Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 25.21 kDa 
• Atom Count: 1930 
• Residue Count: 204 
• Unique protein chains: 1

4HHV

Crystal structure of ceramide transfer protein pleckstrin homology domain

• DOI: 10.2210/pdb4HHV/pdb

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


• Deposited: 2012-10-10 Released: 2013-11-27 
• Deposition Author(s): Prashek, J., Truong, T., Yao, X.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.204 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 

Literature

Crystal Structure of the Pleckstrin Homology Domain from the Ceramide Transfer Protein: Implications for Conformational Change upon Ligand Binding.

Prashek, J., Truong, T., Yao, X.

(2013) PLoS One 8: e79590-e79590

• PubMed: 24260258 
• DOI: 10.1371/journal.pone.0079590
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Ceramide transfer protein (CERT) is responsible for the nonvesicular trafficking of ceramide from the endoplasmic reticulum (ER) to the trans Golgi network where it is converted to sphingomyelin (SM). The N-terminal pleckstrin homology (PH) domain is required for Golgi targeting of CERT by recognizing the phosphatidylinositol 4-phosphate (PtdIns(4)P) enriched in the Golgi membrane. We report a crystal structure of the CERT PH domain. This structure contains a sulfate that is hydrogen bonded with residues in the canonical ligand-binding pocket of PH domains. Our nuclear magnetic resonance (NMR) chemical shift perturbation (CSP) analyses show sulfate association with CERT PH protein resembles that of PtdIns(4)P, suggesting that the sulfate bound structure likely mimics the holo form of CERT PH protein. Comparison of the sulfate bound structure with the apo form solution structure shows structural rearrangements likely occur upon ligand binding, suggesting conformational flexibility in the ligand-binding pocket. This structural flexibility likely explains CERT PH domain's low affinity for PtdIns(4)P, a property that is distinct from many other PH domains that bind to their phosphoinositide ligands tightly. This unique structural feature of CERT PH domain is probably tailored towards the transfer activity of CERT protein where it needs to shuttle between ER and Golgi and therefore requires short resident time on ER and Golgi membranes.

---

Organizational Affiliation: 

Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri Kansas City, Kansas City, Missouri, United States of America.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Collagen type IV alpha-3-binding protein	A, B	105	Homo sapiens	Mutation(s): 0  Gene Names: CERT, COL4A3BP, STARD11, CERT1
Find proteins for Q9Y5P4 (Homo sapiens) Go to UniProtKB:  Q9Y5P4
NIH Common Fund Data Resources
PHAROS  Q9Y5P4 GTEx  ENSG00000113163

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	A, B	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	B	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CL	A, B	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.204 
• R-Value Work: 0.179 
• R-Value Observed: 0.180 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.131	α = 90
b = 54.979	β = 90
c = 98.988	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-10-10 
• Released Date: 2013-11-27 
Deposition Author(s): Prashek, J., Truong, T., Yao, X.

Revision History 

• Version 1.0: 2013-11-27
  Type: Initial release
  
• Version 1.1: 2013-12-25
  Changes: Database references