Hemagglutinin (HA) is the receptor-binding and membrane fusion glycoprotein
of influenza virus and the target for infectivity-neutralizing antibodies. The
structures of three conformations of the ...ectodomain of the 1968 Hong Kong
influenza virus HA have been determined by X-ray crystallography: the
single-chain precursor, HA0; the metastable neutral-pH conformation found on
virus, and the fusion pH-induced conformation. These structures provide a
framework for designing and interpreting the results of experiments on the
activity of HA in receptor binding, the generation of emerging and reemerging
epidemics, and membrane fusion during viral entry. Structures of HA in complex
with sialic acid receptor analogs, together with binding experiments, provide
details of these low-affinity interactions in terms of the sialic acid
substituents recognized and the HA residues involved in recognition.
Neutralizing antibody-binding sites surround the receptor-binding pocket on the
membrane-distal surface of HA, and the structures of the complexes between
neutralizing monoclonal Fabs and HA indicate possible neutralization
mechanisms. Cleavage of the biosynthetic precursor HA0 at a prominent loop in
its structure primes HA for subsequent activation of membrane fusion at
endosomal pH (
Figure 1
). Priming involves
insertion of the fusion peptide into a charged pocket in the precursor;
activation requires its extrusion towards the fusion target membrane, as the N
terminus of a newly formed trimeric coiled coil, and repositioning of the
C-terminal membrane anchor near the fusion peptide at the same end of a
rod-shaped molecule. Comparison of this new HA conformation, which has been
formed for membrane fusion, with the structures determined for other virus
fusion glycoproteins suggests that these molecules are all in the
fusion-activated conformation and that the juxtaposition of the membrane anchor
and fusion peptide, a recurring feature, is involved in the fusion mechanism.
Extension of these comparisons to the soluble N-ethyl-maleimide-sensitive
factor attachment protein receptor (SNARE) protein complex of vesicle fusion
allows a similar conclusion.
Envelope glycoproteins of human and simian immunodeficiency virus (HIV and SIV) undergo a series of conformational changes when they interact with receptor (CD4) and co-receptor on the surface of a ...potential host cell, leading ultimately to fusion of viral and cellular membranes. Structures of fragments of gp120 and gp41 from the envelope protein are known, in conformations corresponding to their post-attachment and postfusion states, respectively. We report the crystal structure, at 4 A resolution, of a fully glycosylated SIV gp120 core, in a conformation representing its prefusion state, before interaction with CD4. Parts of the protein have a markedly different organization than they do in the CD4-bound state. Comparison of the unliganded and CD4-bound structures leads to a model for events that accompany receptor engagement of an envelope glycoprotein trimer. The two conformations of gp120 also present distinct antigenic surfaces. We identify the binding site for a compound that inhibits viral entry.
Herpes simplex virus (HSV) entry into cells requires binding of the envelope glycoprotein D (gD) to one of several cell surface receptors. The 50 C‐terminal residues of the gD ectodomain are ...essential for virus entry, but not for receptor binding. We have determined the structure of an unliganded gD molecule that includes these C‐terminal residues. The structure reveals that the C‐terminus is anchored near the N‐terminal region and masks receptor‐binding sites. Locking the C‐terminus in the position observed in the crystals by an intramolecular disulfide bond abolished receptor binding and virus entry, demonstrating that this region of gD moves upon receptor binding. Similarly, a point mutant that would destabilize the C‐terminus structure was nonfunctional for entry, despite increased affinity for receptors. We propose that a controlled displacement of the gD C‐terminus upon receptor binding is an essential feature of HSV entry, ensuring the timely activation of membrane fusion.
The three-dimensional structures of avian H5 and swine H9 influenza hemagglutinins (HAs) from viruses closely related to those that caused outbreaks of human disease in Hong Kong in 1997 and 1999 ...were determined bound to avian and human cell receptor analogs. Emerging influenza pandemics have been accompanied by the evolution of receptor-binding specificity from the preference of avian viruses for sialic acid receptors in α2,3 linkage to the preference of human viruses for α2,6 linkages. The four new structures show that HA binding sites specific for human receptors appear to be wider than those preferring avian receptors and how avian and human receptors are distinguished by atomic contacts at the glycosidic linkage. α2,3-Linked sialosides bind the avian HA in a trans conformation to form an α2,3 linkage-specific motif, made by the glycosidic oxygen and 4-OH of the penultimate galactose, that is complementary to the hydrogen-bonding capacity of Gln-226, an avian-specific residue. α2,6-Linked sialosides bind in a cis conformation, exposing the glycosidic oxygen to solution and nonpolar atoms of the receptor to Leu-226, a human-specific residue. The new structures are compared with previously reported crystal structures of HA/sialoside complexes of the H3 subtype that caused the 1968 Hong Kong Influenza virus pandemic and analyzed in relation to HA sequences of all 15 subtypes and to receptor affinity data to make clearer how receptor-binding sites of HAs from avian viruses evolve as the virus adapts to humans.
The transporter associated with antigen processing (TAP) is an ABC transporter formed of two subunits, TAP1 and TAP2, each of which has an N‐terminal membrane‐spanning domain and a C‐terminal ABC ...ATPase domain. We report the structure of the C‐terminal ABC ATPase domain of TAP1 (cTAP1) bound to ADP. cTAP1 forms an L‐shaped molecule with two domains, a RecA‐like domain and a small α‐helical domain. The diphosphate group of ADP interacts with the P‐loop as expected. Residues thought to be involved in γ‐phosphate binding and hydrolysis show flexibility in the ADP‐bound state as evidenced by their high B‐factors. Comparisons of cTAP1 with other ABC ATPases from the ABC transporter family as well as ABC ATPases involved in DNA maintenance and repair reveal key regions and residues specific to each family. Three ATPase subfamilies are identified which have distinct adenosine recognition motifs, as well as distinct subdomains that may be specific to the different functions of each subfamily. Differences between TAP1 and TAP2 in the nucleotide‐binding site may be related to the observed asymmetry during peptide transport.
An αβ T‐cell receptor (αβTCR)/hemagglutinin (HA) peptide/human leukocyte antigen (HLA)‐DR1 complex was stabilized by flexibly linking the HA peptide with the human HA1.7 αβTCR, to increase the local ...concentration of the interacting proteins once the peptide has been loaded onto the major histocompatibility complex (MHC) molecule. The structure of the complex, determined by X‐ray crystallography, has a binding mode similar to that of the human B7 αβTCR on a pMHCI molecule. Twelve of the 15 MHC residues contacted are at the same positions observed earlier in class I MHC/peptide/TCR complexes. One contact, to an MHC loop outside the peptide‐binding site, is conserved and specific to pMHCII complexes. TCR gene usage in the response to HA/HLA‐DR appears to conserve charged interactions between three lysines of the peptide and acidic residues on the TCR.
Recent structural studies of protein complexes involved in neurotransmitter release and intracellular vesicle trafficking reveal similarities with the structures of a group of virus membrane fusion ...proteins. In both cases hydrophobic sequences, embedded in the membranes to be fused, are located at the same end of a rod-shaped complex composed of a bundle of long alpha helices. This molecular arrangement is proposed to cause close membrane apposition as the complexes are assembled for membrane fusion.
The alpha/beta T cell receptor (TCR) HA1.7 specific for the hemagglutinin (HA) antigen peptide from influenza A virus is HLA-DR1 restricted but cross-reactive for the HA peptide presented by the ...allo-major histocompatibility complex (MHC) class II molecule HLA-DR4. We report here the structure of the HA1.7/DR4/HA complex, determined by X-ray crystallography at a resolution of 2.4 A. The overall structure of this complex is very similar to the previously reported structure of the HA1.7/DR1/HA complex. Amino acid sequence differences between DR1 and DR4, which are located deep in the peptide binding groove and out of reach for direct contact by the TCR, are able to indirectly influence the antigenicity of the pMHC surface by changing the conformation of HA peptide residues at position P5 and P6. Although TCR HA1.7 is cross-reactive for HA presented by DR1 and DR4 and tolerates these conformational differences, other HA-specific TCRs are sensitive to these changes. We also find a dependence of the width of the MHC class II peptide-binding groove on the sequence of the bound peptide by comparing the HA1.7/DR4/HA complex with the structure of DR4 presenting a collagen peptide. This structural study of TCR cross-reactivity emphasizes how MHC sequence differences can affect TCR binding indirectly by moving peptide atoms.
Inhibitory natural killer (NK) cell receptors down-regulate the cytotoxicity of NK cells upon recognition of specific class I major histocompatibility complex (MHC) molecules on target cells. We ...report here the crystal structure of the inhibitory human killer cell immunoglobulin-like receptor 2DL1 (KIR2DL1) bound to its class I MHC ligand, HLA-Cw4. The KIR2DL1-HLA-Cw4 interface exhibits charge and shape complementarity. Specificity is mediated by a pocket in KIR2DL1 that hosts the Lys80 residue of HLA-Cw4. Many residues conserved in HLA-C and in KIR2DL receptors make different interactions in KIR2DL1-HLA-Cw4 and in a previously reported KIR2DL2-HLA-Cw3 complex. A dimeric aggregate of KIR-HLA-C complexes was observed in one KIR2DL1-HLA-Cw4 crystal. Most of the amino acids that differ between human and chimpanzee KIRs with HLA-C specificities form solvent-accessible clusters outside the KIR-HLA interface, which suggests undiscovered interactions by KIRs.
A complex between HLA-DR3 and a fragment of invariant chain called CLIP was isolated from a human cell line defective in antigen presentation and its X-ray crystal structure determined. Previous data ...indicate that this complex is an intermediate in class II histocompatibility maturation, occurring between invariant chain-DR3 and antigenic peptide-DR3 complexes. The structure shows that the CLIP fragment binds to DR3 in a way almost identical to that in which antigenic peptides bind class II histocompatibility glycoproteins. The structure is the substrate for the loading of antigenic peptides by an exchange process catalysed by DM.
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