PDBsum entry 1or3

Lipid binding protein

PDB id: 1or3

Contents

Protein chain

136 a.a. *

Waters ×158

* Residue conservation analysis

PDB id:

1or3

Name:

Lipid binding protein

Title:

Apolipoprotein e3 (apoe3), trigonal truncation mutant 165

Structure:

Protein (apolipoprotein e). Chain: a. Fragment: receptor binding domain. Synonym: apoe3. Engineered: yes. Other_details: selenomethionine mutant used in mad phasing experiment

Source:

Homo sapiens. Human. Organism_taxid: 9606. Strain: bl21, b834(de)met-. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.73Å R-factor: 0.229 R-free: 0.238

Authors:

B.Rupp,B.W.Segelke

Key ref:

B.W.Segelke et al. (2000). Conformational flexibility in the apolipoprotein E amino-terminal domain structure determined from three new crystal forms: implications for lipid binding. Protein Sci, 9, 886-897. PubMed id: 10850798 DOI: 10.1110/ps.9.5.886

Date:

01-Dec-98 Release date: 24-May-00

Protein chain

P02649  (APOE_HUMAN) -  Apolipoprotein E from Homo sapiens

Seq: 317 a.a.

Struc: 136 a.a.

DOI no: 10.1110/ps.9.5.886

Protein Sci 9:886-897 (2000)

PubMed id: 10850798

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

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

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 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.

Selected figure(s)

Figure 3.
Fig. 3. SOLOMON map covering 80s loop. The initial map after density modification and phase extension with SOLOMON ~Abra- hams & Leslie, 1996! shows the 80s loop is clearly traceable in model-free maps. The H2--H3 connecting loop, or 80s loop, has not been previously observed in any of the numerous structure determinations of apoE and variants. The quality of this map demonstrates clearly the advantage of current crystallographic techniques for revealing new details. The 80s loop adopts a pseudo-b conformation that is stabilized by side-chain--main-chain hydrogen bonds ~not shown!. The 80s loop is rich in acidic residues and is probably involved in initial lipid binding through charge complementarity with positively charged phosphatidylcholine head groups.

Figure 5.
Fig. 5. Electrostatics of packing. A: The antiparallel packing arrangement of three symmetry-related four-helix bundles in the ortho-1 crystal form is shown. The bundles are represented as a ribbon diagram and are shown superimposed with semitranslucent isocontours of the electrostatic poten- tial. Red surface represents negative potential ~contoured at 23 mV! and blue surface represents positive potential ~contoured at 4 mV!. For illus- trative purposes, the molecules are displayed somewhat apart from their actual packing arrangement. It is apparent that in this arrangement favor- able electrostatic interactions take place such that positive and negative electrostatic potentials are juxtaposed. This figure was generated with MOL- SCRIPT ~Kraulis, 1991!, SPOCK ~Christopher, 1997!, and RASTER3D ~Merritt & Bacon, 1997!. B: Relative orientation of packed molecules in the three crystal forms, superimposed on one molecule of the pseudodimer. Perspective is down the principal axis of the four-helix bundle. The model from the ortho-1 form is shown in red, the trigonal form in magenta, and the ortho-2 form in yellow. While maintaining the commonality of the antiparallel arrangement, packing is not identical in any two crystal forms. The pseudodimers of the ortho-2 and ortho-1 forms differ by a small translational shift, while the pseudodimer of the trigonal crystal form is related to that of ortho-1 by an additional, nearly 908 rotation. This figure was generated with MIDAS ~Ferrin et al., 1988!. C: Schematic of the interactions of the electrostatic lobes in different packing arrangements. The arrow represents the principal axis of the helix bundle, the blue oval represents the positive lobe of electrostatic potential, and the red oval represents the negative lobe of electrostatic potential. The upper sections of the sketch represent the packing plane, the lower sections represent a cross-section thereof ~left panel, ortho forms; right panel, trigonal form!. In both packing arrangements, positive and negative electrostatic potential are juxtaposed.

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (2000, 9, 886-897) copyright 2000.

Figures were selected by the author.