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PDBsum entry 1vca
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Cell adhesion protein
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PDB id
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1vca
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Contents |
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* Residue conservation analysis
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PDB id:
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Cell adhesion protein
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Title:
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Crystal structure of an integrin-binding fragment of vascular cell adhesion molecule-1 at 1.8 angstroms resolution
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Structure:
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Human vascular cell adhesion molecule-1. Chain: a, b. Synonym: vcam-d1,2. Engineered: yes
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Strain: hw1110. Expressed in: escherichia coli. Expression_system_taxid: 562
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Resolution:
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Authors:
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E.Y.Jones,K.Harlos,M.J.Bottomley,R.C.Robinson,P.C.Driscoll, R.M.Edwards,J.M.Clements,T.J.Dudgeon,D.I.Stuart
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Key ref:
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E.Y.Jones
et al.
(1995).
Crystal structure of an integrin-binding fragment of vascular cell adhesion molecule-1 at 1.8 A resolution.
Nature,
373,
539-544.
PubMed id:
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Date:
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21-Mar-95
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Release date:
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15-Sep-95
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PROCHECK
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Headers
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References
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P19320
(VCAM1_HUMAN) -
Vascular cell adhesion protein 1 from Homo sapiens
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Seq:
Struc:
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739 a.a.
199 a.a.
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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Nature
373:539-544
(1995)
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PubMed id:
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Crystal structure of an integrin-binding fragment of vascular cell adhesion molecule-1 at 1.8 A resolution.
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E.Y.Jones,
K.Harlos,
M.J.Bottomley,
R.C.Robinson,
P.C.Driscoll,
R.M.Edwards,
J.M.Clements,
T.J.Dudgeon,
D.I.Stuart.
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ABSTRACT
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The cell-surface glycoprotein vascular cell adhesion molecule-1 (VCAM-1; ref. 1)
mediates intercellular adhesion by specific binding to the integrin very-late
antigen-4 (VLA-4, alpha 4 beta 1; ref. 3). VCAM-1, with the intercellular
adhesion molecules ICAM-1, ICAM-2, ICAM-3 and the mucosal vascular addressin
MAd-CAM-1, forms an integrin-binding subgroup of the immunoglobulin superfamily.
In addition to their clinical relevance in inflammation, these molecules act as
cellular receptors for viral and parasitic agents. The predominant form of
VCAM-1 in vivo has an amino-terminal extracellular region comprising seven
immunoglobulin-like domains. Functional studies have identified a conserved
integrin-binding motif in domains 1 and 4, variants of which are present in the
N-terminal domain of all members of the immunoglobulin superfamily subgroup. We
report here the crystal structure of a VLA-4-binding fragment composed of the
first two domains of VCAM-1. The integrin-binding motif (Q38IDSPL) is highly
exposed and forms the N-terminal region of the loop between beta-strands C and D
of domain 1. This motif exhibits a distinctive conformation which we predict
will be common to all the integrin-binding IgSF molecules. These, and additional
data, map VLA-4 binding to the face of the CFG beta-sheet, the surface
previously identified as the site for intercellular adhesive interactions
between members of the immunoglobulin superfamily.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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X.L.Yu,
T.Hu,
J.M.Du,
J.P.Ding,
X.M.Yang,
J.Zhang,
B.Yang,
X.Shen,
Z.Zhang,
W.D.Zhong,
N.Wen,
H.Jiang,
P.Zhu,
and
Z.N.Chen
(2008).
Crystal structure of HAb18G/CD147: implications for immunoglobulin superfamily homophilic adhesion.
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J Biol Chem,
283,
18056-18065.
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PDB code:
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J.Takagi
(2007).
Structural basis for ligand recognition by integrins.
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Curr Opin Cell Biol,
19,
557-564.
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H.Buschmann,
J.Chan,
L.Sanchez-Pulido,
M.A.Andrade-Navarro,
J.H.Doonan,
and
C.W.Lloyd
(2006).
Microtubule-associated AIR9 recognizes the cortical division site at preprophase and cell-plate insertion.
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Curr Biol,
16,
1938-1943.
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A.Zubia,
L.Mendoza,
S.Vivanco,
E.Aldaba,
T.Carrascal,
B.Lecea,
A.Arrieta,
T.Zimmerman,
F.Vidal-Vanaclocha,
and
F.P.Cossío
(2005).
Application of Stereocontrolled Stepwise [3+2] Cycloadditions to the Preparation of Inhibitors of alpha(4)beta(1)-Integrin-Mediated Hepatic Melanoma Metastasis.
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Angew Chem Int Ed Engl,
44,
2903-2907.
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M.Król,
I.Roterman,
B.Piekarska,
L.Konieczny,
J.Rybarska,
B.Stopa,
and
P.Spólnik
(2005).
Analysis of correlated domain motions in IgG light chain reveals possible mechanisms of immunological signal transduction.
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Proteins,
59,
545-554.
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H.J.Huttunen,
and
H.Rauvala
(2004).
Amphoterin as an extracellular regulator of cell motility: from discovery to disease.
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J Intern Med,
255,
351-366.
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J.Dando,
K.W.Wilkinson,
S.Ortlepp,
D.J.King,
and
R.L.Brady
(2002).
A reassessment of the MAdCAM-1 structure and its role in integrin recognition.
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Acta Crystallogr D Biol Crystallogr,
58,
233-241.
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PDB code:
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M.A.Arnaout,
S.L.Goodman,
and
J.P.Xiong
(2002).
Coming to grips with integrin binding to ligands.
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Curr Opin Cell Biol,
14,
641-651.
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Z.Li,
M.J.Calzada,
J.M.Sipes,
J.A.Cashel,
H.C.Krutzsch,
D.S.Annis,
D.F.Mosher,
and
D.D.Roberts
(2002).
Interactions of thrombospondins with alpha4beta1 integrin and CD47 differentially modulate T cell behavior.
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J Cell Biol,
157,
509-519.
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M.Kvansakul,
M.Hopf,
A.Ries,
R.Timpl,
and
E.Hohenester
(2001).
Structural basis for the high-affinity interaction of nidogen-1 with immunoglobulin-like domain 3 of perlecan.
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EMBO J,
20,
5342-5346.
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PDB code:
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P.Taylor,
M.Bilsland,
and
M.D.Walkinshaw
(2001).
A new conformation of the integrin-binding fragment of human VCAM-1 crystallizes in a highly hydrated packing arrangement.
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Acta Crystallogr D Biol Crystallogr,
57,
1579-1583.
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PDB code:
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C.C.Deivanayagam,
R.L.Rich,
M.Carson,
R.T.Owens,
S.Danthuluri,
T.Bice,
M.Höök,
and
S.V.Narayana
(2000).
Novel fold and assembly of the repetitive B region of the Staphylococcus aureus collagen-binding surface protein.
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Structure,
8,
67-78.
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PDB codes:
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D.J.Stauber,
A.D.DiGabriele,
and
W.A.Hendrickson
(2000).
Structural interactions of fibroblast growth factor receptor with its ligands.
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Proc Natl Acad Sci U S A,
97,
49-54.
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PDB code:
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I.Callebaut,
D.Gilgès,
I.Vigon,
and
J.P.Mornon
(2000).
HYR, an extracellular module involved in cellular adhesion and related to the immunoglobulin-like fold.
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Protein Sci,
9,
1382-1390.
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K.S.Taraszka,
J.M.Higgins,
K.Tan,
D.A.Mandelbrot,
J.H.Wang,
and
M.B.Brenner
(2000).
Molecular basis for leukocyte integrin alpha(E)beta(7) adhesion to epithelial (E)-cadherin.
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J Exp Med,
191,
1555-1567.
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M.A.Bowen,
A.A.Aruffo,
and
J.Bajorath
(2000).
Cell surface receptors and their ligands: in vitro analysis of CD6-CD166 interactions.
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Proteins,
40,
420-428.
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M.J.Humphries
(2000).
Integrin cell adhesion receptors and the concept of agonism.
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Trends Pharmacol Sci,
21,
29-32.
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X.Jiang,
O.Gurel,
E.A.Mendiaz,
G.W.Stearns,
C.L.Clogston,
H.S.Lu,
T.D.Osslund,
R.S.Syed,
K.E.Langley,
and
W.A.Hendrickson
(2000).
Structure of the active core of human stem cell factor and analysis of binding to its receptor kit.
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EMBO J,
19,
3192-3203.
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PDB code:
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C.Kasper,
H.Rasmussen,
V.Berezin,
E.Bock,
and
I.K.Larsen
(1999).
Expression, crystallization and preliminary X-ray analysis of the two amino-terminal Ig domains of the neural cell adhesion molecule (NCAM).
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Acta Crystallogr D Biol Crystallogr,
55,
1598-1600.
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F.Peri,
D.Grell,
P.Dumy,
Y.Yokokawa,
K.Welzenbach,
G.Weitz-Schmidt,
and
M.Mutter
(1999).
Assembly of binding loops on aromatic templates as VCAM-1 mimetics.
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J Pept Sci,
5,
313-322.
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J.M.Casasnovas,
C.Pieroni,
and
T.A.Springer
(1999).
Lymphocyte function-associated antigen-1 binding residues in intercellular adhesion molecule-2 (ICAM-2) and the integrin binding surface in the ICAM subfamily.
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Proc Natl Acad Sci U S A,
96,
3017-3022.
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M.Bycroft,
A.Bateman,
J.Clarke,
S.J.Hamill,
R.Sandford,
R.L.Thomas,
and
C.Chothia
(1999).
The structure of a PKD domain from polycystin-1: implications for polycystic kidney disease.
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EMBO J,
18,
297-305.
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PDB code:
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R.W.Berg,
Y.Yang,
K.Lehnert,
and
G.W.Krissansen
(1999).
Mouse M290 is the functional homologue of the human mucosal lymphocyte integrin HML-1: antagonism between the integrin ligands E-cadherin and RGD tripeptide.
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Immunol Cell Biol,
77,
337-344.
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C.Quan,
N.J.Skelton,
K.Clark,
D.Y.Jackson,
M.E.Renz,
H.H.Chiu,
S.M.Keating,
M.H.Beresini,
S.Fong,
and
D.R.Artis
(1998).
Transfer of a protein binding epitope to a minimal designed peptide.
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Biopolymers,
47,
265-275.
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I.D.Campbell
(1998).
The modular architecture of leukocyte cell-surface receptors.
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Immunol Rev,
163,
11-18.
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J.Bella,
P.R.Kolatkar,
C.W.Marlor,
J.M.Greve,
and
M.G.Rossmann
(1998).
The structure of the two amino-terminal domains of human ICAM-1 suggests how it functions as a rhinovirus receptor and as an LFA-1 integrin ligand.
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Proc Natl Acad Sci U S A,
95,
4140-4145.
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PDB code:
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J.L.Banères,
F.Roquet,
M.Green,
H.LeCalvez,
and
J.Parello
(1998).
The cation-binding domain from the alpha subunit of integrin alpha5 beta1 is a minimal domain for fibronectin recognition.
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J Biol Chem,
273,
24744-24753.
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J.M.Casasnovas,
T.Stehle,
J.H.Liu,
J.H.Wang,
and
T.A.Springer
(1998).
A dimeric crystal structure for the N-terminal two domains of intercellular adhesion molecule-1.
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Proc Natl Acad Sci U S A,
95,
4134-4139.
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PDB code:
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J.M.Higgins,
D.A.Mandlebrot,
S.K.Shaw,
G.J.Russell,
E.A.Murphy,
Y.T.Chen,
W.J.Nelson,
C.M.Parker,
and
M.B.Brenner
(1998).
Direct and regulated interaction of integrin alphaEbeta7 with E-cadherin.
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J Cell Biol,
140,
197-210.
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J.Wang,
and
T.A.Springer
(1998).
Structural specializations of immunoglobulin superfamily members for adhesion to integrins and viruses.
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Immunol Rev,
163,
197-215.
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M.J.Humphries,
and
P.Newham
(1998).
The structure of cell-adhesion molecules.
|
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Trends Cell Biol,
8,
78-83.
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N.Verdaguer,
N.Sevilla,
M.L.Valero,
D.Stuart,
E.Brocchi,
D.Andreu,
E.Giralt,
E.Domingo,
M.G.Mateu,
and
I.Fita
(1998).
A similar pattern of interaction for different antibodies with a major antigenic site of foot-and-mouth disease virus: implications for intratypic antigenic variation.
|
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J Virol,
72,
739-748.
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R.Urfer,
P.Tsoulfas,
L.O'Connell,
J.A.Hongo,
W.Zhao,
and
L.G.Presta
(1998).
High resolution mapping of the binding site of TrkA for nerve growth factor and TrkC for neurotrophin-3 on the second immunoglobulin-like domain of the Trk receptors.
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J Biol Chem,
273,
5829-5840.
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S.Ichikawa,
H.Hatanaka,
T.Yuuki,
N.Iwamoto,
S.Kojima,
C.Nishiyama,
K.Ogura,
Y.Okumura,
and
F.Inagaki
(1998).
Solution structure of Der f 2, the major mite allergen for atopic diseases.
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J Biol Chem,
273,
356-360.
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PDB codes:
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S.J.Davis,
S.Ikemizu,
M.K.Wild,
and
P.A.van der Merwe
(1998).
CD2 and the nature of protein interactions mediating cell-cell recognition.
|
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Immunol Rev,
163,
217-236.
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Y.Yokosaki,
N.Matsuura,
S.Higashiyama,
I.Murakami,
M.Obara,
M.Yamakido,
N.Shigeto,
J.Chen,
and
D.Sheppard
(1998).
Identification of the ligand binding site for the integrin alpha9 beta1 in the third fibronectin type III repeat of tenascin-C.
|
| |
J Biol Chem,
273,
11423-11428.
|
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A.P.May,
R.C.Robinson,
R.T.Aplin,
P.Bradfield,
P.R.Crocker,
and
E.Y.Jones
(1997).
Expression, crystallization, and preliminary X-ray analysis of a sialic acid-binding fragment of sialoadhesin in the presence and absence of ligand.
|
| |
Protein Sci,
6,
717-721.
|
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C.Chothia,
and
E.Y.Jones
(1997).
The molecular structure of cell adhesion molecules.
|
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Annu Rev Biochem,
66,
823-862.
|
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C.G.Gahmberg,
M.Tolvanen,
and
P.Kotovuori
(1997).
Leukocyte adhesion--structure and function of human leukocyte beta2-integrins and their cellular ligands.
|
| |
Eur J Biochem,
245,
215-232.
|
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C.Kisker,
H.Schindelin,
A.Pacheco,
W.A.Wehbi,
R.M.Garrett,
K.V.Rajagopalan,
J.H.Enemark,
and
D.C.Rees
(1997).
Molecular basis of sulfite oxidase deficiency from the structure of sulfite oxidase.
|
| |
Cell,
91,
973-983.
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PDB code:
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D.J.Leahy
(1997).
Implications of atomic-resolution structures for cell adhesion.
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Annu Rev Cell Dev Biol,
13,
363-393.
|
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D.L.Bodian,
S.J.Davis,
B.P.Morgan,
and
N.K.Rushmere
(1997).
Mutational analysis of the active site and antibody epitopes of the complement-inhibitory glycoprotein, CD59.
|
| |
J Exp Med,
185,
507-516.
|
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E.Domingo,
and
J.J.Holland
(1997).
RNA virus mutations and fitness for survival.
|
| |
Annu Rev Microbiol,
51,
151-178.
|
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|
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G.V.Louie,
W.Yang,
M.E.Bowman,
and
S.Choe
(1997).
Crystal structure of the complex of diphtheria toxin with an extracellular fragment of its receptor.
|
| |
Mol Cell,
1,
67-78.
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PDB code:
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J.C.Loftus,
and
R.C.Liddington
(1997).
Cell adhesion in vascular biology. New insights into integrin-ligand interaction.
|
| |
J Clin Invest,
99,
2302-2306.
|
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J.P.Newton,
C.D.Buckley,
E.Y.Jones,
and
D.L.Simmons
(1997).
Residues on both faces of the first immunoglobulin fold contribute to homophilic binding sites of PECAM-1/CD31.
|
| |
J Biol Chem,
272,
20555-20563.
|
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K.L.Fisher,
J.Lu,
L.Riddle,
K.J.Kim,
L.G.Presta,
and
S.C.Bodary
(1997).
Identification of the binding site in intercellular adhesion molecule 1 for its receptor, leukocyte function-associated antigen 1.
|
| |
Mol Biol Cell,
8,
501-515.
|
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P.Newham,
S.E.Craig,
G.N.Seddon,
N.R.Schofield,
A.Rees,
R.M.Edwards,
E.Y.Jones,
and
M.J.Humphries
(1997).
Alpha4 integrin binding interfaces on VCAM-1 and MAdCAM-1. Integrin binding footprints identify accessory binding sites that play a role in integrin specificity.
|
| |
J Biol Chem,
272,
19429-19440.
|
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R.J.Gumina,
P.J.Newman,
D.Kenny,
D.C.Warltier,
and
G.J.Gross
(1997).
The leukocyte cell adhesion cascade and its role in myocardial ischemia-reperfusion injury.
|
| |
Basic Res Cardiol,
92,
201-213.
|
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S.Fong,
S.Jones,
M.E.Renz,
H.H.Chiu,
A.M.Ryan,
L.G.Presta,
and
D.Jackson
(1997).
Mucosal addressin cell adhesion molecule-1 (MAdCAM-1). Its binding motif for alpha 4 beta 7 and role in experimental colitis.
|
| |
Immunol Res,
16,
299-311.
|
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T.Sugimori,
D.L.Griffith,
and
M.A.Arnaout
(1997).
Emerging paradigms of integrin ligand binding and activation.
|
| |
Kidney Int,
51,
1454-1462.
|
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|
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A.Bateman,
M.Jouet,
J.MacFarlane,
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PDB codes:
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Where a reference describes a PDB structure, the PDB
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