6K68

Application of anti-helix antibodies in protein structure determination (8420-3MNZ)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.289 
  • R-Value Observed: 0.291 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Application of antihelix antibodies in protein structure determination.

Kim, J.W.Kim, S.Lee, H.Cho, G.Kim, S.C.Lee, H.Jin, M.S.Lee, J.O.

(2019) Proc Natl Acad Sci U S A 116: 17786-17791

  • DOI: https://doi.org/10.1073/pnas.1910080116
  • Primary Citation of Related Structures:  
    6K3M, 6K64, 6K65, 6K67, 6K68, 6K69, 6K6A, 6K6B

  • PubMed Abstract: 

    Antibodies are indispensable tools in protein engineering and structural biology. Antibodies suitable for structural studies should recognize the 3-dimensional (3D) conformations of target proteins. Generating such antibodies and characterizing their complexes with antigens take a significant amount of time and effort. Here, we show that we can expand the application of well-characterized antibodies by "transplanting" the epitopes that they recognize to proteins with completely different structures and sequences. Previously, several antibodies have been shown to recognize the alpha-helical conformation of antigenic peptides. We demonstrate that these antibodies can be made to bind to a variety of unrelated "off-target" proteins by modifying amino acids in the preexisting alpha helices of such proteins. Using X-ray crystallography, we determined the structures of the engineered protein-antibody complexes. All of the antibodies bound to the epitope-transplanted proteins, forming accurately predictable structures. Furthermore, we showed that binding of these antihelix antibodies to the engineered target proteins can modulate their catalytic activities by trapping them in selected functional states. Our method is simple and efficient, and it will have applications in protein X-ray crystallography, electron microscopy, and nanotechnology.


  • Organizational Affiliation

    School of Life Sciences, Gwangju Institute of Science and Technology, Buk-gu, Gwangju 61005, Korea; misunjin@gist.ac.kr jieoh@postech.ac.kr.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3MNZ Variable heavy chain
A, C, F, J
115Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
3MNZ Variable light chain
B, D, G, K
116Mus musculusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Protein A
E, H, I, L
73Staphylococcus aureusMutation(s): 0 
UniProt
Find proteins for P02976 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore P02976 
Go to UniProtKB:  P02976
Entity Groups  
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UniProt GroupP02976
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.318 
  • R-Value Work: 0.289 
  • R-Value Observed: 0.291 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.951α = 90
b = 95.017β = 90
c = 179.561γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic OfNRF-2014R1A2A1A10050436
National Research Foundation (Korea)Korea, Republic OfNRF-2017M3A9F6029753

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2019-09-18
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-20
    Changes: Source and taxonomy
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description