7MLH | pdb_00007mlh

Crystal structure of human IgE (2F10) in complex with Der p 2.0103


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.247 (Depositor), 0.249 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.217 (DCC) 

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 7MLH

This is version 1.3 of the entry. See complete history

Literature

Human IgE monoclonal antibody recognition of mite allergen Der p 2 defines structural basis of an epitope for IgE cross-linking and anaphylaxis in vivo.

Khatri, K.Richardson, C.M.Glesner, J.Kapingidza, A.B.Mueller, G.A.Zhang, J.Dolamore, C.Vailes, L.D.Wunschmann, S.Peebles Jr., R.S.Chapman, M.D.Smith, S.A.Chruszcz, M.Pomes, A.

(2022) PNAS Nexus 1: pgac054-pgac054

  • DOI: https://doi.org/10.1093/pnasnexus/pgac054
  • Primary Citation Related Structures: 
    7MLH

  • PubMed Abstract: 

    Immunoglobulin E (IgE) antibody is a critical effector molecule for adaptive allergen-induced immune responses, which affect up to 40% of the population worldwide. Allergens are usually innocuous molecules but induce IgE antibody production in allergic subjects. Allergen cross-linking of IgE bound to its high affinity receptor (FcεRI) on mast cells and basophils triggers release of histamine and other mediators that cause allergic symptoms. Little is known about the direct allergen-IgE antibody interaction due to the polyclonal nature of serum IgE and the low frequency of IgE-producing B cells in blood. Here, we report the X-ray crystal structure of a house dust mite allergen, Der p 2, in complex with Fab of a human IgE monoclonal antibody (mAb) isolated by hybridoma technology using human B cells from an allergic subject. This IgE mAb, 2F10, has the correct pairing of heavy and light chains as it occurs in vivo . Key amino acids forming the IgE epitope on Der p 2 were identified. Mutation of these residues ablated their functional ability to cross-link IgE in a mouse model of passive systemic anaphylaxis. These analyses revealed an important conformational epitope associated with the IgE antibody repertoire to a major mite allergen.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA.

Macromolecule Content 

  • Total Structure Weight: 124.13 kDa 
  • Atom Count: 8,935 
  • Modeled Residue Count: 1,099 
  • Deposited Residue Count: 1,138 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
IgE Light Chain
A, D
212Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Der p 2 variant 3
B, F
129Dermatophagoides pteronyssinusMutation(s): 0 
UniProt
Find proteins for P49278 (Dermatophagoides pteronyssinus)
Explore P49278 
Go to UniProtKB:  P49278
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49278
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
IgE Heavy chain
C, E
228Homo sapiensMutation(s): 0 

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
G [auth A]
H [auth A]
I [auth A]
K [auth B]
L [auth B]
G [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth C],
O [auth C],
P [auth D],
Q [auth D],
R [auth D],
U [auth E],
V [auth E],
W [auth E],
X [auth E]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL

Query on CL



Download:Ideal Coordinates CCD File
J [auth A],
S [auth D],
T [auth D]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.247 (Depositor), 0.249 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.217 (DCC) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.776α = 90
b = 231.458β = 94.338
c = 51.791γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI077653

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-04
    Type: Initial release
  • Version 1.1: 2022-11-16
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-11-13
    Changes: Structure summary