Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 40.85 kDa 
• Atom Count: 2816 
• Residue Count: 331 
• Unique protein chains: 2

5JJD

crystal structure of the ceramide transfer protein PH and START domain complex

• DOI: 10.2210/pdb5JJD/pdb

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


• Deposited: 2016-04-23 Released: 2017-07-05 
• Deposition Author(s): Prashek, J., Bouyain, S., Yao, X.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.245 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 

Literature

Interaction between the PH and START domains of ceramide transfer protein competes with phosphatidylinositol 4-phosphate binding by the PH domain.

Prashek, J., Bouyain, S., Fu, M., Li, Y., Berkes, D., Yao, X.

(2017) J Biol Chem 292: 14217-14228

• PubMed: 28652409 
• DOI: 10.1074/jbc.M117.780007
• Primary Citation of Related Structures:  
  5JJD


• PubMed Abstract: 
  

De novo synthesis of the sphingolipid sphingomyelin requires non-vesicular transport of ceramide from the endoplasmic reticulum to the Golgi by the multidomain protein ceramide transfer protein (CERT). CERT's N-terminal pleckstrin homology (PH) domain targets it to the Golgi by binding to phosphatidylinositol 4-phosphate (PtdIns(4)P) in the Golgi membrane, whereas its C-terminal StAR-related lipid transfer domain (START) carries out ceramide transfer. Hyperphosphorylation of a serine-rich motif immediately after the PH domain decreases both PtdIns(4)P binding and ceramide transfer by CERT. This down-regulation requires both the PH and START domains, suggesting a possible inhibitory interaction between the two domains. In this study we show that isolated PH and START domains interact with each other. The crystal structure of a PH-START complex revealed that the START domain binds to the PH domain at the same site for PtdIns(4)P-binding, suggesting that the START domain competes with PtdIns(4)P for association with the PH domain. We further report that mutations disrupting the PH-START interaction increase both PtdIns(4)P-binding affinity and ceramide transfer activity of a CERT-serine-rich phosphorylation mimic. We also found that these mutations increase the Golgi localization of CERT inside the cell, consistent with enhanced PtdIns(4)P binding of the mutant. Collectively, our structural, biochemical, and cellular investigations provide important structural insight into the regulation of CERT function and localization.

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Organizational Affiliation: 

From the Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, Missouri 64110, [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen type IV alpha-3-binding protein	A	106	Homo sapiens	Mutation(s): 0  Gene Names: COL4A3BP, CERT, STARD11, CERT1
Find proteins for Q9Y5P4 (Homo sapiens) Explore Q9Y5P4  Go to UniProtKB:  Q9Y5P4
NIH Common Fund Data Resources
PHAROS  Q9Y5P4 GTEx  ENSG00000113163

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Collagen type IV alpha-3-binding protein	B	246	Homo sapiens	Mutation(s): 0  Gene Names: COL4A3BP, CERT, STARD11, CERT1
Find proteins for Q9Y5P4 (Homo sapiens) Explore Q9Y5P4  Go to UniProtKB:  Q9Y5P4
NIH Common Fund Data Resources
PHAROS  Q9Y5P4 GTEx  ENSG00000113163

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	B	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	B	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.245 
• R-Value Work: 0.201 
• R-Value Observed: 0.203 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.761	α = 90
b = 60.914	β = 90
c = 95.804	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-04-23 
• Released Date: 2017-07-05 
Deposition Author(s): Prashek, J., Bouyain, S., Yao, X.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1 R15 GM113200-01

Revision History 

• Version 1.0: 2017-07-05
  Type: Initial release
  
• Version 1.1: 2017-09-13
  Changes: Author supporting evidence
• Version 1.2: 2019-01-16
  Changes: Data collection, Database references
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence