4NJ9

Crystal structure of Fab 8B10 in complex with MPTS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Adaptive Mutations Alter Antibody Structure and Dynamics during Affinity Maturation.

Adhikary, R.Yu, W.Oda, M.Walker, R.C.Chen, T.Stanfield, R.L.Wilson, I.A.Zimmermann, J.Romesberg, F.E.

(2015) Biochemistry 54: 2085-2093

  • DOI: 10.1021/bi501417q
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • While adaptive mutations can bestow new functions on proteins via the introduction or optimization of reactive centers, or other structural changes, a role for the optimization of protein dynamics also seems likely but has been more difficult to eval ...

    While adaptive mutations can bestow new functions on proteins via the introduction or optimization of reactive centers, or other structural changes, a role for the optimization of protein dynamics also seems likely but has been more difficult to evaluate. Antibody (Ab) affinity maturation is an example of adaptive evolution wherein the adaptive mutations may be identified and Abs may be raised to specific targets that facilitate the characterization of protein dynamics. Here, we report the characterization of three affinity matured Abs that evolved from a common germline precursor to bind the chromophoric antigen (Ag), 8-methoxypyrene-1,3,6-trisulfonate (MPTS). In addition to characterizing the sequence, molecular recognition, and structure of each Ab, we characterized the dynamics of each complex by determining their mechanical response to an applied force via three-pulse photon echo peak shift (3PEPS) spectroscopy and deconvoluting the response into elastic, anelastic, and plastic components. We find that for one Ab, affinity maturation was accomplished via the introduction of a single functional group that mediates a direct contact with MPTS and results in a complex with little anelasticity or plasticity. In the other two cases, more mutations were introduced but none directly contact MPTS, and while their effects on structure are subtle, their effects on anelasticity and plasticity are significant, with the level of plasticity correlated with specificity, suggesting that the optimization of protein dynamics may have contributed to affinity maturation. A similar optimization of structure and dynamics may contribute to the evolution of other proteins.


    Organizational Affiliation

    §Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 1-5, Hangi-cho, Shimogamo, Sakyo-ku, Kyoto 606-8522, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
8B10 light chain
L
218N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
8B10 heavy chain
H
229N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
H, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
2M9
Query on 2M9

Download SDF File 
Download CCD File 
H
8-methoxypyrene-1,3,6-trisulfonic acid
C17 H12 O10 S3
CTERCLHSWSQHSD-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 37.133α = 90.00
b = 58.441β = 90.00
c = 212.852γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
DENZOdata reduction
Blu-Icedata collection
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-11-12
    Type: Initial release
  • Version 1.1: 2015-01-21
    Type: Refinement description
  • Version 1.2: 2015-03-25
    Type: Database references, Structure summary
  • Version 1.3: 2015-04-08
    Type: Database references
  • Version 1.4: 2017-06-14
    Type: Database references, Source and taxonomy