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PDBsum entry 1knb
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Cell receptor recognition PDB id
1knb

 

 

 

 

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Contents
Protein chain
186 a.a. *
Waters ×435
* Residue conservation analysis
PDB id:
1knb
Name: Cell receptor recognition
Title: Crystal structure of the receptor-binding domain of adenovirus type 5 fiber protein at 1.7 angstroms resolution
Structure: Adenovirus type 5 fiber protein. Chain: a. Engineered: yes
Source: Human adenovirus 5. Organism_taxid: 28285. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Trimer (from PQS)
Resolution:
1.70Å     R-factor:   0.158    
Authors: D.Xia,L.J.Henry,R.D.Gerard,J.Deisenhofer
Key ref:
D.Xia et al. (1994). Crystal structure of the receptor-binding domain of adenovirus type 5 fiber protein at 1.7 A resolution. Structure, 2, 1259-1270. PubMed id: 7704534 DOI: 10.1016/S0969-2126(94)00126-X
Date:
06-Jan-95     Release date:   31-Mar-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P11818  (SPIKE_ADE05) -  Fiber protein from Human adenovirus C serotype 5
Seq:
Struc: 		 
Seq:
Struc: 		581 a.a.
186 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
DOI no: 10.1016/S0969-2126(94)00126-X Structure 2:1259-1270 (1994)
PubMed id: 7704534  
 
 
Crystal structure of the receptor-binding domain of adenovirus type 5 fiber protein at 1.7 A resolution.
D.Xia, L.J.Henry, R.D.Gerard, J.Deisenhofer.
 
  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.
 
  Selected figure(s)  
 
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].
 
  The above figures are reprinted by permission from Cell Press: Structure (1994, 2, 1259-1270) copyright 1994.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

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Receptors mediating adenovirus attachment and internalization.
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PDB codes: 1kac 1nob
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Characterization of an adenovirus vector containing a heterologous peptide epitope in the HI loop of the fiber knob.
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A single locus on human chromosome 21 directs the expression of a receptor for adenovirus type 2 in mouse A9 cells.
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Adenovirus 3 penton dodecahedron exhibits structural changes of the base on fibre binding.
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Domains required for assembly of adenovirus type 2 fiber trimers.
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Viruses.
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Epitopes and hemagglutination binding domain on subgenus B:2 adenovirus fibers.
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  7588601 S.S.Hong, and P.Boulanger (1995).
Protein ligands of the human adenovirus type 2 outer capsid identified by biopanning of a phage-displayed peptide library on separate domains of wild-type and mutant penton capsomers.
  EMBO J, 14, 4714-4727.  
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. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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