The Crystal Structure of H-2Dd MHC Class I Complexed with the HIV-1-Derived Peptide P18-I10 at 2.4 Å Resolution

Achour, Adnane; Persson, Karina; Harris, Robert A.; Sundbäck, Jonas; Sentman, Charles L.; Lindqvist, Ylva; Schneider, Günter; Kärre, Klas

doi:10.1016/s1074-7613(00)80602-0

Cited by 70 publications

(74 citation statements)

References 65 publications

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“…This fourth anchor residue is due to the presence of two Trp residues (at positions 97 and 114 of D d ), which form a wall within the binding groove that forces the peptide to arch over the wall to anchor the C-terminal residue (39), and permits that peptide positions 6, 7, and 8 protrude above the protein surface and have high solvent accessibility. As a consequence, the side chains of these residues are more accessible for recognition by specific CTL.…”

Section: Discussionmentioning

confidence: 99%

“…Of these, at least one of them is different to the decamer peptide previously assumed (20) as the optimal synthetic peptide in the ENV glycoprotein-specific CTL immune response, and unexpectedly lacks the terminal NH 3 ϩ group anchor. Effect of N-and C-terminal Extensions on MHC/Peptide/ CTL Interaction-Resolution of the crystal structure of the R10I peptide bound to D d (38,39), as well as analysis of the pool of natural endogenous peptides presented by D d (40), jointly provide a basis for predicting the binding conformation of the shorter as well as maybe longer peptides found in this study. To complement this set of information, antigenicity for CTL, as well as D d /peptide complex stability, was assayed for an extended series of synthetic peptides.…”

Section: Fig 5 Identification By Mass Spectrometry Of G9i In Infectmentioning

confidence: 95%

“…However, another group reported later that this monocharged nonapeptide was essentially not antigenic (20), and this latter report was widely accepted as an indication that the optimal synthetic peptide was, by far, R10I. This was supported by the excellent fit of the R10I peptide into the D d molecule, as revealed by crystallographic studies (38,39). On this light, it was unexpected to find this monocharged G9I species as a result of endogenous processing.…”

Section: Physiological Processing Generates At Least Two Different D mentioning

confidence: 96%

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An Endogenous HIV Envelope-derived Peptide without the Terminal NH3+ Group Anchor Is Physiologically Presented by Major Histocompatibility Complex Class I Molecules

Samino

López

Guil

et al. 2004

Journal of Biological Chemistry

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Section: Discussionmentioning

confidence: 99%

Section: Fig 5 Identification By Mass Spectrometry Of G9i In Infectmentioning

confidence: 95%

Section: Physiological Processing Generates At Least Two Different D mentioning

confidence: 96%

See 1 more Smart Citation

An Endogenous HIV Envelope-derived Peptide without the Terminal NH3+ Group Anchor Is Physiologically Presented by Major Histocompatibility Complex Class I Molecules

Samino

López

Guil

et al. 2004

Journal of Biological Chemistry

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“…5). Especially, the side chain of Arg 35 (H-2D d heavy chain) is involved in hydrogen bonding with ␤ 2 m in the crystal structure of H-2D d (42,43). Disruption of this hydrogen bond by R35A mutation might change the orientation of ␤ 2 m against ␣1/␣2 domain and thereby severely impair the Ly49A binding to H-2D d .…”

Section: Effect Of Mutation In Conserved Residues In ␣1 Domain Of H-2mentioning

confidence: 99%

“…The crystal structure of H-2D d revealed that Ala 99 and Asp 77 are located in a critical position to bind two anchoring residues of the peptide, Pro at position 3 and Arg at position 5, respectively (42,43). Consequently, H-2D d with these mutations might not bind peptide or acquire new peptide specificities.…”

Section: Effect Of Mutation In Conserved Residues In ␣1 Domain Of H-2mentioning

confidence: 99%

The NK Cell MHC Class I Receptor Ly49A Detects Mutations on H-2Dd Inside and Outside of the Peptide Binding Groove

Matsumoto

Yokoyama

Kojima

et al. 2001

The Journal of Immunology

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N atural killer cells are a group of lymphocytes that spontaneously lyse certain tumor targets (1). The finding that cell lines defective for MHC class I expression were efficiently lysed by NK cells led to the missing self hypothesis: NK cells kill cells that lack normal expression of MHC class I molecules (2). Recent studies have established that NK cells express inhibitory receptors for MHC class I molecules (3, 4). The receptors can be classified into two groups by their structural characteristics. One group that includes human killer cell Ig-like receptors is characterized by two or three Ig-like domains in the extracellular region and configuration of type I transmembrane proteins (5, 6). NK cell MHC class I receptors of Ig-type have thus far been found only in primates, but not in rodents. gp49B1, which belongs to the Ig superfamily, is expressed on mouse NK cells (7,8); however, the ligand for gp49B1 may not be MHC class I. Another group of NK cell MHC class I receptors is characterized by disulfide-linked dimer of type II transmembrane protein with an extracellular region homologous to carbohydrate recognition domain of C-type lectin. This group includes the Ly49 family in mice (9 -12) and rats (13) and CD94/NKG2 heterodimer found in humans (14) and rodents (15, 16).The inhibitory receptors of both groups have one or two immune receptor tyrosine-based inhibitory motifs (ITIM) 3 characterized by an IXYXXL sequence in the cytoplasmic region (17). Upon ligand recognition, the Tyr residue in the ITIM is phosphorylated and recruits the Src homology domain-containing protein tyrosine phosphatase 1 with Src homology 2 domains. The recruited Src homology domain-containing protein tyrosine phosphatase 1 is believed to dephosphorylate unknown critical substrates to shut down positive signaling. There are activating type of MHC class I receptors of C-type lectin and Ig-type with extracellular domains similar to those of the inhibitory receptors. Instead of cytoplasmic ITIM, the activating receptors have characteristic charged amino acid residues in the transmembrane region, and by that associate with DAP12, an adapter component with cytoplasmic immune receptor tyrosine-based activating motif (18). Engagement of such receptors initiates an activation signaling cascade analogous to T or B cell receptor signaling.Mouse NK cells express the Ly49 family of receptors, which includes Ͼ10 members (9 -12, 19). Several lines of evidence demonstrate that Ly49A, a primary member of Ly49 family, is an inhibitory receptor that specifically recognizes a conformational epitope on H- The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked advertisement in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

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Effect of glycosylation on structure and dynamics of MHC class I glycoprotein: A molecular dynamics study

Mandal

Mukhopadhyay

2001

Biopolymers

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Complex carbohydrates linked to glycoproteins are recently being implicated to play a variety of biological roles. The lack of well‐resolved crystallographic coordinates of the carbohydrates makes it difficult to assess the contributions of the glycan chain on protein structure and dynamics. We have modeled two different oligosaccharides NeuNAc2Gal3Man3GlcNAc5Fuc and Man3GlcNAc4 to generate two glycosylation variants of major histocompatibility complex (MHC) class I glycoprotein. Molecular dynamics simulations of the isolated fourteen‐ and seven‐residue oligosaccharides have been done in vacuo and in solution. The dynamics of the two glycoforms of MHC class I protein have been simulated in solution in the free as well as in the peptide‐bound form. Good agreement between the calculated solution conformations of the oligosaccharides in isolated and conjugated forms and the average conformations obtained from x‐ray or NMR data was observed for most of the glycosidic linkages. These molecular dynamics simulations of the isolated glycan chains and the glycoconjugates reveal the details of the conformational flexibility of the glycan chains; they also provide atomic level details of protein–carbohydrate interactions and the effect of the ligand binding on the carbohydrate structure and dynamics. It was found that though there is some flexibility in some of the glycosidic linkages in the isolated oligosaccharides, in the protein‐conjugated form the linkages adopt more restricted conformations. The glycan chains protrude out into the solvent and might hinder the lateral association of the proteins. The presence of the bulky glycan chains does not affect the average backbone fold of the protein but induces local changes in protein structure and dynamics. It has been noted that the extent of the changes depends upon the nature of the attached glycan chain. The glycan chains do not appear to influence the peptide binding property of the protein directly, but may stabilize the protein residues that are involved in ligand binding. © 2001 John Wiley & Sons, Inc. Biopolymers 59: 11–23, 2001

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The Crystal Structure of H-2Dd MHC Class I Complexed with the HIV-1-Derived Peptide P18-I10 at 2.4 Å Resolution

Cited by 70 publications

References 65 publications

An Endogenous HIV Envelope-derived Peptide without the Terminal NH3+ Group Anchor Is Physiologically Presented by Major Histocompatibility Complex Class I Molecules

An Endogenous HIV Envelope-derived Peptide without the Terminal NH3+ Group Anchor Is Physiologically Presented by Major Histocompatibility Complex Class I Molecules

The NK Cell MHC Class I Receptor Ly49A Detects Mutations on H-2Dd Inside and Outside of the Peptide Binding Groove

Effect of glycosylation on structure and dynamics of MHC class I glycoprotein: A molecular dynamics study

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