1RJC

Crystal structure of the camelid single domain antibody cAb-Lys2 in complex with hen egg white lysozyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Strong in vivo maturation compensates for structurally restricted H3 loops in antibody repertoires.

De Genst, E.Silence, K.Ghahroudi, M.A.Decanniere, K.Loris, R.Kinne, J.Wyns, L.Muyldermans, S.

(2005) J.Biol.Chem. 280: 14114-14121

  • DOI: 10.1074/jbc.M413011200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A central paradigm in immunology states that successful generation of high affinity antibodies necessitates an immense primary repertoire of antigen-combining sites. Much of the diversity of this repertoire is provided by varying one antigen binding ...

    A central paradigm in immunology states that successful generation of high affinity antibodies necessitates an immense primary repertoire of antigen-combining sites. Much of the diversity of this repertoire is provided by varying one antigen binding loop, created by inserting randomly a D (diversity) gene out of a small pool between the V and J genes. It is therefore assumed that any particular D-encoded region surrounded by different V and J regions adopts a different conformation. We have solved the structure of two lysozyme-specific variable domains of heavy-chain antibodies isolated from two strictly unrelated dromedaries. These antibodies recombined identical D gene sequences to different V and J precursors with significant variance in their V(D)J junctions. Despite these large differences, the D-encoded loop segments adopt remarkably identical architectures, thus directing the antibodies toward identical epitopes. Furthermore, a striking convergent maturation process occurred in the V region, adapting both binders for their sub-nanomolar affinity association with lysozyme. Hence, on a structural level, humoral immunity may rely more on well developed maturation and selection systems than on the acquisition of large primary repertoires.


    Organizational Affiliation

    Laboratory of Cellular and Molecular Immunology, Department of Molecular and Cellular Interactions, Vlaams Interuniversitair Instituut voor Biotechnologie, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium. edegenst@vub.ac.be




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
camelid heavy chain antibody
A
137N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Lysozyme C
B
129Gallus gallusMutation(s): 0 
Gene Names: LYZ
EC: 3.2.1.17
Find proteins for P00698 (Gallus gallus)
Go to Gene View: LYZ
Go to UniProtKB:  P00698
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.4 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.220 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.020α = 90.00
b = 68.360β = 90.00
c = 72.050γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CNSrefinement
CCP4data scaling
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-02-01
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance