Cryo-Electron Microscopy Structure of an Adenovirus-Integrin Complex Indicates Conformational Changes in both Penton Base and Integrin

A structure of adenovirus type 12 (HAdV12) complexed with a soluble form of integrin αvβ5 was determined by cryo-electron microscopy (cryoEM) image reconstruction. Subnanometer resolution (8 Å) was achieved for the icosahedral capsid with moderate resolution (27 Å) for integrin density above each penton base. Modeling with αvβ3 and α_IIbβ3 crystal structures indicates that a maximum of four integrins fit over the pentameric penton base. The close spacing (∼60 Å) of the RGD protrusions on penton base precludes integrin binding in the same orientation to neighboring RGD sites. Flexible penton-base RGD loops and incoherent averaging of bound integrin molecules explain the moderate resolution observed for the integrin density. A model with four integrins bound to a penton base suggests that integrin might extend one RGD-loop in the direction that could induce a conformational change in the penton base involving clockwise untwisting of the pentamer. A global conformational change in penton base could be one step on the way to the release of Ad vertex proteins during cell entry. Comparison of the cryoEM structure with bent and extended models for the integrin ectodomain reveals that integrin adopts an extended conformation when bound to the Ad penton base, a multivalent viral ligand. These findings shed further light on the structural basis of integrin binding to biologically relevant ligands, as well as on the molecular events leading to HAdV cell entry.A growing number of viruses have been identified as using one of the 24 types of integrin heterodimers as a receptor for cell entry (32). Integrins are cell surface molecules involved in the regulation of adhesion, migration, growth, and differentiation (11). The large multidomained extracellular segments of α and β integrin subunits bind a variety of ligands, including viral ligands, while the smaller intracellular domains interact with cytoskeletal proteins (Fig. ​(Fig.1A).1A). These extracellular and intracellular interactions facilitate bidirectional signaling, with the initiating events occurring either outside of the cell (outside-in signaling) or within the cell (inside-out signaling) (24). Integrin clustering has been established as having an important role in outside-in signaling (9, 19, 20, 44). Clustering results in the formation of focal adhesions, which are organized intracellular complexes, that facilitate downstream signaling cascades within the cell (24).Open in a separate windowFIG. 1.Integrin domains and conformations. (A) Structural domains of integrin αv and β chains, including the extracellular domains, transmembrane-spanning regions, and small cytoplasmic domains, shown in extended schematic forms. The domains are represented as 10Å-resolution density maps based on crystallographic coordinates. The membrane is represented by a gray bar. (Modified from Stewart and Nemerow (32) and reprinted with permission from Elsevier.) (B) Models for soluble αvβ5 integrin with Fos/Jun dimerization domains. Each chain has a six residue glycine-rich linker between the ectodomain and the Fos or Jun dimerization domain. The model of a bent integrin conformation (left) was built as a composite of αvβ3 integrin crystal structures, PDB-IDs 1L5G and 1U8C (42, 43), and the crystal structure of c-Fos/c-Jun bound to DNA, PDB-ID 1FOS (6). The model of an extended integrin conformation (right) is similar to the extended model docked into the HAdV12/αvβ5 cryo structure (Fig. ​(Fig.8B8B).Studies of adenovirus (Ad) interactions with αv integrins provided some of the first evidence of the virus-induced signaling events (13, 14). The Ad penton base capsid protein, which sits at the 12 vertices of the icosahedral capsid, has five prominent Arg-Gly-Asp (RGD) containing loops that are flexible and protrude from the viral surface (31, 48). Receptor-mediated endocytosis of Ad is stimulated by interaction of the RGD-containing penton base with αvβ3 and αvβ5 integrins (34). This interaction leads to receptor clustering, followed by tyrosine phosphorylation/activation of focal adhesion kinase, as well as activation of p130CAS, phosphatidylinositol 3-OH-kinase, and the Rho family of small GTPases, and subsequent actin polymerization and Ad internalization (32). Integrin signaling events also lead to production of proinflammatory cytokines (23) and may result in increased survival of certain host cells through subsequent signaling to protein kinase B (AKT) (25).Multiple studies indicate that after interaction with an RGD-containing ligand a straightening of the integrin extracellular domains occurs, leading to the “extension” or “switchblade” model for integrin activation (16, 45). In the extension model the headpiece domains, which are closest to the RGD interaction site, have a “closed” conformation in the low-affinity, unliganded state. This state is characterized by the close proximity of the α and β subunits at the “knees” or midpoints of the extracellular segments. In contrast, the high-affinity, ligand-bound state in the extension model is distinguished by an “open” headpiece conformation with separation at the knees of the extracellular segments. The location of the RGD binding site between the α-subunit β-propellor and the β-subunit I domain was first visualized in the crystal structure of the αvβ3 extracellular segment with a bound RGD peptide (43). In this structure the RGD site is folded back toward the membrane, and the integrin is in a closed conformation. The closed conformation has also been observed in crystal structures of the αvβ3 ectodomain without an RGD peptide (41) and the α_IIbβ3 ectodomain (47).The open integrin conformation has been characterized as having a large separation of up to ∼70 Å between the knees of α and β subunits (16). Four slightly different open headpiece conformations were observed in crystal structures of the α_IIbβ3 headpiece with bound fibrinogen-mimetic therapeutics (38). These structures show that the change from a closed to an open headpiece conformation is accompanied by a piston-like motion of helix α7 in the β-chain I domain and a large swing of the β-chain hybrid domain of up to 69°, as well as extension and separation of the two integrin chains. Comparison of the available αvβ3 and α_IIbβ3 crystal structures is providing information on the interdomain angle variation and flexibility between domains (47).One aspect of the extension model is that separation of the C-terminal, intracellular portions of the α and β subunits leads to inside-out activation. This concept is supported by nuclear magnetic resonance structures of the cytoplasmic tails of α_IIbβ3 showing that the membrane-proximal helices engage in a weak interaction that can be disrupted by constitutively activating mutations or by talin, a protein found in high concentrations in focal adhesions (33). The concept that the integrin α and β subunits must also separate during outside-in signaling is supported by a study involving a disulfide-bonded mutant of α_IIbβ3 integrin (46). When the α and β subunits are linked in the vicinity of the transmembrane helices the mutant α_IIbβ3 is still able to bind ligand, mediate adhesion, and undergo antibody-induced clustering. However, the disulfide-bonded mutant exhibits defects in focal adhesion formation and focal adhesion kinase activation. Reduction of the disulfide bond or single cysteine mutants rescues signaling.A competing model for integrin activation, called the “deadbolt” model, proposes only small conformational changes in the integrin β-chain I domain upon RGD binding (2). This model is based on crystal structures of the αvβ3 ectodomain with or without an RGD peptide (41, 43). Both of these αvβ3 structures reveal a bent integrin conformation with a closed headpiece conformation. However, the RGD peptide was soaked into a preformed crystal of αvβ3 and crystal contacts may have prevented conformational changes.There are relatively few and only moderate resolution structures of virus-integrin complexes. A moderate resolution cryoEM structure has been determined for the Picornavirus echovirus 1 (EV1) in complex with the I domain of the α2 integrin subunit (39). Docking of crystal structures of EV1 and the α2 I domain into the cryoEM density indicates that the I domain binds within a canyon on the surface of EV1 and that five integrins could potentially bind at one vertex of the icosahedral capsid. Confocal fluorescence microscopy experiments indicated that EV1 causes integrin clustering on human osteosarcoma cells stably transfected with α2 integrin. However, it could not be determined whether the bound integrins were in the inactive (bent) or active (extended) conformation.Moderate resolution (∼21 Å) cryoEM structures of Ad type 2 (HAdV2) and HAdV12 in complex with a soluble form of αvβ5 integrin revealed a ring of integrin density over each penton base capsid protein (5). Better-defined integrin density was observed in the HAdV12/integrin complex, supporting the idea suggested from sequence alignments that the RGD loop of the HAdV12 penton base is shorter and less flexible than that of HAdV2. This study also suggested that the precise spatial arrangement of the five RGD protrusions on the penton base might promote integrin clustering, which may lead to the intracellular signaling events required for virus internalization into a host cell. A similar spacing of RGD-containing integrin-binding sites around the fivefold axis of icosahedral virions has been noted for Ad, foot-and-mouth disease virus, and coxsackievirus A9 (32).We present here a significantly higher-resolution cryoEM structure of HAdV12 complexed with soluble αvβ5 that provides insight into the Ad-integrin interaction. The resolution of the icosahedral capsid portion of the Ad-integrin complex was improved to 8 Å, and the capsid shows clearly resolved α-helices, which allows accurate docking of the penton base crystal structure within the cryoEM density. The resolution of the integrin density is more moderate due to flexibility of the RGD-containing surface loop of penton base and incoherent averaging of integrin heterodimers. Nevertheless, modeling studies with available integrin crystal structures have enabled us to distinguish between a bent or extended conformation (Fig. ​(Fig.1B)1B) when αvβ5 binds to the multivalent ligand presented by the Ad penton base. The cryoEM structural analysis also indicates that integrin induces a conformational change in penton base.