Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 24.92 kDa 
• Atom Count: 1871 
• Modelled Residue Count: 205 
• Deposited Residue Count: 209 
• Unique protein chains: 1

2EUM

Crystal structure of human Glycolipid Transfer Protein complexed with 8:0 Lactosylceramide

• PDB DOI: 10.2210/pdb2EUM/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: 2.30 Å
• R-Value Free: 0.250 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 

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: 10.1371/journal.pbio.0040362
• Primary Citation of 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.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycolipid transfer protein	A	209	Homo sapiens	Mutation(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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G84224TW GlyCosmos:  G84224TW GlyGen:  G84224TW

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SPH	C [auth A]	SPHINGOSINE C18 H37 N O2 WWUZIQQURGPMPG-MSOLQXFVSA-N
OCA	D [auth A]	OCTANOIC ACID (CAPRYLIC ACID) C8 H16 O2 WWZKQHOCKIZLMA-UHFFFAOYSA-N
D10	F [auth A]	DECANE C10 H22 DIOQZVSQGTUSAI-UHFFFAOYSA-N
OCT	E [auth A]	N-OCTANE C8 H18 TVMXDCGIABBOFY-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900004	B	beta-lactose	Oligosaccharide / Nutrient		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.250 
• R-Value Work: 0.184 
• R-Value Observed: 0.187 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.509	α = 90
b = 49.264	β = 122.57
c = 68.66	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

• Deposited Date: 2005-10-28 
• 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: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Advisory, Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary