PDBsum entry 1yuk

Cell adhesion

PDB id: 1yuk

Contents

Protein chains

94 a.a. *

120 a.a. *

Ligands

NDG ×2

Waters ×219

* Residue conservation analysis

PDB id:

1yuk

Name:

Cell adhesion

Title:

The crystal structure of the psi/hybrid domain/ i-egf1 segment from the human integrin beta2 at 1.8 resolution

Structure:

Integrin beta-2 a chain. Chain: a. Fragment: psi domain. Synonym: cell surface adhesion glycoproteins lfa- 1/cr3/p150,95 beta- subunit, cd18, complement receptor c3 beta- subunit. Engineered: yes. Integrin beta-2 b chain. Chain: b. Fragment: i-egf domain.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

1.80Å R-factor: 0.234 R-free: 0.253

Authors:

M.Shi,K.Sundramurthy,B.Liu,S.M.Tan,S.K.Law,J.Lescar

Key ref:

M.Shi et al. (2005). The crystal structure of the plexin-semaphorin-integrin domain/hybrid domain/I-EGF1 segment from the human integrin beta2 subunit at 1.8-A resolution. J Biol Chem, 280, 30586-30593. PubMed id: 15965234 DOI: 10.1074/jbc.M502525200

Date:

14-Feb-05 Release date: 19-Jul-05

Protein chain

P05107  (ITB2_HUMAN) -  Integrin beta-2 from Homo sapiens

Seq: 769 a.a.

Struc: 94 a.a.

Protein chain

P05107  (ITB2_HUMAN) -  Integrin beta-2 from Homo sapiens

Seq: 769 a.a.

Struc: 120 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DOI no: 10.1074/jbc.M502525200

J Biol Chem 280:30586-30593 (2005)

PubMed id: 15965234

The crystal structure of the plexin-semaphorin-integrin domain/hybrid domain/I-EGF1 segment from the human integrin beta2 subunit at 1.8-A resolution.

M.Shi, K.Sundramurthy, B.Liu, S.M.Tan, S.K.Law, J.Lescar.

ABSTRACT

Integrins are modular (alphabeta) heterodimeric proteins that mediate cell adhesion and convey signals across the plasma membrane. Interdomain motions play a key role in signal transduction by propagating structural changes through the molecule, thus controlling the activation state and adhesive properties of the integrin. We expressed a soluble fragment of the human integrin beta2 subunit comprising the plexin-semaphorin-integrin domain (PSI)/hybrid domain/I-EGF1 fragment and present its crystal structure at 1.8-A resolution. The structure reveals an elongated molecule with a rigid architecture stabilized by nine disulfide bridges. The PSI domain is located centrally and participates in the formation of extended interfaces with the hybrid domain and I-EGF1 domains, respectively. The hybrid domain/PSI interface involves the burial of an Arg residue, and contacts between PSI and I-EGF1 are mainly mediated by well conserved Arg and Trp residues. Conservation of key interacting residues across the various integrin beta subunits sequences suggests that our structure represents a good model for the entire integrin family. Superposition with the integrin beta3 receptor in its bent conformation suggests that an articulation point is present at the linkage between its I-EGF1 and I-EGF2 modules and underlines the importance of this region for the control of integrin-mediated cell adhesion.

Selected figure(s)

Figure 4.
FIG. 4. A, superposition of the I-EGF1 domain (red, Protein Data Bank code 1YUK [PDB] , this work) with the I-EGF4 from integrin [3] (blue, Protein Data Bank code 1JV2 [PDB] ) and the EGF domain of P-selectin (turquoise, Protein Data Bank code 1FSB [PDB] ). The disulfide bonds C3-C6 and C7-C8 are well conserved, constraining the fold of the C-terminal part of the EGF module. The cysteine bridge (C2-C4) is absent in the I-EGF1 domain. Large conformational variations are observed between the N-terminal ends of the three structures. The present I-EGF1 structure lacks strand 4 leaving its strand 3 unpaired (see text). B, schematic representation of the I-EGF1 structure of human integrin [2]. The three disulfide bonds C1-C5, C3-C6, and C7-C8 are indicated. It should be noted that the cysteines are numbered according to the typical integrin-EGF domain with 8 cysteines; in this case, C2 and C4 are missing. The Arg and Leu residues that replace C2 and C4, respectively, according to the published sequence alignment (17) are in a yellow background.

Figure 5.
FIG. 5. Interaction between domains. Buried water molecules are represented by stars, and hydrogen bonds are represented by broken lines. A, interactions at the hybrid domain (yellow) and the PSI domain (green) interface: the invariant Arg86 residue is located centrally making several polar contacts indicated by broken lines. B, interactions at the PSI domain (green) and the I-EGF1 domain (red) interface: residues taking part in the interaction are labeled. Also labeled is the Ile^455 in the I-EGF1 domain that may play an important role in the interaction with the I-EGF2 domain.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2005, 280, 30586-30593) copyright 2005.

Figures were selected by an automated process.