6K6A

Application of anti-helix antibodies in protein structure determination (8188cys-3LRHcys)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.1 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.USA 116: 17786-17791

  • DOI: 10.1073/pnas.1910080116
  • Primary Citation of Related Structures:  

  • 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 ...

    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.,School of Life Sciences, Gwangju Institute of Science and Technology, Buk-gu, Gwangju 61005, Korea.,Department of Chemistry, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 34141, Korea.,Institute of Biotechnology, Chungnam National University, Yuseong-gu, Daejeon 34134, Korea.,Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon 34141, Korea.,Department of Life Sciences, Pohang University of Science and Technology, Nam-gu, Pohang 37673, Korea; misunjin@gist.ac.kr jieoh@postech.ac.kr.,Department of Life Sciences, Pohang University of Science and Technology, Nam-gu, Pohang 37673, Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3LRH intrabody
B, A
135N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Engineered Protein A
C, D
79N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.169 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 37.227α = 87.16
b = 40.603β = 75.20
c = 61.691γ = 65.50
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

  • Version 1.0: 2019-08-14
    Type: Initial release
  • Version 1.1: 2019-09-18
    Type: Data collection, Database references