5D1X

IsdB NEAT2 bound by D4-30


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.271 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Germline-encoded neutralization of a Staphylococcus aureus virulence factor by the human antibody repertoire.

Yeung, Y.A.Foletti, D.Deng, X.Abdiche, Y.Strop, P.Glanville, J.Pitts, S.Lindquist, K.Sundar, P.D.Sirota, M.Hasa-Moreno, A.Pham, A.Melton Witt, J.Ni, I.Pons, J.Shelton, D.Rajpal, A.Chaparro-Riggers, J.

(2016) Nat Commun 7: 13376-13376

  • DOI: https://doi.org/10.1038/ncomms13376
  • Primary Citation of Related Structures:  
    5D1Q, 5D1X, 5D1Z

  • PubMed Abstract: 

    Staphylococcus aureus is both an important pathogen and a human commensal. To explore this ambivalent relationship between host and microbe, we analysed the memory humoral response against IsdB, a protein involved in iron acquisition, in four healthy donors. Here we show that in all donors a heavily biased use of two immunoglobulin heavy chain germlines generated high affinity (pM) antibodies that neutralize the two IsdB NEAT domains, IGHV4-39 for NEAT1 and IGHV1-69 for NEAT2. In contrast to the typical antibody/antigen interactions, the binding is primarily driven by the germline-encoded hydrophobic CDRH-2 motifs of IGHV1-69 and IGHV4-39, with a binding mechanism nearly identical for each antibody derived from different donors. Our results suggest that IGHV1-69 and IGHV4-39, while part of the adaptive immune system, may have evolved under selection pressure to encode a binding motif innately capable of recognizing and neutralizing a structurally conserved protein domain involved in pathogen iron acquisition.


  • Organizational Affiliation

    Rinat R&D, Pfizer Inc., 230 East Grand Avenue, South San Francisco, California 94080, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
D4-30 Light Chain219Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
D4-30 Heavy Chain259Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
P5 Heavy Chain274Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
P5 Light Chain216Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Iron-regulated surface determinant protein B118Staphylococcus aureus subsp. aureus USA300Mutation(s): 0 
Gene Names: isdBfrpBsasJsirHSAUSA300_1028
UniProt
Find proteins for Q2FZF0 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2FZF0 
Go to UniProtKB:  Q2FZF0
Entity Groups  
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UniProt GroupQ2FZF0
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.21 Å
  • R-Value Free: 0.310 
  • R-Value Work: 0.269 
  • R-Value Observed: 0.271 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 111.251α = 90
b = 111.251β = 90
c = 105.226γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2016-08-10 
  • Deposition Author(s): Deng, X.

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-12-07
    Changes: Database references