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PDBsum entry 1wiq

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Glycoprotein PDB id
1wiq

 

 

 

 

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Contents
Protein chain
363 a.a. *
* Residue conservation analysis
PDB id:
1wiq
Name: Glycoprotein
Title: Structure of t-cell surface glycoprotein cd4, trigonal crystal form
Structure: T-cell surface glycoprotein cd4. Chain: a, b. Fragment: extracellular fragment. Synonym: cd4. Other_details: trigonal crystal form
Source: Homo sapiens. Human. Organism_taxid: 9606
Resolution:
5.00Å     R-factor:   0.422     R-free:   0.442
Authors: H.Wu,P.D.Kwong,W.A.Hendrickson
Key ref: H.Wu et al. (1997). Dimeric association and segmental variability in the structure of human CD4. Nature, 387, 527-530. PubMed id: 9168119
Date:
18-Dec-96     Release date:   07-Jul-97    
PROCHECK
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 Headers
 References

Protein chains
Pfam   ArchSchema ?
P01730  (CD4_HUMAN) -  T-cell surface glycoprotein CD4 from Homo sapiens
Seq:
Struc:
458 a.a.
363 a.a.
Key:    PfamA domain  Secondary structure

 

 
Nature 387:527-530 (1997)
PubMed id: 9168119  
 
 
Dimeric association and segmental variability in the structure of human CD4.
H.Wu, P.D.Kwong, W.A.Hendrickson.
 
  ABSTRACT  
 
CD4 is a co-receptor in the cellular immune response. It increases the avidity of association between a T cell and an antigen-presenting cell by interacting with non-polymorphic portions of the complex between class II major histocompatibility complex (MHC) and T-cell receptor (TCR) molecules, and it contributes directly to signal transduction through its cytoplasmic association with the lymphocyte kinase Lck. CD4 also serves as the high-affinity receptor for cellular attachment and entry of the human immunodeficiency virus (HIV). The extracellular portion of CD4 comprises four immunoglobulin-like domains (D1-D4). This part of human CD4 (residues 1-369) has been characterized as a recombinant soluble protein (sCD4), and crystal structures have been described for the human D1D2 fragment and for the rat D3D4 fragment. We have now determined the structures of intact sCD4 in three crystal lattices. These structures have a hinge-like variability at the D1D2 to D3D4 junction that might be important in immune recognition and HIV fusion, and a common dimeric association through D4 domains. Dynamic light scattering measurements and chemical crosslinking of sCD4 corroborate dimerization at high protein concentration. We suggest that such dimers mayhave relevance as mediators of signal transduction in T cells.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21468932 B.Wei, N.Han, H.Z.Liu, A.Rayner, and S.Rayner (2011).
Use of mutual information arrays to predict coevolving sites in the full length HIV gp120 protein for subtypes B and C.
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20890395 G.Vasiliver-Shamis, M.L.Dustin, and C.E.Hioe (2010).
HIV-1 Virological Synapse is not Simply a Copycat of the Immunological Synapse.
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21134642 M.M.Freeman, M.S.Seaman, S.Rits-Volloch, X.Hong, C.Y.Kao, D.D.Ho, and B.Chen (2010).
Crystal structure of HIV-1 primary receptor CD4 in complex with a potent antiviral antibody.
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PDB code: 3o2d
20463063 R.Song, D.Franco, C.Y.Kao, F.Yu, Y.Huang, and D.D.Ho (2010).
Epitope mapping of ibalizumab, a humanized Anti-CD4 monoclonal antibody with anti-HIV-1 activity in infected patients.
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19933330 C.Cicala, E.Martinelli, J.P.McNally, D.J.Goode, R.Gopaul, J.Hiatt, K.Jelicic, S.Kottilil, K.Macleod, A.O'Shea, N.Patel, D.Van Ryk, D.Wei, M.Pascuccio, L.Yi, L.McKinnon, P.Izulla, J.Kimani, R.Kaul, A.S.Fauci, and J.Arthos (2009).
The integrin alpha4beta7 forms a complex with cell-surface CD4 and defines a T-cell subset that is highly susceptible to infection by HIV-1.
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18045872 Ashish, I.J.Juncadella, R.Garg, C.D.Boone, J.Anguita, and J.K.Krueger (2008).
Conformational Rearrangement within the Soluble Domains of the CD4 Receptor Is Ligand-specific.
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Structure of reovirus sigma1 in complex with its receptor junctional adhesion molecule-A.
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PDB code: 3eoy
18846098 N.R.Gascoigne (2008).
Do T cells need endogenous peptides for activation?
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18497748 R.Conners, D.J.Hill, E.Borodina, C.Agnew, S.J.Daniell, N.M.Burton, R.B.Sessions, A.R.Clarke, L.E.Catto, D.Lammie, T.Wess, R.L.Brady, and M.Virji (2008).
The Moraxella adhesin UspA1 binds to its human CEACAM1 receptor by a deformable trimeric coiled-coil.
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PDB code: 2qih
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Modeling of human CCR5 as Target for HIV-I and Virtual Screening with Marine Therapeutic compounds.
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Cis interactions of immunoreceptors with MHC and non-MHC ligands.
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Rapid evolution by positive Darwinian selection in T-cell antigen CD4 in primates.
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CCR5 interactions with the variable 3 loop of gp120.
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XIAP induces NF-kappaB activation via the BIR1/TAB1 interaction and BIR1 dimerization.
  Mol Cell, 26, 689-702.
PDB codes: 2poi 2pom 2pop
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The Laminin 511/521-binding site on the Lutheran blood group glycoprotein is located at the flexible junction of Ig domains 2 and 3.
  Blood, 110, 3398-3406.
PDB codes: 2pet 2pf6
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Eukaryotic expression: developments for structural proteomics.
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16519733 G.W.Lynch, S.Turville, B.Carter, A.J.Sloane, A.Chan, N.Muljadi, S.Li, L.Low, P.Armati, R.Raison, H.Zoellner, P.Williamson, A.Cunningham, and W.B.Church (2006).
Marked differences in the structures and protein associations of lymphocyte and monocyte CD4: resolution of a novel CD4 isoform.
  Immunol Cell Biol, 84, 154-165.  
16551255 M.G.Rudolph, R.L.Stanfield, and I.A.Wilson (2006).
How TCRs bind MHCs, peptides, and coreceptors.
  Annu Rev Immunol, 24, 419-466.  
  16762062 R.Bourgeois, J.Mercier, I.Paquette-Brooks, and E.A.Cohen (2006).
Association between disruption of CD4 receptor dimerization and increased human immunodeficiency virus type 1 entry.
  Retrovirology, 3, 31.  
15893666 C.C.Huang, F.Stricher, L.Martin, J.M.Decker, S.Majeed, P.Barthe, W.A.Hendrickson, J.Robinson, C.Roumestand, J.Sodroski, R.Wyatt, G.M.Shaw, C.Vita, and P.D.Kwong (2005).
Scorpion-toxin mimics of CD4 in complex with human immunodeficiency virus gp120 crystal structures, molecular mimicry, and neutralization breadth.
  Structure, 13, 755-768.
PDB codes: 1yyl 1yym
16284180 C.C.Huang, M.Tang, M.Y.Zhang, S.Majeed, E.Montabana, R.L.Stanfield, D.S.Dimitrov, B.Korber, J.Sodroski, I.A.Wilson, R.Wyatt, and P.D.Kwong (2005).
Structure of a V3-containing HIV-1 gp120 core.
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PDB code: 2b4c
16185162 K.Vermeire, and D.Schols (2005).
Anti-HIV agents targeting the interaction of gp120 with the cellular CD4 receptor.
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Substrate-induced interconversion of protein quaternary structure isoforms.
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Interfacial metal and antibody recognition.
  Proc Natl Acad Sci U S A, 102, 14575-14580.
PDB codes: 2adg 2adi 2adj
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Virus yoga: the role of flexibility in virus host cell recognition.
  Trends Microbiol, 12, 162-169.  
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Interleukin-16 and peptide derivatives as immunomodulatory therapy in allergic lung disease.
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15534202 K.L.Arnett, S.C.Harrison, and D.C.Wiley (2004).
Crystal structure of a human CD3-epsilon/delta dimer in complex with a UCHT1 single-chain antibody fragment.
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PDB code: 1xiw
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Proteomic analysis of DC-SIGN on dendritic cells detects tetramers required for ligand binding but no association with CD4.
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15247914 Q.J.Li, A.R.Dinner, S.Qi, D.J.Irvine, J.B.Huppa, M.M.Davis, and A.K.Chakraborty (2004).
CD4 enhances T cell sensitivity to antigen by coordinating Lck accumulation at the immunological synapse.
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15326605 Y.H.Sanejouand (2004).
Domain swapping of CD4 upon dimerization.
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15131118 Y.Pan, B.Ma, O.Keskin, and R.Nussinov (2004).
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15557001 Z.Y.Sun, S.T.Kim, I.C.Kim, A.Fahmy, E.L.Reinherz, and G.Wagner (2004).
Solution structure of the CD3epsilondelta ectodomain and comparison with CD3epsilongamma as a basis for modeling T cell receptor topology and signaling.
  Proc Natl Acad Sci U S A, 101, 16867-16872.
PDB code: 1xmw
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Crystal structure of human junctional adhesion molecule 1: implications for reovirus binding.
  Proc Natl Acad Sci U S A, 100, 5366-5371.
PDB code: 1nbq
12970440 A.F.Labrijn, P.Poignard, A.Raja, M.B.Zwick, K.Delgado, M.Franti, J.Binley, V.Vivona, C.Grundner, C.C.Huang, M.Venturi, C.J.Petropoulos, T.Wrin, D.S.Dimitrov, J.Robinson, P.D.Kwong, R.T.Wyatt, J.Sodroski, and D.R.Burton (2003).
Access of antibody molecules to the conserved coreceptor binding site on glycoprotein gp120 is sterically restricted on primary human immunodeficiency virus type 1.
  J Virol, 77, 10557-10565.  
14563351 E.L.Lynch, F.F.Little, K.C.Wilson, D.M.Center, and W.W.Cruikshank (2003).
Immunomodulatory cytokines in asthmatic inflammation.
  Cytokine Growth Factor Rev, 14, 489-502.  
12433920 G.J.Babcock, M.Farzan, and J.Sodroski (2003).
Ligand-independent dimerization of CXCR4, a principal HIV-1 coreceptor.
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14705812 G.W.Lynch, E.K.Slaytor, F.D.Elliott, A.Saurajen, S.G.Turville, A.J.Sloane, P.U.Cameron, A.L.Cunningham, and G.M.Halliday (2003).
CD4 is expressed by epidermal Langerhans' cells predominantly as covalent dimers.
  Exp Dermatol, 12, 700-711.  
12787753 J.H.Wang, and M.J.Eck (2003).
Assembling atomic resolution views of the immunological synapse.
  Curr Opin Immunol, 15, 286-293.  
12962625 S.Majeed, G.Ofek, A.Belachew, C.C.Huang, T.Zhou, and P.D.Kwong (2003).
Enhancing protein crystallization through precipitant synergy.
  Structure, 11, 1061-1070.
PDB code: 1ps5
12627395 T.Stehle, and T.S.Dermody (2003).
Structural evidence for common functions and ancestry of the reovirus and adenovirus attachment proteins.
  Rev Med Virol, 13, 123-132.  
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Axonin-1/TAG-1 mediates cell-cell adhesion by a cis-assisted trans-interaction.
  J Biol Chem, 277, 4551-4557.  
11980704 K.Tan, B.D.Zelus, R.Meijers, J.H.Liu, J.M.Bergelson, N.Duke, R.Zhang, A.Joachimiak, K.V.Holmes, and J.H.Wang (2002).
Crystal structure of murine sCEACAM1a[1,4]: a coronavirus receptor in the CEA family.
  EMBO J, 21, 2076-2086.
PDB code: 1l6z
11988465 M.G.Rudolph, J.G.Luz, and I.A.Wilson (2002).
Structural and thermodynamic correlates of T cell signaling.
  Annu Rev Biophys Biomol Struct, 31, 121-149.  
11790535 R.König (2002).
Interactions between MHC molecules and co-receptors of the TCR.
  Curr Opin Immunol, 14, 75-83.  
12208966 S.H.Xiang, P.D.Kwong, R.Gupta, C.D.Rizzuto, D.J.Casper, R.Wyatt, L.Wang, W.A.Hendrickson, M.L.Doyle, and J.Sodroski (2002).
Mutagenic stabilization and/or disruption of a CD4-bound state reveals distinct conformations of the human immunodeficiency virus type 1 gp120 envelope glycoprotein.
  J Virol, 76, 9888-9899.  
11380681 C.L.Van Broekhoven, and J.G.Altin (2001).
A novel system for convenient detection of low-affinity receptor-ligand interactions: chelator-lipid liposomes engrafted with recombinant CD4 bind to cells expressing MHC class II.
  Immunol Cell Biol, 79, 274-284.  
11468396 G.Jogl, X.Tao, Y.Xu, and L.Tong (2001).
COMO: a program for combined molecular replacement.
  Acta Crystallogr D Biol Crystallogr, 57, 1127-1134.  
11727516 H.Kornfeld, and W.W.Cruikshank (2001).
Prospects for IL-16 in the treatment of AIDS.
  Expert Opin Biol Ther, 1, 425-432.  
11535811 J.H.Wang, R.Meijers, Y.Xiong, J.H.Liu, T.Sakihama, R.Zhang, A.Joachimiak, and E.L.Reinherz (2001).
Crystal structure of the human CD4 N-terminal two-domain fragment complexed to a class II MHC molecule.
  Proc Natl Acad Sci U S A, 98, 10799-10804.
PDB code: 1jl4
11390574 J.P.Moore, P.W.Parren, and D.R.Burton (2001).
Genetic subtypes, humoral immunity, and human immunodeficiency virus type 1 vaccine development.
  J Virol, 75, 5721-5729.  
11244037 P.Poignard, E.O.Saphire, P.W.Parren, and D.R.Burton (2001).
gp120: Biologic aspects of structural features.
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11095740 A.Ozinsky, D.M.Underhill, J.D.Fontenot, A.M.Hajjar, K.D.Smith, C.B.Wilson, L.Schroeder, and A.Aderem (2000).
The repertoire for pattern recognition of pathogens by the innate immune system is defined by cooperation between toll-like receptors.
  Proc Natl Acad Sci U S A, 97, 13766-13771.  
10986460 D.J.Thiel, M.H.le Du, R.L.Walter, A.D'Arcy, C.Chène, M.Fountoulakis, G.Garotta, F.K.Winkler, and S.E.Ealick (2000).
Observation of an unexpected third receptor molecule in the crystal structure of human interferon-gamma receptor complex.
  Structure, 8, 927-936.
PDB code: 1fg9
10617620 H.Appel, L.Gauthier, J.Pyrdol, and K.W.Wucherpfennig (2000).
Kinetics of T-cell receptor binding by bivalent HLA-DR.Peptide complexes that activate antigen-specific human T-cells.
  J Biol Chem, 275, 312-321.  
10617658 M.Miyahara, H.Nakanishi, K.Takahashi, K.Satoh-Horikawa, K.Tachibana, and Y.Takai (2000).
Interaction of nectin with afadin is necessary for its clustering at cell-cell contact sites but not for its cis dimerization or trans interaction.
  J Biol Chem, 275, 613-618.  
10644369 P.D.Kwong, R.Wyatt, Q.J.Sattentau, J.Sodroski, and W.A.Hendrickson (2000).
Oligomeric modeling and electrostatic analysis of the gp120 envelope glycoprotein of human immunodeficiency virus.
  J Virol, 74, 1961-1972.  
11188697 P.D.Kwong, R.Wyatt, S.Majeed, J.Robinson, R.W.Sweet, J.Sodroski, and W.A.Hendrickson (2000).
Structures of HIV-1 gp120 envelope glycoproteins from laboratory-adapted and primary isolates.
  Structure, 8, 1329-1339.
PDB codes: 1g9m 1g9n
  10892807 S.Arold, F.Hoh, S.Domergue, C.Birck, M.A.Delsuc, M.Jullien, and C.Dumas (2000).
Characterization and molecular basis of the oligomeric structure of HIV-1 nef protein.
  Protein Sci, 9, 1137-1148.  
11118070 U.Esser, R.F.Speck, K.C.Deen, R.E.Atchison, R.Sweet, and M.A.Goldsmith (2000).
Molecular function of the CD4 D1 domain in coreceptor-mediated entry by HIV type 1.
  AIDS Res Hum Retroviruses, 16, 1845-1854.  
9990061 G.Fernández-Miguel, B.Alarcón, A.Iglesias, H.Bluethmann, M.Alvarez-Mon, E.Sanz, and A.de la Hera (1999).
Multivalent structure of an alphabetaT cell receptor.
  Proc Natl Acad Sci U S A, 96, 1547-1552.  
10458774 G.W.Lynch, A.J.Sloane, V.Raso, A.Lai, and A.L.Cunningham (1999).
Direct evidence for native CD4 oligomers in lymphoid and monocytoid cells.
  Eur J Immunol, 29, 2590-2602.  
10595395 J.Roland, A.Berezov, M.I.Greene, R.Murali, D.Piatier-Tonneau, C.Devaux, and L.Briant (1999).
The synthetic CD4 exocyclic CDR3.AME(82-89) inhibits NF-kappaB nuclear translocation, HIV-1 promoter activation, and viral gene expression.
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Molecular interactions between extracellular components of the T-cell receptor signaling complex.
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Covalent homodimers of murine secretory component induced by epitope substitution unravel the capacity of the polymeric Ig receptor to dimerize noncovalently in the absence of IgA ligand.
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Probability analysis of variational crystallization and its application to gp120, the exterior envelope glycoprotein of type 1 human immunodeficiency virus (HIV-1).
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Enhanced expression, native purification, and characterization of CCR5, a principal HIV-1 coreceptor.
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The downregulation of CD4 and MHC-I by primate lentiviruses: a paradigm for the modulation of cell surface receptors.
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Constitutive cell surface association between CD4 and CCR5.
  Proc Natl Acad Sci U S A, 96, 7496-7501.  
10438516 Y.Liu, W.W.Cruikshank, T.O'Loughlin, P.O'Reilly, D.M.Center, and H.Kornfeld (1999).
Identification of a CD4 domain required for interleukin-16 binding and lymphocyte activation.
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Potent T cell activation with dimeric peptide-major histocompatibility complex class II ligand: the role of CD4 coreceptor.
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Preferential expression of TCR V alpha regions in CD4/CD8 subsets: class discrimination or co-receptor recognition?
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9699624 E.A.Berger (1998).
And the best picture is--the HIV gp120 envelope, please!
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The modular architecture of leukocyte cell-surface receptors.
  Immunol Rev, 163, 11-18.  
9597142 J.D.Klemm, S.L.Schreiber, and G.R.Crabtree (1998).
Dimerization as a regulatory mechanism in signal transduction.
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9806633 J.Delon, C.Grégoire, B.Malissen, S.Darche, F.Lemaître, P.Kourilsky, J.P.Abastado, and A.Trautmann (1998).
CD8 expression allows T cell signaling by monomeric peptide-MHC complexes.
  Immunity, 9, 467-473.  
9539702 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.
  Proc Natl Acad Sci U S A, 95, 4134-4139.
PDB code: 1ic1
9700512 J.Wang, and T.A.Springer (1998).
Structural specializations of immunoglobulin superfamily members for adhesion to integrins and viruses.
  Immunol Rev, 163, 197-215.  
9603449 N.Coudronnière, J.Corbeil, V.Robert-Hebmann, J.M.Mesnard, and C.Devaux (1998).
The Ick protein tyrosine kinase is not involved in antibody-mediated CD4 (CDR3-loop) signal transduction that inhibits HIV-1 transcription.
  Eur J Immunol, 28, 1445-1457.  
9739096 Q.J.Sattentau (1998).
HIV gp120: double lock strategy foils host defences.
  Structure, 6, 945-949.  
9479578 R.Murali, and M.I.Greene (1998).
Structure-based design of immunologically active therapeutic peptides.
  Immunol Res, 17, 163-169.  
9523116 R.Zamoyska (1998).
CD4 and CD8: modulators of T-cell receptor recognition of antigen and of immune responses?
  Curr Opin Immunol, 10, 82-87.  
9703515 X.D.Su, L.N.Gastinel, D.E.Vaughn, I.Faye, P.Poon, and P.J.Bjorkman (1998).
Crystal structure of hemolin: a horseshoe shape with implications for homophilic adhesion.
  Science, 281, 991-995.
PDB code: 1bih
9700515 Z.Weng, and C.DeLisi (1998).
Toward a predictive understanding of molecular recognition.
  Immunol Rev, 163, 251-266.  
9413981 D.S.Dimitrov (1997).
How do viruses enter cells? The HIV coreceptors teach us a lesson of complexity.
  Cell, 91, 721-730.  
9342320 M.Karpusas, M.Nolte, C.B.Benton, W.Meier, W.N.Lipscomb, and S.Goelz (1997).
The crystal structure of human interferon beta at 2.2-A resolution.
  Proc Natl Acad Sci U S A, 94, 11813-11818.
PDB code: 1au1
9368747 R.N.Germain (1997).
T-cell signaling: the importance of receptor clustering.
  Curr Biol, 7, R640-R644.  
9566118 Z.Huang, S.Li, and R.Korngold (1997).
Immunoglobulin superfamily proteins: structure, mechanisms, and drug discovery.
  Biopolymers, 43, 367-382.  
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 code is shown on the right.

 

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