3PHQ

Crystal structure of S64-4 in complex with KDO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural insights into parallel strategies for germline antibody recognition of lipopolysaccharide from Chlamydia.

Evans, D.W.Muller-Loennies, S.Brooks, C.L.Brade, L.Kosma, P.Brade, H.Evans, S.V.

(2011) Glycobiology 21: 1049-1059

  • DOI: 10.1093/glycob/cwr041
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structure of the antigen-binding fragment from the monoclonal antibody S64-4 in complex with a pentasaccharide bisphosphate fragment from chlamydial lipopolysaccharide has been determined by x-ray diffraction to 2.6 Å resolution. Like the well-ch ...

    The structure of the antigen-binding fragment from the monoclonal antibody S64-4 in complex with a pentasaccharide bisphosphate fragment from chlamydial lipopolysaccharide has been determined by x-ray diffraction to 2.6 Å resolution. Like the well-characterized antibody S25-2, S64-4 displays a pocket formed by the residues of germline sequence corresponding to the heavy and light chain V gene segments that binds the terminal Kdo residue of the antigen; however, although S64-4 shares the same heavy chain V gene segment as S25-2, it has a different light chain V gene segment. The new light chain V gene segment codes for a combining site that displays greater affinity, different specificity, and allows a novel antigen conformation that brings a greater number of antigen residues into the combining site than possible in S25-2. Further, while antibodies in the S25-2 family use complementarity determining region (CDR) H3 to discriminate among antigens, S64-4 achieves its specificity via the new light chain V gene segment and resulting change in antigen conformation. These structures reveal an intriguing parallel strategy where two different combinations of germline-coded V gene segments can act as starting points for the generation of germline antibodies against chlamydial antigens and show how anti-carbohydrate antibodies can exploit the conformational flexibility of this class of antigens to achieve high affinity and specificity independently of CDR H3.


    Organizational Affiliation

    Department of Biochemistry and Microbiology, University of Victoria, PO Box 3055 STN CSC, Victoria, BC, Canada V8P 3P6.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
S64-4 Fab (IgG1) light chain
A
217N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
S64-4 Fab (IgG1) heavy chain
B
222N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KDO
Query on KDO

Download SDF File 
Download CCD File 
B
3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
C8 H14 O8
NNLZBVFSCVTSLA-HXUQBWEZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.840α = 90.00
b = 81.150β = 90.00
c = 94.190γ = 90.00
Software Package:
Software NamePurpose
CrystalCleardata reduction
CrystalCleardata collection
PHASERphasing
d*TREKdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2011-07-27
    Type: Database references
  • Version 1.3: 2019-07-17
    Type: Data collection, Refinement description