6LDV

Structure antibody F9 in complex with methylated peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for antigen recognition by methylated lysine-specific antibodies.

Ishii, M.Nakakido, M.Caaveiro, J.M.M.Kuroda, D.Okumura, C.J.Maruyama, T.Entzminger, K.Tsumoto, K.

(2020) J Biol Chem 296: 100176-100176

  • DOI: 10.1074/jbc.RA120.015996
  • Primary Citation of Related Structures:  
    6LDV, 6LDW, 6LDX, 6LDY

  • PubMed Abstract: 
  • Proteins are modulated by a variety of posttranslational modifications including methylation. Despite its importance, the majority of protein methylation modifications discovered by mass spectrometric analyses are functionally uncharacterized, partly due to the difficulty in obtaining reliable methylsite-specific antibodies ...

    Proteins are modulated by a variety of posttranslational modifications including methylation. Despite its importance, the majority of protein methylation modifications discovered by mass spectrometric analyses are functionally uncharacterized, partly due to the difficulty in obtaining reliable methylsite-specific antibodies. To elucidate how functional methylsite-specific antibodies recognize the antigens and lead to development of novel method to create such antibodies, we use an immunized library paired with phage display to create rabbit monoclonal antibodies recognizing trimethylated Lys260 of MAP3K2 as a representative substrate. We isolated several methylsite-specific antibodies which contained unique complementarity determining region sequence.  We characterized the mode of antigen recognition by each of these antibodies using structural and biophysical analyses, revealing the molecular details, such as  binding affinity toward methylated / unmethylated antigens and s structural motif that is responsible for recognition of methylated lysine residue, by which each antibody recognized the target antigen. In addition, the comparison with the results of western blotting analysis suggests a critical antigen recognition mode to generate cross-reactivity to protein and peptide antigen of the antibodies.  Computational simulations effectively recapitulated our biophysical data, capturing the antibodies of differing affinity and specificity. Our exhaustive characterization provides molecular architectures of functional methylsite-specific antibodies and thus should contribute to the development of a general method to generate functional methylsite-specific antibodies by de novo design.


    Organizational Affiliation

    Bioengineering, The University of Tokyo, Japan.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fab heavy chainA [auth H]241Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fab light chainB [auth L]239Oryctolagus cuniculusMutation(s): 0 
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
GLY-M3L-GLY-GLY-THR-TYR-PROC [auth P]14Homo sapiensMutation(s): 0 
Gene Names: MAP3K2MAPKKK2MEKK2
EC: 2.7.11.25
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2U5 (Homo sapiens)
Explore Q9Y2U5 
Go to UniProtKB:  Q9Y2U5
PHAROS:  Q9Y2U5
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.764α = 90
b = 63.526β = 90
c = 125.856γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-25
    Type: Initial release
  • Version 1.1: 2020-12-23
    Changes: Database references
  • Version 1.2: 2021-07-14
    Changes: Database references