5D1Z

IsdB NEAT1 bound by clone D4-10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.17 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 

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: 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Y10 Light ChainA,
I [auth H]
214Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Y10 Heavy ChainB,
H [auth G]
264Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
D4-10 Light ChainC,
F [auth E]
214Homo sapiensMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
D4-10 Heavy ChainD,
G [auth F]
270Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Iron-regulated surface determinant protein BE [auth I],
J
157Staphylococcus aureus subsp. aureus MSSA476Mutation(s): 0 
Gene Names: isdBfrpBsasJsirHSAS1063
UniProt & NIH Common Fund Data Resources
Find proteins for Q69YH5 (Homo sapiens)
Explore Q69YH5 
Go to UniProtKB:  Q69YH5
PHAROS:  Q69YH5
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UniProt GroupQ69YH5
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.17 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.236 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.292α = 90
b = 147.005β = 90
c = 165.045γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2016-09-14 
  • Deposition Author(s): Deng, X.

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2016-12-07
    Changes: Database references