PDBsum entry 1t0p

Immune system

PDB id

1t0p

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Contents

			Protein chains

					174 a.a. *


					86 a.a. *

			Ligands

					NAG ×2

			Metals

					_MG

			Waters ×169

* Residue conservation analysis

PDB id:

1t0p

Links

Name:

Immune system

Title:

Structural basis of icam recognition by integrin alpahlbeta2 revealed in the complex structure of binding domains of icam-3 and alphalbeta2 at 1.65 a

Structure:

Integrin alpha-l. Chain: a. Fragment: i domain. Synonym: cell surface glycoprotein cd11a. Antigen cd11a (p180). Lymphocyte function-associated antigen 1. Cd11a. Engineered: yes. Intercellular adhesion molecule-3. Chain: b. Fragment: domain 1.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Expressed in: cricetulus griseus. Expression_system_taxid: 10029. Expression_system_cell: lec cells.

Biol. unit:

Dimer (from PQS)

Resolution:

1.66Å

R-factor:

0.220

R-free:

0.241

Authors:

G.Song,Y.T.Yang,J.H.Liu,M.Shimaoko,T.A.Springer,J.H.Wang

Key ref:

G.Song et al. (2005). An atomic resolution view of ICAM recognition in a complex between the binding domains of ICAM-3 and integrin alphaLbeta2. Proc Natl Acad Sci U S A, 102, 3366-3371. PubMed id: 15728350 DOI: 10.1073/pnas.0500200102

Date:

12-Apr-04

Release date:

08-Mar-05

PROCHECK

	Headers

	References

Protein chain

P20701 (ITAL_HUMAN) - Integrin alpha-L from Homo sapiens

Seq: Struc:

Seq: Struc:

Seq: Struc:					1170 a.a. 174 a.a.*

Protein chain

P32942 (ICAM3_HUMAN) - Intercellular adhesion molecule 3 from Homo sapiens

Seq: Struc:

Seq: Struc:					547 a.a. 86 a.a.*

Key:

PfamA domain

Secondary structure

CATH domain

* PDB and UniProt seqs differ at 5 residue positions (black crosses)

DOI no: 10.1073/pnas.0500200102	Proc Natl Acad Sci U S A 102:3366-3371 (2005)
PubMed id: 15728350

An atomic resolution view of ICAM recognition in a complex between the binding domains of ICAM-3 and integrin alphaLbeta2.
G.Song, Y.Yang, J.H.Liu, J.M.Casasnovas, M.Shimaoka, T.A.Springer, J.H.Wang.

ABSTRACT

Within the Ig superfamily (IgSF), intercellular adhesion molecules (ICAMs) form a subfamily that binds the leukocyte integrin alphaLbeta2. We report a 1.65-A-resolution crystal structure of the ICAM-3 N-terminal domain (D1) in complex with the inserted domain, the ligand-binding domain of alphaLbeta2. This high-resolution structure and comparisons among ICAM subfamily members establish that the binding of ICAM-3 D1 onto the inserted domain represents a common docking mode for ICAM subfamily members. The markedly different off-rates of ICAM-1, -2, and -3 appear to be determined by the hydrophobicity of residues that surround a metal coordination bond in the alphaLbeta2-binding interfaces. Variation in composition of glycans on the periphery of the interfaces influences on-rate.

Selected figure(s)



	Figure 3. Fig. 3. The ICAM-3/ [L] [2] binding interface. (A) The interface residues are shown in light cyan and light gold for ICAM-3 and the I domain, respectively. The metal ion, oxygens, and nitrogens are shown as magenta, red, and blue spheres, respectively. Water molecules are shown as red spheres. Metal coordination is shown by black dashed lines. Hydrogen bonds and a salt bridge between Lys-42 in ICAM-3 and Glu-241 in the I domain are represented by silver dashed lines. Residues involved in the hydrophobic patch are colored in silver. For clarity, MIDAS residues are omitted. (B) Structural elements that stabilize the conformation of the CD loop of ICAM-3. The CD and EF loops are colored in yellow and green, respectively. Only relevant side chains are shown in this figure for clarity. Hydrophobic, neutral hydrophilic, and basic residues are colored in orange, cyan, and blue, respectively. The broken lines represent hydrogen bonds, whereas the silver ball is a bound water molecule. A was prepared with RIBBONS (43), and B was prepared with SETOR (44).		Figure 4. Fig. 4. Surface representation of the binding faces of ICAM-3 and -1. Negatively and positively charged residues are colored red and blue, respectively. Hydrophobic and neutral hydrophilic residues are colored white and yellow, respectively. Some important residues are labeled. The binding footprints are encircled with green dashed lines. Prepared with GRASP (45).

Figures were selected by an automated process.

Literature references that cite this PDB file's key reference

PubMed id

Reference

19575676

R.P.McEver, and C.Zhu (2010).
Rolling cell adhesion.

Annu Rev Cell Dev Biol, 26, 363-396.

19805116

H.Zhang, J.H.Liu, W.Yang, T.Springer, M.Shimaoka, and J.H.Wang (2009).
Structural basis of activation-dependent binding of ligand-mimetic antibody AL-57 to integrin LFA-1.

Proc Natl Acad Sci U S A, 106, 18345-18350.

PDB codes:

3hi5 3hi6

19276170

K.Tan, M.Duquette, A.Joachimiak, and J.Lawler (2009).
The crystal structure of the signature domain of cartilage oligomeric matrix protein: implications for collagen, glycosaminoglycan and integrin binding.

FASEB J, 23, 2490-2501.

PDB code:

3fby

19153605

Y.Li, C.Cao, W.Jia, L.Yu, M.Mo, Q.Wang, Y.Huang, J.M.Lim, M.Ishihara, L.Wells, P.Azadi, H.Robinson, Y.W.He, L.Zhang, and R.A.Mariuzza (2009).
Structure of the F-spondin domain of mindin, an integrin ligand and pattern recognition molecule.

EMBO J, 28, 286-297.

PDB code:

3d34

18691975

H.Zhang, J.M.Casasnovas, M.Jin, J.H.Liu, C.G.Gahmberg, T.A.Springer, and J.H.Wang (2008).
An unusual allosteric mobility of the C-terminal helix of a high-affinity alphaL integrin I domain variant bound to ICAM-5.

Mol Cell, 31, 432-437.

PDB code:

3bn3

18554252

Iskandarsyah, B.A.Tejo, U.S.Tambunan, G.Verkhivker, and T.J.Siahaan (2008).
Structural modifications of ICAM-1 cyclic peptides to improve the activity to inhibit heterotypic adhesion of T cells.

Chem Biol Drug Des, 72, 27-33.

17935964

A.R.Aricescu, and E.Y.Jones (2007).
Immunoglobulin superfamily cell adhesion molecules: zippers and signals.

Curr Opin Cell Biol, 19, 543-550.

17201681

B.H.Luo, C.V.Carman, and T.A.Springer (2007).
Structural basis of integrin regulation and signaling.

Annu Rev Immunol, 25, 619-647.

17942298

J.Takagi (2007).
Structural basis for ligand recognition by integrins.

Curr Opin Cell Biol, 19, 557-564.

17233909

O.D.Perez, D.Mitchell, and G.P.Nolan (2007).
Differential role of ICAM ligands in determination of human memory T cell differentiation.

BMC Immunol, 8, 2.

17702677

T.Vorup-Jensen, T.T.Waldron, N.Astrof, M.Shimaoka, and T.A.Springer (2007).
The connection between metal ion affinity and ligand affinity in integrin I domains.

Biochim Biophys Acta, 1774, 1148-1155.

17096550

E.P.Wojcikiewicz, M.H.Abdulreda, X.Zhang, and V.T.Moy (2006).
Force spectroscopy of LFA-1 and its ligands, ICAM-1 and ICAM-2.

Biomacromolecules, 7, 3188-3195.

16354667

G.Song, G.A.Lazar, T.Kortemme, M.Shimaoka, J.R.Desjarlais, D.Baker, and T.A.Springer (2006).
Rational design of intercellular adhesion molecule-1 (ICAM-1) variants for antagonizing integrin lymphocyte function-associated antigen-1-dependent adhesion.

J Biol Chem, 281, 5042-5049.

16963559

M.Shimaoka, M.Kim, E.H.Cohen, W.Yang, N.Astrof, D.Peer, A.Salas, A.Ferrand, and T.A.Springer (2006).
AL-57, a ligand-mimetic antibody to integrin LFA-1, reveals chemokine-induced affinity up-regulation in lymphocytes.

Proc Natl Acad Sci U S A, 103, 13991-13996.

17125150

R.L.Rich, and D.G.Myszka (2006).
Survey of the year 2005 commercial optical biosensor literature.

J Mol Recognit, 19, 478-534.

17023419

W.Yang, C.V.Carman, M.Kim, A.Salas, M.Shimaoka, and T.A.Springer (2006).
A small molecule agonist of an integrin, alphaLbeta2.

J Biol Chem, 281, 37904-37912.

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.