1BZ4

APOLIPOPROTEIN E3 (APO-E3), TRUNCATION MUTANT 165


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Conformational flexibility in the apolipoprotein E amino-terminal domain structure determined from three new crystal forms: implications for lipid binding.

Segelke, B.W.Forstner, M.Knapp, M.Trakhanov, S.D.Parkin, S.Newhouse, Y.M.Bellamy, H.D.Weisgraber, K.H.Rupp, B.

(2000) Protein Sci 9: 886-897

  • DOI: 10.1110/ps.9.5.886
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • An amino-terminal fragment of human apolipoprotein E3 (residues 1-165) has been expressed and crystallized in three different crystal forms under similar crystallization conditions. One crystal form has nearly identical cell dimensions to the previou ...

    An amino-terminal fragment of human apolipoprotein E3 (residues 1-165) has been expressed and crystallized in three different crystal forms under similar crystallization conditions. One crystal form has nearly identical cell dimensions to the previously reported orthorhombic (P2(1)2(1)2(1)) crystal form of the amino-terminal 22 kDa fragment of apolipoprotein E (residues 1-191). A second orthorhombic crystal form (P2(1)2(1)2(1) with cell dimensions differing from the first form) and a trigonal (P3(1)21) crystal form were also characterized. The structures of the first orthorhombic and the trigonal form were determined by seleno-methionine multiwavelength anomalous dispersion, and the structure of the second orthorhombic form was determined by molecular replacement using the structure from the trigonal form as a search model. A combination of modern experimental and computational techniques provided high-quality electron-density maps, which revealed new features of the apolipoprotein E structure, including an unambiguously traced loop connecting helices 2 and 3 in the four-helix bundle and a number of multiconformation side chains. The three crystal forms contain a common intermolecular, antiparallel packing arrangement. The electrostatic complimentarity observed in this antiparallel packing resembles the interaction of apolipoprotein E with the monoclonal antibody 2E8 and the low density lipoprotein receptor. Superposition of the model structures from all three crystal forms reveals flexibility and pronounced kinks in helices near one end of the four-helix bundle. This mobility at one end of the molecule provides new insights into the structural changes in apolipoprotein E that occur with lipid association.


    Organizational Affiliation

    Lawrence Livermore National Laboratory, Biology and Biotechnology Research Program, University of California, Livermore 94550, USA.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN (APOLIPOPROTEIN E)A144Homo sapiensMutation(s): 0 
Gene Names: APOE
Find proteins for P02649 (Homo sapiens)
Explore P02649 
Go to UniProtKB:  P02649
NIH Common Fund Data Resources
PHAROS  P02649
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.207 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.783α = 90
b = 53.2β = 90
c = 84.777γ = 90
Software Package:
Software NamePurpose
SOLVEphasing
X-PLORmodel building
CCP4model building
X-PLORrefinement
UCSD-systemdata reduction
UCSD-systemdata scaling
X-PLORphasing
CCP4phasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 1998-11-05 
  • Released Date: 1998-11-11 
  • Deposition Author(s): Rupp, B., Segelke, B.

Revision History 

  • Version 1.0: 1998-11-11
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description