2OBD

Crystal Structure of Cholesteryl Ester Transfer Protein


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 4.2 of the entry. See complete history


Literature

Crystal structure of cholesteryl ester transfer protein reveals a long tunnel and four bound lipid molecules.

Qiu, X.Mistry, A.Ammirati, M.J.Chrunyk, B.A.Clark, R.W.Cong, Y.Culp, J.S.Danley, D.E.Freeman, T.B.Geoghegan, K.F.Griffor, M.C.Hawrylik, S.J.Hayward, C.M.Hensley, P.Hoth, L.R.Karam, G.A.Lira, M.E.Lloyd, D.B.McGrath, K.M.Stutzman-Engwall, K.J.Subashi, A.K.Subashi, T.A.Thompson, J.F.Wang, I.K.Zhao, H.Seddon, A.P.

(2007) Nat Struct Mol Biol 14: 106-113

  • DOI: https://doi.org/10.1038/nsmb1197
  • Primary Citation of Related Structures:  
    2OBD

  • PubMed Abstract: 

    Cholesteryl ester transfer protein (CETP) shuttles various lipids between lipoproteins, resulting in the net transfer of cholesteryl esters from atheroprotective, high-density lipoproteins (HDL) to atherogenic, lower-density species. Inhibition of CETP raises HDL cholesterol and may potentially be used to treat cardiovascular disease. Here we describe the structure of CETP at 2.2-A resolution, revealing a 60-A-long tunnel filled with two hydrophobic cholesteryl esters and plugged by an amphiphilic phosphatidylcholine at each end. The two tunnel openings are large enough to allow lipid access, which is aided by a flexible helix and possibly also by a mobile flap. The curvature of the concave surface of CETP matches the radius of curvature of HDL particles, and potential conformational changes may occur to accommodate larger lipoprotein particles. Point mutations blocking the middle of the tunnel abolish lipid-transfer activities, suggesting that neutral lipids pass through this continuous tunnel.


  • Organizational Affiliation

    Pfizer Global Research and Development, Eastern Point Road, Groton, Connecticut 06430, USA. xiayang.qiu@pfizer.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cholesteryl ester transfer protein476Homo sapiensMutation(s): 6 
Gene Names: CETP
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P11597 (Homo sapiens)
Explore P11597 
Go to UniProtKB:  P11597
PHAROS:  P11597
GTEx:  ENSG00000087237 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11597
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P11597-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
B
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PCW
Query on PCW

Download Ideal Coordinates CCD File 
F [auth A],
G [auth A]
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE
C44 H85 N O8 P
SNKAWJBJQDLSFF-NVKMUCNASA-O
2OB
Query on 2OB

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
CHOLESTERYL OLEATE
C45 H78 O2
RJECHNNFRHZQKU-RMUVNZEASA-N
EPE
Query on EPE

Download Ideal Coordinates CCD File 
H [auth A]4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
I [auth A],
J [auth A]
PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
K [auth A]TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.78α = 90
b = 70.32β = 90
c = 187.62γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2007-01-23 
  • Deposition Author(s): Qiu, X.

Revision History  (Full details and data files)

  • Version 1.0: 2007-01-23
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2017-11-29
    Changes: Advisory, Atomic model, Derived calculations, Non-polymer description, Structure summary
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 4.0: 2021-10-20
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Source and taxonomy, Structure summary
  • Version 4.1: 2023-12-27
    Changes: Data collection
  • Version 4.2: 2024-11-13
    Changes: Structure summary