PDBsum entry 2ipk

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protein Protein-protein interface(s) links
Immune system PDB id
Protein chains
179 a.a. *
190 a.a. *
14 a.a. *
232 a.a. *
Waters ×419
* Residue conservation analysis
PDB id:
Name: Immune system
Title: Crystal structure of the mhc class ii molecule hla-dr1 in complex with the fluorogenic peptide, acpkxvkqntlklat (x=3- [5-(dimethylamino)-1,3-dioxo-1,3-dihydro-2h-isoindol-2-yl]- l-alanine) and the superantigen, sec3 variant 3b2
Structure: Hla class ii histocompatibility antigen, dr alpha chain. Chain: a. Fragment: extracellular domain, residues 26-207. Synonym: mhc class ii antigen dra. Engineered: yes. Hla class ii histocompatibility antigen, drb1-1 beta chain. Chain: b.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: hla-dra. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: hla-drb1. Synthetic: yes. Other_details: synthesized peptide naturally found in
2.30Å     R-factor:   0.203     R-free:   0.224
Authors: T.T.Nguyen,L.J.Stern
Key ref:
P.Venkatraman et al. (2007). Fluorogenic probes for monitoring peptide binding to class II MHC proteins in living cells. Nat Chem Biol, 3, 222-228. PubMed id: 17351628 DOI: 10.1038/nchembio868
12-Oct-06     Release date:   13-Mar-07    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P01903  (DRA_HUMAN) -  HLA class II histocompatibility antigen, DR alpha chain
254 a.a.
179 a.a.
Protein chain
Pfam   ArchSchema ?
P04229  (2B11_HUMAN) -  HLA class II histocompatibility antigen, DRB1-1 beta chain
266 a.a.
190 a.a.
Protein chain
Pfam   ArchSchema ?
A8CDU0  (A8CDU0_9INFA) -  Hemagglutinin (Fragment)
104 a.a.
13 a.a.*
Protein chain
Pfam   ArchSchema ?
P0A0L5  (ENTC3_STAAU) -  Enterotoxin type C-3
266 a.a.
232 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   3 terms 
  Biological process     immune response   3 terms 


DOI no: 10.1038/nchembio868 Nat Chem Biol 3:222-228 (2007)
PubMed id: 17351628  
Fluorogenic probes for monitoring peptide binding to class II MHC proteins in living cells.
P.Venkatraman, T.T.Nguyen, M.Sainlos, O.Bilsel, S.Chitta, B.Imperiali, L.J.Stern.
A crucial step in the immune response is the binding of antigenic peptides to major histocompatibility complex (MHC) proteins. Class II MHC proteins present their bound peptides to CD4(+) T cells, thereby helping to activate both the humoral and the cellular arms of the adaptive immune response. Peptide loading onto class II MHC proteins is regulated temporally, spatially and developmentally in antigen-presenting cells. To help visualize these processes, we have developed a series of novel fluorogenic probes that incorporate the environment-sensitive amino acid analogs 6-N,N-dimethylamino-2-3-naphthalimidoalanine and 4-N,N-dimethylaminophthalimidoalanine. Upon binding to class II MHC proteins these fluorophores show large changes in emission spectra, quantum yield and fluorescence lifetime. Peptides incorporating these fluorophores bind specifically to class II MHC proteins on antigen-presenting cells and can be used to follow peptide binding in vivo. Using these probes we have tracked a developmentally regulated cell-surface peptide-binding activity in primary human monocyte-derived dendritic cells.
  Selected figure(s)  
Figure 1.
(a) Chemical structures of DANA, 4-DAPA and 6-DMNA. (b) In the crystal structure of the DR1–HA peptide complex, a tyrosine residue is buried deep into the hydrophobic P1 pocket^5. DANA, 4-DAPA and 6-DMNA were modeled in silico into this pocket in place of tyrosine. Residues shown lining the pocket are (clockwise from upper right) Phe 54, Phe 32, Trp 43 (behind), Ile 7, Trp 153, Phe 48, Thr 90, Val 91, Tyr 83, Gly 86 and Val 85. The side chains of Asn 82 and His 81 (upper left) form hydrogen bonds with the peptide main chain at the mouth of the P1 pocket. Other residues lining the pocket but not shown are Phe 24, Phe 26 and Phe 48. (c) Binding of fluorogenic peptides to DR1 assessed using a competitive binding assay. DR1 was incubated with biotin–HA peptide and various concentrations of unlabeled inhibitor peptides, and biotin-HA binding was quantified by a sandwich ELISA assay using streptavidin alkaline phosphatase. Binding of Fmoc-(4-DAPA) was assessed to evaluate nonspecific binding of the fluorophore. IC[50] values for these and other peptides (Supplementary Table 1) were determined as described (Supplementary Methods).
Figure 3.
(a) (4-DAPA)-HA was incubated with HLA-DR1 as described for (4-DAPA)-RSMA[4]L, and the complex formed was purified by gel filtration. Fluorescence of DR-(4-DAPA)-HA was compared with that of the free peptide. (b) Activation of HA1.7 T-cell receptor hybridoma by antigen-presenting cells pulsed with HA (filled circles) or (4-DAPA)-HA (closed triangles) peptides. T-cell activation reported as counts per minute (c.p.m.) measured in a thymidine incorporation bioassay for IL-2 as secreted by activated T cells. Error bars indicate s.d. of triplicate measurements. (c–e) Crystal structure of (4-DAPA)-HA bound to DR1. (c) (4-DAPA)-HA peptide shown with surface representation of the DR1 peptide binding site, with the 4-DAPA side chain shown with yellow bonds extending down into the P1 pocket (top); unmodified HA peptide from the crystal structure of the DR1-HA-SEC (3B2) complex (PDB ID 1JWU) shown after alignment of MHC peptide binding domain, with tyrosine side chain at the P1 position shown with cyan bonds (bottom). (d) 2F[o] - F[c] omit map of the region around the P1 pocket with all residues shown removed from the model before map calculation. (e) Section through the P1 pocket, showing the HA peptide tyrosine side chain and the (4-DAPA)-HA fluorophore, along with the corresponding ordered water molecules, colored as in c. Panels c–e made using PyMOL^30.
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Chem Biol (2007, 3, 222-228) copyright 2007.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21123113 C.C.Clement, O.Rotzschke, and L.Santambrogio (2011).
The lymph as a pool of self-antigens.
  Trends Immunol, 32, 6.  
21109888 D.Zhang, K.Vangala, S.Li, M.Yanney, H.Xia, S.Zou, and A.Sygula (2011).
Acid cleavable surface enhanced raman tagging for protein detection.
  Analyst, 136, 520-526.  
19962774 G.S.Loving, M.Sainlos, and B.Imperiali (2010).
Monitoring protein interactions and dynamics with solvatochromic fluorophores.
  Trends Biotechnol, 28, 73-83.  
19194572 A.R.Katritzky, and T.Narindoshvili (2009).
Fluorescent amino acids: advances in protein-extrinsic fluorophores.
  Org Biomol Chem, 7, 627-634.  
19821578 G.Loving, and B.Imperiali (2009).
Thiol-reactive derivatives of the solvatochromic 4-N,N-dimethylamino-1,8-naphthalimide fluorophore: a highly sensitive toolset for the detection of biomolecular interactions.
  Bioconjug Chem, 20, 2133-2141.  
19388649 M.Sainlos, W.S.Iskenderian, and B.Imperiali (2009).
A general screening strategy for peptide-based fluorogenic ligands: probes for dynamic studies of PDZ domain-mediated interactions.
  J Am Chem Soc, 131, 6680-6682.  
  19739174 V.Sharma, and D.S.Lawrence (2009).
Uber-responsive peptide-based sensors of signaling proteins.
  Angew Chem Int Ed Engl, 48, 7290-7292.  
19151084 V.V.Shvadchak, A.S.Klymchenko, Rocquigny, and Y.Mély (2009).
Sensing peptide-oligonucleotide interactions by a two-color fluorescence label: application to the HIV-1 nucleocapsid protein.
  Nucleic Acids Res, 37, e25.  
18808123 G.Loving, and B.Imperiali (2008).
A versatile amino acid analogue of the solvatochromic fluorophore 4-N,N-dimethylamino-1,8-naphthalimide: a powerful tool for the study of dynamic protein interactions.
  J Am Chem Soc, 130, 13630-13638.  
18385732 R.Weissleder, and M.J.Pittet (2008).
Imaging in the era of molecular oncology.
  Nature, 452, 580-589.  
18236039 S.B.Raymond, J.Skoch, I.D.Hills, E.E.Nesterov, T.M.Swager, and B.J.Bacskai (2008).
Smart optical probes for near-infrared fluorescence imaging of Alzheimer's disease pathology.
  Eur J Nucl Med Mol Imaging, 35, S93-S98.  
17372601 J.W.Yewdell, and A.Lev (2007).
Self-reporting peptides illuminate the MHC groove.
  Nat Chem Biol, 3, 201-202.  
18079720 M.Sainlos, and B.Imperiali (2007).
Tools for investigating peptide-protein interactions: peptide incorporation of environment-sensitive fluorophores via on-resin derivatization.
  Nat Protoc, 2, 3201-3209.  
18079721 M.Sainlos, and B.Imperiali (2007).
Tools for investigating peptide-protein interactions: peptide incorporation of environment-sensitive fluorophores through SPPS-based 'building block' approach.
  Nat Protoc, 2, 3210-3218.  
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.