PDBsum entry 1b4f

Signal transduction

PDB id: 1b4f

Contents

Protein chains

(+ 2 more) 74 a.a. *

Waters ×685

* Residue conservation analysis

PDB id:

1b4f

Name:

Signal transduction

Title:

Oligomeric structure of the human ephb2 receptor sam domain

Structure:

Ephb2. Chain: a, b, c, d, e, f, g, h. Fragment: sam domain. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Tissue: vascular. Cell: renal microvascular endothelial. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Biol. unit:

Not given

Resolution:

1.95Å R-factor: 0.228 R-free: 0.273

Authors:

C.D.Thanos,K.E.Goodwill,J.U.Bowie

Key ref:

C.D.Thanos et al. (1999). Oligomeric structure of the human EphB2 receptor SAM domain. Science, 283, 833-836. PubMed id: 9933164 DOI: 10.1126/science.283.5403.833

Date:

20-Dec-98 Release date: 16-Feb-99

Protein chains

P29323  (EPHB2_HUMAN) -  Ephrin type-B receptor 2 from Homo sapiens

Seq: 1055 a.a.

Struc: 74 a.a.

Enzyme reactions

• Enzyme class: E.C.2.7.10.1 - receptor protein-tyrosine kinase.
• Reaction: L-tyrosyl-[protein] + ATP = O-phospho-L-tyrosyl-[protein] + ADP + H⁺

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

Added reference

DOI no: 10.1126/science.283.5403.833

Science 283:833-836 (1999)

PubMed id: 9933164

Oligomeric structure of the human EphB2 receptor SAM domain.

C.D.Thanos, K.E.Goodwill, J.U.Bowie.

ABSTRACT

The sterile alpha motif (SAM) domain is a protein interaction module that is present in diverse signal-transducing proteins. SAM domains are known to form homo- and hetero-oligomers. The crystal structure of the SAM domain from an Eph receptor tyrosine kinase, EphB2, reveals two large interfaces. In one interface, adjacent monomers exchange amino-terminal peptides that insert into a hydrophobic groove on each neighbor. A second interface is composed of the carboxyl-terminal helix and a nearby loop. A possible oligomer, constructed from a combination of these binding modes, may provide a platform for the formation of larger protein complexes.

Selected figure(s)

Figure 1.
Fig. 1. The arm-exchange interface. (A) Ribbon structure of the EphB2 SAM domain. The L-form of the polypeptide is outlined in blue, the S-form is outlined in yellow, and Tyr8 is shown in ball and stick representation. The areas of the structure that interact with other proteins are highlighted in red. In our numbering, Tyr26 corresponds to Tyr929 in the EphB1 receptor (23). (B) Close-up view of the L-form peptide insertion. In the L-form, Tyr8 packs into a hydrophobic pocket (Phe^11 is not shown, Phe^38, Met70, Trp17, and Val69) and hydrogen bonds through an ordered water molecule to Ser66. (C) Close-up view of the S-form peptide insertion. In the S-form, Tyr8 inserts into the same pocket as in the L-form, but it hydrogen bonds to Trp17 through an ordered water molecule. Residue Phe^11C (L-form) and helix 1 are shown in transparent representation to better illustrate the packing around Tyr8 and the architecture of Trp17 in the hydrophobic patch. The figures were made with MOLSCRIPT (33).

Figure 3.
Fig. 3. Model of the SAM domain oligomer. (A) Ribbon diagram. Packing of the monomer with a combination of arm-exchange interfaces and b-region interfaces creates an oligomer. In the ribbon diagram, the S- and L-forms are colored yellow and blue as in Fig. 1. (B) Surface diagram. Each monomer is rendered with a unique color to illustrate the packing at each interface. A 1.4 Å probe radius was used to calculate the molecular surface area. This figure was made with MOLMOL (33). (C) Electrostatic potential surface of the oligomer. The asymmetric distribution of charge on each face of the oligomer is shown. Red is negative, white is neutral, and blue is positive. The electrostatic surface was contoured between 10 k[B]T/e and +10 k[B]T/e, where k[B] is the Boltzmann constant, T is temperature, and e is the electronic charge. This figure was made with GRASP (33).

The above figures are reprinted by permission from the AAAs: Science (1999, 283, 833-836) copyright 1999.

Figures were selected by the author.