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 
  • R-Value Observed: 0.217 

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
  • Structures With Same Primary Citation

  • 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

    ∥Department of Chemistry and Biochemistry and San Diego Supercomputer Center, University of California, San Diego, La Jolla, California 92093, United States.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
8B10 light chainL218Mus musculusMutation(s): 0 
Gene Names: Igk
Find proteins for Q52L95 (Mus musculus)
Explore Q52L95 
Go to UniProtKB:  Q52L95
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
8B10 heavy chainH229Mus musculusMutation(s): 0 
Find proteins for Q9D8L4 (Mus musculus)
Explore Q9D8L4 
Go to UniProtKB:  Q9D8L4
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2M9
Query on 2M9

Download CCD File 
H
8-methoxypyrene-1,3,6-trisulfonic acid
C17 H12 O10 S3
CTERCLHSWSQHSD-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
H, L
ZINC ION
Zn
PTFCDOFLOPIGGS-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 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.133α = 90
b = 58.441β = 90
c = 212.852γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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