Biological Assembly 1  

 3D View: Structure | Electron Density

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 12.64 kDa 
• Atom Count: 855 
• Residue Count: 102 
• Unique protein chains: 1

1SJV

Three-Dimensional Structure of a Llama VHH Domain Swapping

• DOI: 10.2210/pdb1SJV/pdb

• Classification: ANTIBIOTIC
• Organism(s): Lama glama
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2004-03-04 Released: 2004-06-01 
• Deposition Author(s): Spinelli, S., Desmyter, A., Frenken, L., Verrips, T., Cambillau, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.225 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 

Literature

Domain swapping of a llama VHH domain builds a crystal-wide beta-sheet structure.

Spinelli, S., Desmyter, A., Frenken, L., Verrips, T., Tegoni, M., Cambillau, C.

(2004) FEBS Lett 564: 35-40

• PubMed: 15094039 
• DOI: 10.1016/S0014-5793(04)00304-7
• Primary Citation of Related Structures:  
  1SJV


• PubMed Abstract: 
  

Among mammals, camelids have a unique immunological system since they produce functional antibodies devoid of light chains and CH1 domains. To bind antigens, whether they are proteins or haptens, camelids use the single domain VH from their heavy chain (VHH). We report here on such a llama VHH domain (VHH-R9) which was raised against a hapten, the RR6 red dye. This VHH possesses the shortest complementarity determining region 3 (CDR3) among all the known VHH sequences and nevertheless binds RR6 efficiently with a K(d) value of 83 nM. However, the crystal structure of VHH-R9 exhibits a striking feature: its CDR3 and its last beta-strand (beta9) do not follow the immunoglobulin VH domain fold, but instead extend out of the VHH molecular boundary and associate with a symmetry-related molecule. The two monomers thus form a domain-swapped dimer which establishes further contacts with symmetry-related molecules and build a crystal-wide beta-sheet structure. The driving force of the dimer formation is probably the strain induced by the short CDR3 together with the cleavage of the first seven residues.

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Organizational Affiliation: 

Architecture et Fonction des Macromolécules Biologiques, UMR-6098, CNRS and Universités d'Aix-Marseille I and II, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
r9	A	114	Lama glama	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.94 Å
• R-Value Free: 0.225 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 
• Space Group: I 4₁ 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.3	α = 90
b = 124.3	β = 90
c = 124.3	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
AMoRE	phasing
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-03-04 
• Released Date: 2004-06-01 
Deposition Author(s): Spinelli, S., Desmyter, A., Frenken, L., Verrips, T., Cambillau, C.

Revision History 

• Version 1.0: 2004-06-01
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance