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PDBsum entry 1qqd
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protein ligands Protein-protein interface(s) links
Immune system PDB id
1qqd

 

 

 

 

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Contents
Protein chains
273 a.a. *
99 a.a. *
Ligands
GLN-TYR-ASP-ASP-
ALA-VAL-TYR-LYS-
LEU
Waters ×35
* Residue conservation analysis
PDB id:
1qqd
Name: Immune system
Title: Crystal structure of hla-cw4, a ligand for the kir2d natural killer cell inhibitory receptor
Structure: Histocompatibility leukocyte antigen (hla)-cw4 (heavy chain). Chain: a. Fragment: extracellular domain. Engineered: yes. Beta-2 microglobulin. Chain: b. Engineered: yes. Hla-cw4 specific peptide.
Source: Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: the peptide was chemically synthesized. The nonameric peptide contains the consensus peptide-binding motif for hla-cw4, which was determined by pool sequencing.
Biol. unit: Trimer (from PQS)
Resolution:
2.70Å     R-factor:   0.223     R-free:   0.275
Authors: Q.R.Fan,D.C.Wiley
Key ref: Q.R.Fan and D.C.Wiley (1999). Structure of human histocompatibility leukocyte antigen (HLA)-Cw4, a ligand for the KIR2D natural killer cell inhibitory receptor. J Exp Med, 190, 113-123. PubMed id: 10429675
Date:
03-Jun-99     Release date:   08-Dec-99    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
P10321  (1C07_HUMAN) -  HLA class I histocompatibility antigen, C alpha chain from Homo sapiens
Seq:
Struc: 		366 a.a.
273 a.a.*
Protein chain
Pfam   ArchSchema ?
P61769  (B2MG_HUMAN) -  Beta-2-microglobulin from Homo sapiens
Seq:
Struc: 		119 a.a.
99 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 22 residue positions (black crosses)

 

 
J Exp Med 190:113-123 (1999)
PubMed id: 10429675  
 
 
Structure of human histocompatibility leukocyte antigen (HLA)-Cw4, a ligand for the KIR2D natural killer cell inhibitory receptor.
Q.R.Fan, D.C.Wiley.
 
  ABSTRACT  
 
The crystal structure of the human class I major histocompatibility complex molecule, human histocompatibility leukocyte antigen (HLA)-Cw4, the ligand for a natural killer (NK) cell inhibitory receptor, has been determined, complexed with a nonameric consensus peptide (QYDDAVYKL). Relative to HLA-A2, the peptide binding groove is widened around the COOH terminus of the alpha 1 helix, which contains residues that determine the specificity of HLA-Cw4 for the inhibitory NK receptor, KIR2D. The structure reveals an unusual pattern of internal hydrogen bonding among peptide residues. The peptide is anchored in four specificity pockets in the cleft and secured by extensive hydrogen bonds between the peptide main chain and the cleft. The surface of HLA-Cw4 has electrostatic complementarity to the surface of the NK cell inhibitory receptor KIR2D.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21216870 A.Merino, R.Malhotra, M.Morton, J.Mulenga, S.Allen, E.Hunter, J.Tang, and R.A.Kaslow (2011).
Impact of a Functional KIR2DS4 Allele on Heterosexual HIV-1 Transmission among Discordant Zambian Couples.
  J Infect Dis, 203, 487-495.  
  20975736 S.Infantes, E.Lorente, J.J.Cragnolini, M.Ramos, R.García, M.Jiménez, S.Iborra, M.Del Val, and D.López (2011).
Unusual viral ligand with alternative interactions is presented by HLA-Cw4 in human respiratory syncytial virus-infected cells.
  Immunol Cell Biol, 89, 558-565.  
  19177349 P.Kumar, A.Vahedi-Faridi, W.Saenger, A.Ziegler, and B.Uchanska-Ziegler (2009).
Conformational changes within the HLA-A1:MAGE-A1 complex induced by binding of a recombinant antibody fragment with TCR-like specificity.
  Protein Sci, 18, 37-49.
PDB code: 3bo8
17446137 G.Yun, J.Tolar, A.K.Yerich, S.G.Marsh, J.Robinson, H.Noreen, B.R.Blazar, and J.S.Miller (2007).
A novel method for KIR-ligand typing by pyrosequencing to predict NK cell alloreactivity.
  Clin Immunol, 123, 272-280.  
17705876 J.C.Tong, Z.H.Zhang, J.T.August, V.Brusic, T.W.Tan, and S.Ranganathan (2007).
In silico characterization of immunogenic epitopes presented by HLA-Cw*0401.
  Immunome Res, 3, 7.  
16533401 I.A.Doytchinova, P.Guan, and D.R.Flower (2006).
EpiJen: a server for multistep T cell epitope prediction.
  BMC Bioinformatics, 7, 131.  
16185332 S.H.Hwang, C.H.Cha, O.J.Kwon, Y.S.Heo, S.S.Hur, M.N.Lee, and H.B.Oh (2005).
Novel HLA-Cw*06 allele, Cw*0612, identified by sequence-based typing.
  Tissue Antigens, 66, 330-331.  
11861620 K.Natarajan, N.Dimasi, J.Wang, R.A.Mariuzza, and D.H.Margulies (2002).
Structure and function of natural killer cell receptors: multiple molecular solutions to self, nonself discrimination.
  Annu Rev Immunol, 20, 853-885.  
10764618 E.O.Long, and S.Rajagopalan (2000).
HLA class I recognition by killer cell Ig-like receptors.
  Semin Immunol, 12, 101-108.  
10764619 M.López-Botet, M.Llano, F.Navarro, and T.Bellón (2000).
NK cell recognition of non-classical HLA class I molecules.
  Semin Immunol, 12, 109-119.  
10611338 D.M.Davis, I.Chiu, M.Fassett, G.B.Cohen, O.Mandelboim, and J.L.Strominger (1999).
The human natural killer cell immune synapse.
  Proc Natl Acad Sci U S A, 96, 15062-15067.  
10607669 K.Maenaka, and E.Y.Jones (1999).
MHC superfamily structure and the immune system.
  Curr Opin Struct Biol, 9, 745-753.  
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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