spacer
spacer
Go to PDB code: 
protein Protein-protein interface(s) links
Structural protein PDB id
1ck4
Jmol
Contents
Protein chains
193 a.a. *
Waters ×215
* Residue conservation analysis
PDB id:
1ck4
Name: Structural protein
Title: Crystal structure of rat a1b1 integrin i-domain.
Structure: Integrin alpha-1. Chain: a, b. Fragment: i-domain. Engineered: yes
Source: Rattus norvegicus. Norway rat. Organism_taxid: 10116. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_cell_line: dh5a.
Resolution:
2.20Å     R-factor:   0.234     R-free:   0.299
Authors: M.Nolte,R.B.Pepinsky,S.Y.Venyaminov,V.Koteliansky, P.J.Gotwals,M.Karpusas
Key ref: M.Nolte et al. (1999). Crystal structure of the alpha1beta1 integrin I-domain: insights into integrin I-domain function. Febs Lett, 452, 379-385. PubMed id: 10386626 DOI: 10.1016/S0014-5793(99)00666-3
Date:
27-Apr-99     Release date:   03-May-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P18614  (ITA1_RAT) -  Integrin alpha-1
Seq:
Struc: 		 
Seq:
Struc: 		 
Seq:
Struc: 		1180 a.a.
193 a.a.
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain

 

 
DOI no: 10.1016/S0014-5793(99)00666-3 Febs Lett 452:379-385 (1999)
PubMed id: 10386626  
 
 
Crystal structure of the alpha1beta1 integrin I-domain: insights into integrin I-domain function.
M.Nolte, R.B.Pepinsky, Venyaminov SYu, V.Koteliansky, P.J.Gotwals, M.Karpusas.
 
  ABSTRACT  
 
The alpha1beta1 integrin is a major cell surface receptor for collagen. Ligand binding is mediated, in part, through a 200 amino acid inserted 'I'-domain contained in the extracellular part of the integrin alpha chain. Integrin I-domains contain a divalent cation binding (MIDAS) site and require cations to interact with integrin ligands. We have determined the crystal structure of recombinant I-domain from the rat alpha1beta1 integrin at 2.2 A resolution in the absence of divalent cations. The alpha1 I-domain adopts the dinucleotide binding fold that is characteristic of all I-domain structures that have been solved to date and has a structure very similar to that of the closely related alpha2beta1 I-domain which also mediates collagen binding. A unique feature of the alpha1 I-domain crystal structure is that the MIDAS site is occupied by an arginine side chain from another I-domain molecule in the crystal, in place of a metal ion. This interaction supports a proposed model for ligand-induced displacement of metal ions. Circular dichroism spectra determined in the presence of Ca2+, Mg2+ and Mn2+ indicate that no changes in the structure of the I-domain occur upon metal ion binding in solution. Metal ion binding induces small changes in UV absorption spectra, indicating a change in the polarity of the MIDAS site environment.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21163365 A.R.Klatt, A.K.Becker, C.D.Neacsu, M.Paulsson, and R.Wagener (2011).
The matrilins: modulators of extracellular matrix assembly.
  Int J Biochem Cell Biol, 43, 320-330.  
21057832 M.Nakajima, Y.Miyamoto, and S.Ikegawa (2011).
Cloning and characterization of the osteoarthritis-associated gene DVWA.
  J Bone Miner Metab, 29, 300-308.  
18587047 N.S.Seo, C.Q.Zeng, J.M.Hyser, B.Utama, S.E.Crawford, K.J.Kim, M.Höök, and M.K.Estes (2008).
Inaugural article: integrins alpha1beta1 and alpha2beta1 are receptors for the rotavirus enterotoxin.
  Proc Natl Acad Sci U S A, 105, 8811-8818.  
16330543 G.Veit, B.Kobbe, D.R.Keene, M.Paulsson, M.Koch, and R.Wagener (2006).
Collagen XXVIII, a novel von Willebrand factor A domain-containing protein with many imperfections in the collagenous domain.
  J Biol Chem, 281, 3494-3504.  
16861231 G.Veit, U.Hansen, D.R.Keene, P.Bruckner, R.Chiquet-Ehrismann, M.Chiquet, and M.Koch (2006).
Collagen XII interacts with avian tenascin-X through its NC3 domain.
  J Biol Chem, 281, 27461-27470.  
14997473 C.Renner, B.Saccà, and L.Moroder (2004).
Synthetic heterotrimeric collagen peptides as mimics of cell adhesion sites of the basement membrane.
  Biopolymers, 76, 34-47.  
15016833 M.Koch, J.Schulze, U.Hansen, T.Ashwodt, D.R.Keene, W.J.Brunken, R.E.Burgeson, P.Bruckner, and L.Bruckner-Tuderman (2004).
A novel marker of tissue junctions, collagen XXII.
  J Biol Chem, 279, 22514-22521.  
14660600 Y.Nymalm, J.S.Puranen, T.K.Nyholm, J.Käpylä, H.Kidron, O.T.Pentikäinen, T.T.Airenne, J.Heino, J.P.Slotte, M.S.Johnson, and T.A.Salminen (2004).
Jararhagin-derived RKKH peptides induce structural changes in alpha1I domain of human integrin alpha1beta1.
  J Biol Chem, 279, 7962-7970.
PDB codes: 1pt6 1qcy
14506275 G.Sengle, B.Kobbe, M.Morgelin, M.Paulsson, and R.Wagener (2003).
Identification and characterization of AMACO, a new member of the von Willebrand factor A-like domain protein superfamily with a regulated expression in the kidney.
  J Biol Chem, 278, 50240-50249.  
12388743 C.A.Whittaker, and R.O.Hynes (2002).
Distribution and evolution of von Willebrand/integrin A domains: widely dispersed domains with roles in cell adhesion and elsewhere.
  Mol Biol Cell, 13, 3369-3387.  
  11876085 D.E.Gullberg, and E.Lundgren-Akerlund (2002).
Collagen-binding I domain integrins--what do they do?
  Prog Histochem Cytochem, 37, 3.  
12234369 J.Takagi, and T.A.Springer (2002).
Integrin activation and structural rearrangement.
  Immunol Rev, 186, 141-163.  
12234368 M.A.Arnaout (2002).
Integrin structure: new twists and turns in dynamic cell adhesion.
  Immunol Rev, 186, 125-140.  
11988479 M.Shimaoka, J.Takagi, and T.A.Springer (2002).
Conformational regulation of integrin structure and function.
  Annu Rev Biophys Biomol Struct, 31, 485-516.  
  11936186 I.Bank, J.Kapyla, A.Grinbaum, R.Doolman, J.Bank, and B.A.Sela (2001).
Analysis of cell-free human alpha1 integrin with a monoclonal antibody to the I-domain: detection in ocular fluid and function as an adhesion substrate.
  Cell Commun Adhes, 8, 113-123.  
10617582 C.G.Knight, L.F.Morton, A.R.Peachey, D.S.Tuckwell, R.W.Farndale, and M.J.Barnes (2000).
The collagen-binding A-domains of integrins alpha(1)beta(1) and alpha(2)beta(1) recognize the same specific amino acid sequence, GFOGER, in native (triple-helical) collagens.
  J Biol Chem, 275, 35-40.  
10933804 C.Marcinkiewicz, R.R.Lobb, M.M.Marcinkiewicz, J.L.Daniel, J.B.Smith, C.Dangelmaier, P.H.Weinreb, D.A.Beacham, and S.Niewiarowski (2000).
Isolation and characterization of EMS16, a C-lectin type protein from Echis multisquamatus venom, a potent and selective inhibitor of the alpha2beta1 integrin.
  Biochemistry, 39, 9859-9867.  
10998238 G.Bitan, L.Scheibler, D.F.Mierke, M.Rosenblatt, and M.Chorev (2000).
Ligand-integrin alpha v beta 3 interaction determined by photoaffinity cross-linking: a challenge to the prevailing model.
  Biochemistry, 39, 11014-11023.  
  10873865 J.Bella, and H.M.Berman (2000).
Integrin-collagen complex: a metal-glutamate handshake.
  Structure, 8, R121-R126.  
10652324 J.Käpylä, J.Ivaska, R.Riikonen, P.Nykvist, O.Pentikäinen, M.Johnson, and J.Heino (2000).
Integrin alpha(2)I domain recognizes type I and type IV collagens by different mechanisms.
  J Biol Chem, 275, 3348-3354.  
10713152 P.Nykvist, H.Tu, J.Ivaska, J.Käpylä, T.Pihlajaniemi, and J.Heino (2000).
Distinct recognition of collagen subtypes by alpha(1)beta(1) and alpha(2)beta(1) integrins. Alpha(1)beta(1) mediates cell adhesion to type XIII collagen.
  J Biol Chem, 275, 8255-8261.  
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.