5D1Z | pdb_00005d1z

IsdB NEAT1 bound by clone D4-10


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.17 ?
  • R-Value Free: 
    0.287 (Depositor), 0.290 (DCC) 
  • R-Value Work: 
    0.233 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 
    0.236 (Depositor) 

wwPDB Validation   3D Report Full Report


This is version 1.2 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Y10 Light ChainA,
I [auth H]
214Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Y10 Heavy ChainB,
H [auth G]
264Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
D4-10 Light ChainC,
F [auth E]
214Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
D4-10 Heavy ChainD,
G [auth F]
270Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence 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
GTEx:  ENSG00000184661 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ69YH5
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.17 ?
  • R-Value Free:  0.287 (Depositor), 0.290 (DCC) 
  • R-Value Work:  0.233 (Depositor), 0.230 (DCC) 
  • R-Value Observed: 0.236 (Depositor) 
Space Group: P 2 21 21
Unit Cell:
Length ( ? )Angle ( ? )
a = 115.292¦Á = 90
b = 147.005¦Â = 90
c = 165.045¦Ă = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



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
  • Version 1.2: 2024-11-20
    Changes: Data collection, Database references, Structure summary
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