PDBsum entry 1fzk

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Immune system PDB id
Protein chains
274 a.a. *
99 a.a. *
PO4 ×2
MPD ×2
Waters ×406
* Residue conservation analysis
PDB id:
Name: Immune system
Title: Mhc class i natural mutant h-2kbm1 heavy chain complexed wit microglobulin and sendai virus nucleoprotein
Structure: H-2 class i histocompatibility antigen, k-b alpha chain: a. Fragment: extracellular domain. Engineered: yes. Mutation: yes. Protein (beta-2-microglobulin). Chain: b. Engineered: yes. Protein (nucleocapsid protein).
Source: Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: drosophila melanogaster. Expression_system_taxid: 7227. Synthetic: yes. Other_details: the peptide was chemically synthesized. The of the peptide is found naturally in sendai virus.
Biol. unit: Trimer (from PQS)
1.70Å     R-factor:   0.204     R-free:   0.213
Authors: M.G.Rudolph,J.A.Speir,A.Brunmark,N.Mattsson,M.R.Jackson,P.A. L.Teyton,I.A.Wilson
Key ref:
M.G.Rudolph et al. (2001). The crystal structures of K(bm1) and K(bm8) reveal that subtle changes in the peptide environment impact thermostability and alloreactivity. Immunity, 14, 231-242. PubMed id: 11290333 DOI: 10.1016/S1074-7613(01)00105-4
03-Oct-00     Release date:   28-Mar-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P01901  (HA1B_MOUSE) -  H-2 class I histocompatibility antigen, K-B alpha chain
369 a.a.
274 a.a.*
Protein chain
Pfam   ArchSchema ?
P01887  (B2MG_MOUSE) -  Beta-2-microglobulin
119 a.a.
99 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 5 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   6 terms 
  Biological process     immune system process   12 terms 
  Biochemical function     protein binding     3 terms  


DOI no: 10.1016/S1074-7613(01)00105-4 Immunity 14:231-242 (2001)
PubMed id: 11290333  
The crystal structures of K(bm1) and K(bm8) reveal that subtle changes in the peptide environment impact thermostability and alloreactivity.
M.G.Rudolph, J.A.Speir, A.Brunmark, N.Mattsson, M.R.Jackson, P.A.Peterson, L.Teyton, I.A.Wilson.
The K(bm1) and K(bm8) natural mutants of the murine MHC class I molecule H-2K(b) were originally identified by allograft rejection. They also bind viral peptides VSV8 and SEV9 with high affinity, but their peptide complexes have substantially decreased thermostability, and the K(bm1) complexes do not elicit alloreactive T cell responses. Crystal structures of the four mutant complexes at 1.7-1.9 A resolution are similar to the corresponding wild-type K(b) structures, except in the vicinity of the mutated residues, which alter the electrostatic potential, topology, hydrogen bonding, and local water structure of the peptide binding groove. Thus, these natural K(b) mutations define the minimal perturbations in the peptide environment that alter antigen presentation to T cells and abolish alloreactivity.
  Selected figure(s)  
Figure 1.
Figure 1. Molecular Structure of K^b and Location of the Mutations in K^bm1 and K^bm8(A) Ribbon diagram of wild-type K^b with peptide (magenta) bound in an extended conformation within the binding groove formed by the α helices and the β sheet floor.(B) Mutated side chains in K^bm1 and K^bm8 are shown in green and orange, respectively, while wild-type side chains are shown in (A).(C) Superimposed Cα tracings of the α[1]α[2] helices of K^b-VSV8 (yellow), K^b-SEV9 (blue), K^bm1-VSV8 (magenta), K^bm1-SEV9 (red), K^bm8-VSV8 (cyan), and K^bm8-SEV9 (green). Peptide-contacting side chains from the helices, some of which have different conformations in the six complexes, are shown
Figure 5.
Figure 5. Comparison of the Interactions at the K^bm8 Mutation Site with K^bThe coloring scheme is the same as in Figure 4 except that the MHC residues at the mutation site are colored orange. The two conformers of Ser-24 in K^bm8-VSV8 are shown in orange and blue. Note the intricate hydrogen bond networks mediated by water molecules at the K^bm8 mutation sites compared to the equivalent wild-type K^b complexes
  The above figures are reprinted by permission from Cell Press: Immunity (2001, 14, 231-242) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20936494 C.Cárdenas, A.Bidon-Chanal, P.Conejeros, G.Arenas, S.Marshall, and F.J.Luque (2010).
Molecular modeling of class I and II alleles of the major histocompatibility complex in Salmo salar.
  J Comput Aided Mol Des, 24, 1035-1051.  
20039862 D.A.Clark, G.Chaouat, K.Wong, R.M.Gorczynski, and R.Kinsky (2010).
Tolerance mechanisms in pregnancy: a reappraisal of the role of class I paternal MHC antigens.
  Am J Reprod Immunol, 63, 93.  
20064447 O.Y.Borbulevych, K.H.Piepenbrink, B.E.Gloor, D.R.Scott, R.F.Sommese, D.K.Cole, A.K.Sewell, and B.M.Baker (2009).
T cell receptor cross-reactivity directed by antigen-dependent tuning of peptide-MHC molecular flexibility.
  Immunity, 31, 885-896.
PDB codes: 3h7b 3h9h 3h9s 3ixa
18083574 M.Koch, S.Camp, T.Collen, D.Avila, J.Salomonsen, H.J.Wallny, A.van Hateren, L.Hunt, J.P.Jacob, F.Johnston, D.A.Marston, I.Shaw, P.R.Dunbar, V.Cerundolo, E.Y.Jones, and J.Kaufman (2007).
Structures of an MHC class I molecule from B21 chickens illustrate promiscuous peptide binding.
  Immunity, 27, 885-899.
PDB codes: 3bev 3bew
17169430 S.E.Brophy, L.L.Jones, P.D.Holler, and D.M.Kranz (2007).
Cellular uptake followed by class I MHC presentation of some exogenous peptides contributes to T cell stimulatory capacity.
  Mol Immunol, 44, 2184-2194.  
16446170 L.J.Carreño, P.A.González, and A.M.Kalergis (2006).
Modulation of T cell function by TCR/pMHC binding kinetics.
  Immunobiology, 211, 47-64.  
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.  
16007091 D.M.Zajonc, C.Cantu, J.Mattner, D.Zhou, P.B.Savage, A.Bendelac, I.A.Wilson, and L.Teyton (2005).
Structure and function of a potent agonist for the semi-invariant natural killer T cell receptor.
  Nat Immunol, 6, 810-818.
PDB code: 1z5l
16181330 T.H.Hansen, L.Lybarger, L.Yu, V.Mitaksov, and D.H.Fremont (2005).
Recognition of open conformers of classical MHC by chaperones and monoclonal antibodies.
  Immunol Rev, 207, 100-111.  
15004033 A.I.Webb, M.A.Dunstone, W.Chen, M.I.Aguilar, Q.Chen, H.Jackson, L.Chang, L.Kjer-Nielsen, T.Beddoe, J.McCluskey, J.Rossjohn, and A.W.Purcell (2004).
Functional and structural characteristics of NY-ESO-1-related HLA A2-restricted epitopes and the design of a novel immunogenic analogue.
  J Biol Chem, 279, 23438-23446.
PDB codes: 1s9w 1s9x 1s9y
15557346 M.J.Miley, I.Messaoudi, B.M.Metzner, Y.Wu, J.Nikolich-Zugich, and D.H.Fremont (2004).
Structural basis for the restoration of TCR recognition of an MHC allelic variant by peptide secondary anchor substitution.
  J Exp Med, 200, 1445-1454.
PDB codes: 1rjy 1rjz 1rk0 1rk1
14555655 R.C.Hillig, M.Hülsmeyer, W.Saenger, K.Welfle, R.Misselwitz, H.Welfle, C.Kozerski, A.Volz, B.Uchanska-Ziegler, and A.Ziegler (2004).
Thermodynamic and structural analysis of peptide- and allele-dependent properties of two HLA-B27 subtypes exhibiting differential disease association.
  J Biol Chem, 279, 652-663.
PDB code: 1jgd
12939341 W.A.Macdonald, A.W.Purcell, N.A.Mifsud, L.K.Ely, D.S.Williams, L.Chang, J.J.Gorman, C.S.Clements, L.Kjer-Nielsen, D.M.Koelle, S.R.Burrows, B.D.Tait, R.Holdsworth, A.G.Brooks, G.O.Lovrecz, L.Lu, J.Rossjohn, and J.McCluskey (2003).
A naturally selected dimorphism within the HLA-B44 supertype alters class I structure, peptide repertoire, and T cell recognition.
  J Exp Med, 198, 679-691.
PDB codes: 1m6o 1n2r
12047359 H.A.Elsner, and R.Blasczyk (2002).
Sequence similarity matching: proposal of a structure-based rating system for bone marrow transplantation.
  Eur J Immunogenet, 29, 229-236.  
11877480 J.Hennecke, and D.C.Wiley (2002).
Structure of a complex of the human alpha/beta T cell receptor (TCR) HA1.7, influenza hemagglutinin peptide, and major histocompatibility complex class II molecule, HLA-DR4 (DRA*0101 and DRB1*0401): insight into TCR cross-restriction and alloreactivity.
  J Exp Med, 195, 571-581.
PDB code: 1j8h
11790533 M.G.Rudolph, and I.A.Wilson (2002).
The specificity of TCR/pMHC interaction.
  Curr Opin Immunol, 14, 52-65.  
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.  
11602635 P.D.Holler, A.R.Lim, B.K.Cho, L.A.Rund, and D.M.Kranz (2001).
CD8(-) T cell transfectants that express a high affinity T cell receptor exhibit enhanced peptide-dependent activation.
  J Exp Med, 194, 1043-1052.  
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.