OCTANE C8 H18 TVMXDCGIABBOFY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.230 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.178 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.867	α = 90
b = 49.304	β = 122.61
c = 68.655	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-14 
Deposition Author(s): Malinina, L., Malakhova, M.L., Kanack, A.T., Abagyan, R., Brown, R.E., Patel, D.J.

Revision History  

• Version 1.0: 2006-11-14
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Derived calculations, Structure summary
• Version 1.5: 2023-08-23
  Changes: Data collection, Database references, Refinement description, Structure summary