5DTF

context-independent anti-hypusine antibody FabHpu98.61 in complex with hypusine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural Analysis and Optimization of Context-Independent Anti-Hypusine Antibodies.

Zhai, Q.He, M.Song, A.Deshayes, K.Dixit, V.M.Carter, P.J.

(2016) J.Mol.Biol. 428: 603-617

  • DOI: 10.1016/j.jmb.2016.01.006
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Context-independent anti-hypusine antibodies that bind to the post-translational modification (PTM), hypusine, with minimal dependence on flanking amino acid sequences, were identified. The antibodies bind to both hypusine and deoxyhypusine or select ...

    Context-independent anti-hypusine antibodies that bind to the post-translational modification (PTM), hypusine, with minimal dependence on flanking amino acid sequences, were identified. The antibodies bind to both hypusine and deoxyhypusine or selectively to hypusine but not to deoxyhypusine. Phage display was used to further enhance the affinity of the antibodies. Affinity maturation of these anti-hypusine antibodies improved their performance in affinity capture of the only currently known hypusinated protein, eukaryotic translation initiation factor 5A. These anti-hypusine antibodies may have utility in the identification of novel hypusinated proteins. Crystal structures of the corresponding Fab fragments were determined in complex with hypusine- or deoxyhypusine-containing peptides. The hypusine or deoxyhypusine moiety was found to reside in a deep pocket formed between VH and VL domains of the Fab fragments. Interaction between the antibodies and hypusine includes an extensive hydrogen bond network. These are, to our knowledge, the first reported structures of context-independent anti-PTM antibodies in complex with the corresponding PTM.


    Organizational Affiliation

    Department of Early Discovery Biochemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Department of Physiological Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.,Department of Antibody Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA. Electronic address: pjc@gene.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fab Hpu98.61 Heavy Chain
H, A
230Oryctolagus cuniculusMutation(s): 0 
Find proteins for P01870 (Oryctolagus cuniculus)
Go to UniProtKB:  P01870
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fab Hpu98.61 Light Chain
L, B
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Peptide: GLY-5CT-GLY-ALA
P
4N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
B, L
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
5CT
Query on 5CT

Download SDF File 
Download CCD File 
B
Hypusine
N~6~-[(2S)-4-amino-2-hydroxybutyl]-L-lysine
C10 H23 N3 O3
BZUIJMCJNWUGKQ-IUCAKERBSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
5CT
Query on 5CT
P
peptide linkingC10 H23 N3 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.212 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 130.120α = 90.00
b = 75.770β = 120.66
c = 120.610γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-09-18 
  • Released Date: 2016-02-17 
  • Deposition Author(s): Zhai, Q., Carter, P.J.

Revision History 

  • Version 1.0: 2016-02-17
    Type: Initial release
  • Version 1.1: 2016-03-02
    Type: Database references
  • Version 1.2: 2016-05-04
    Type: Non-polymer description