2R1X

Crystal structure of S25-2 Fab in complex with Kdo analogues


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Exploration of specificity in germline monoclonal antibody recognition of a range of natural and synthetic epitopes.

Brooks, C.L.Muller-Loennies, S.Brade, L.Kosma, P.Hirama, T.MacKenzie, C.R.Brade, H.Evans, S.V.

(2008) J.Mol.Biol. 377: 450-468

  • DOI: 10.1016/j.jmb.2008.01.018
  • Primary Citation of Related Structures:  2R1W, 2R1Y, 2R23, 2R2B, 2R2E, 2R2H, 3BPC

  • PubMed Abstract: 
  • To explore the molecular basis of antigen recognition by germline antibodies, we have determined to high resolution the structures of the near-germline monoclonal antibody S25-2 in complex with seven distinct carbohydrate antigens based on the bacter ...

    To explore the molecular basis of antigen recognition by germline antibodies, we have determined to high resolution the structures of the near-germline monoclonal antibody S25-2 in complex with seven distinct carbohydrate antigens based on the bacterial sugar 3-deoxy-alpha-D-manno-oct-2-ulosonic acid (Kdo). In contrast to previous findings, the inherited germline Kdo monosaccharide binding site is not restricted to this bacterial sugar but is able to accommodate an array of substitutions and chemical modifications of Kdo, including naturally occurring antigens containing the related monosaccharide d-glycero-alpha-d-talo-oct-2-ulosonic acid as well as nonterminal Kdo residues. However, we show by surface plasmon resonance and ELISA how antibody S25-2 specificity is so dependent on the context in which the antigen is presented that a free disaccharide displays strong binding while the same lipid-A-bound disaccharide does not bind. These structures provide insight into how inherited germline genes code for immunoglobulins of limited flexibility that are capable of binding a range of epitopes from which affinity-matured antibodies are generated.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fab, antibody fragment (IgG1k), light chain
A
219Mus musculusGene Names: Igkv8-30 (Gm10883)
Find proteins for Q52L64 (Mus musculus)
Go to UniProtKB:  Q52L64
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab, antibody fragment (IgG1k), heavy chain
B
222Mus musculusN/A
Find proteins for A2NU21 (Mus musculus)
Go to UniProtKB:  A2NU21
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
KDA
Query on KDA

Download SDF File 
Download CCD File 
B
(3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID)-2-O-ALLYL
C11 H18 O8
LEEKAQBTVJRLOA-UEWQFTGXSA-N
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
KDD
Query on KDD

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Download CCD File 
A
2,6-anhydro-3,5-dideoxy-D-ribo-oct-2-enonic acid
5-deoxy-4-epi-2,3-dehydro-alpha-D-manno-oct-2-ulosonic acid
C8 H12 O6
DVEBLXNKVWKMJU-PBXRRBTRSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KDDKd: 16000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 45.940α = 90.00
b = 81.490β = 90.00
c = 131.420γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
CrystalCleardata reduction
REFMACrefinement
PHASERphasing
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-12-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance