PDBsum entry 1knb

Cell receptor recognition

PDB id

1knb

Contents

			Protein chain

					186 a.a.

			Waters ×435

References listed in PDB file

Key reference

Title

Crystal structure of the receptor-Binding domain of adenovirus type 5 fiber protein at 1.7 a resolution.

Authors

D.Xia, L.J.Henry, R.D.Gerard, J.Deisenhofer.

Ref.

Structure, 1994, 2, 1259-1270. [DOI no: 10.1016/S0969-2126(94)00126-X]

PubMed id

7704534

Abstract

BACKGROUND: Adenoviral infection begins with the binding of virion to the surface of host cells. Specific attachment is achieved through interactions between host-cell receptors and the adenovirus fiber protein and is mediated by the globular carboxy-terminal domain of the adenovirus fiber protein, termed the carboxy-terminal knob domain. RESULTS: The crystal structure of the carboxy-terminal knob domain of the adenovirus type 5 (Ad5) fiber protein has been determined at 1.7 A resolution. Each knob monomer forms an eight-stranded antiparallel beta-sandwich structure. In the crystal lattice, the knob monomers form closely interacting trimers which possess a deep surface depression centered around the three-fold molecular symmetry axis and three symmetry-related valleys. CONCLUSIONS: The amino acid residues lining the wall of the central surface depression and the three symmetry-related floors of the valleys are strictly conserved in the knob domains of Ad5 and adenovirus type 2 (Ad2) fiber proteins, which share the same cellular receptor. The beta-sandwich structure of the knob monomer demonstrates a unique folding topology which is different from that of other known antiparallel beta-sandwich structures. The large buried surface area and numerous polar interactions in the trimer indicate that this form of the knob protein is predominant in solution, suggesting a possible assembly pathway for the native fiber protein.



	Figure 7. Figure 7. Space-filling model of the trimeric knob protein, showing the deep surface depression centered on the three-fold axis, and the valleys formed by the R-sheets and HI loops. Red: amino acid residues of Ad5 that differ from those of Ad2. Yellow: residues identical in Ad5 and Ad2. Green: residues identical in Ad5 and Ad2 but different from residues that are identical in Ad7 and Ad3. The main conserved regions are in the central surface depression around the three-fold symmetry axis and on the floor the valley. This diagram was produced with the program INSIGHT II (Biosym Technologies Inc.,9685 Scranton Road, San Diego, CA 92121-2777, USA). Figure 7. Space-filling model of the trimeric knob protein, showing the deep surface depression centered on the three-fold axis, and the valleys formed by the R-sheets and HI loops. Red: amino acid residues of Ad5 that differ from those of Ad2. Yellow: residues identical in Ad5 and Ad2. Green: residues identical in Ad5 and Ad2 but different from residues that are identical in Ad7 and Ad3. The main conserved regions are in the central surface depression around the three-fold symmetry axis and on the floor the valley. This diagram was produced with the program INSIGHT II (Biosym Technologies Inc.,9685 Scranton Road, San Diego, CA 92121-2777, USA).		Figure 8. Figure 8. Surface profile around the central depression and the residues lining the wall of the depression of the knob trimer. The profile is calculated as the distance from the molecular surface to a reference plane which is placed in front of the knob molecule normal to the three-fold molecular axis. Red color indicates the smallest, and dark blue color the largest, distance from the molecular surface to the reference plane. The key shows the main distance ranges and their corresponding colors. The depression is vert, similar 15 Å deep and residues in the depression are mostly hydrophilic. The diagram was prepared using the program Roadmap [56]. Figure 8. Surface profile around the central depression and the residues lining the wall of the depression of the knob trimer. The profile is calculated as the distance from the molecular surface to a reference plane which is placed in front of the knob molecule normal to the three-fold molecular axis. Red color indicates the smallest, and dark blue color the largest, distance from the molecular surface to the reference plane. The key shows the main distance ranges and their corresponding colors. The depression is [3]not, vert, similar 15 Å deep and residues in the depression are mostly hydrophilic. The diagram was prepared using the program Roadmap [[4]56].