4NJA

Crystal structure of Fab 6C8 in complex with MPTS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 

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Ligand Structure Quality Assessment 


This is version 1.3 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:  
    4NJ9, 4NJA

  • 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 evaluate ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
6C8 light chainA [auth L]218Mus musculusMutation(s): 0 
Gene Names: Igk
UniProt
Find proteins for P01660 (Mus musculus)
Explore P01660 
Go to UniProtKB:  P01660
Find proteins for Q52L95 (Mus musculus)
Explore Q52L95 
Go to UniProtKB:  Q52L95
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ52L95P01660
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
6C8 heavy chainB [auth H]233Mus musculusMutation(s): 0 
Gene Names: HC
UniProt
Find proteins for A0A0F7R1P3 (Mus musculus)
Explore A0A0F7R1P3 
Go to UniProtKB:  A0A0F7R1P3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0F7R1P3
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2M9
Query on 2M9

Download Ideal Coordinates CCD File 
F [auth H]8-methoxypyrene-1,3,6-trisulfonic acid
C17 H12 O10 S3
CTERCLHSWSQHSD-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
G [auth H]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth L],
H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
D [auth L],
E [auth L]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.66α = 90
b = 127.837β = 90
c = 47.785γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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