3Q1S

HIV-1 neutralizing antibody Z13e1 in complex with epitope display protein

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structure-Based Design of a Protein Immunogen that Displays an HIV-1 gp41 Neutralizing Epitope.

Stanfield, R.L., Julien, J.P., Pejchal, R., Gach, J.S., Zwick, M.B., Wilson, I.A.

(2011) J Mol Biol 414: 460-476

  • DOI: 10.1016/j.jmb.2011.10.014
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • Antibody Z13e1 is a relatively broadly neutralizing anti-human immunodeficiency virus type 1 antibody that recognizes the membrane-proximal external region (MPER) of the human immunodeficiency virus type 1 envelope glycoprotein gp41. Based on the cry ...

    Antibody Z13e1 is a relatively broadly neutralizing anti-human immunodeficiency virus type 1 antibody that recognizes the membrane-proximal external region (MPER) of the human immunodeficiency virus type 1 envelope glycoprotein gp41. Based on the crystal structure of an MPER epitope peptide in complex with Z13e1 Fab, we identified an unrelated protein, interleukin (IL)-22, with a surface-exposed region that is structurally homologous in its backbone to the gp41 Z13e1 epitope. By grafting the gp41 Z13e1 epitope sequence onto the structurally homologous region in IL-22, we engineered a novel protein (Z13-IL22-2) that contains the MPER epitope sequence for use as a potential immunogen and as a reagent for the detection of Z13e1-like antibodies. The Z13-IL22-2 protein binds Fab Z13e1 with a K(d) of 73 nM. The crystal structure of Z13-IL22-2 in complex with Fab Z13e1 shows that the epitope region is faithfully replicated in the Fab-bound scaffold protein; however, isothermal calorimetry studies indicate that Fab binding to Z13-IL22-2 is not a lock-and-key event, leaving open the question of whether conformational changes upon binding occur in the Fab, in Z13-IL-22, or in both.

    Organizational Affiliation: 

    Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. robyn@scripps.edu



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Z13e1 Fab light chainL212Homo sapiensMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Z13e1 Fab heavy chainH230Homo sapiensMutation(s): 0 
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Interleukin-22I151Homo sapiensMutation(s): 5 
Gene Names: IL22, ILTIF, ZCYTO18, UNQ3099/PRO10096
Find proteins for Q9GZX6 (Homo sapiens)
Explore Q9GZX6 
Go to UniProtKB:  Q9GZX6
NIH Common Fund Data Resources
PHAROS  Q9GZX6
GTEx  ENSG00000127318
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download CCD File 
H, I, L
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
IPA
Query on IPA
Download CCD File 
L
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.210 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.623α = 90
b = 99.216β = 90
c = 105.533γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-11-02
    Type: Initial release
  • Version 1.1: 2012-01-11
    Changes: Database references