GspB Siglec domain

Experimental Data Snapshot

  • Resolution: 1.30 Å
  • R-Value Free: 0.144 
  • R-Value Work: 0.131 
  • R-Value Observed: 0.131 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


Origins of glycan selectivity in streptococcal Siglec-like adhesins suggest mechanisms of receptor adaptation.

Bensing, B.A.Stubbs, H.E.Agarwal, R.Yamakawa, I.Luong, K.Solakyildirim, K.Yu, H.Hadadianpour, A.Castro, M.A.Fialkowski, K.P.Morrison, K.M.Wawrzak, Z.Chen, X.Lebrilla, C.B.Baudry, J.Smith, J.C.Sullam, P.M.Iverson, T.M.

(2022) Nat Commun 13: 2753-2753

  • DOI: https://doi.org/10.1038/s41467-022-30509-y
  • Primary Citation of Related Structures:  
    6EF7, 6EF9, 6EFA, 6EFB, 6EFC, 6EFD, 6EFF, 6EFI, 6X3K, 6X3Q, 7KMJ

  • PubMed Abstract: 

    Bacterial binding to host receptors underlies both commensalism and pathogenesis. Many streptococci adhere to protein-attached carbohydrates expressed on cell surfaces using Siglec-like binding regions (SLBRs). The precise glycan repertoire recognized may dictate whether the organism is a strict commensal versus a pathogen. However, it is currently not clear what drives receptor selectivity. Here, we use five representative SLBRs and identify regions of the receptor binding site that are hypervariable in sequence and structure. We show that these regions control the identity of the preferred carbohydrate ligand using chimeragenesis and single amino acid substitutions. We further evaluate how the identity of the preferred ligand affects the interaction with glycoprotein receptors in human saliva and plasma samples. As point mutations can change the preferred human receptor, these studies suggest how streptococci may adapt to changes in the environmental glycan repertoire.

  • Organizational Affiliation

    Division of Infectious Diseases, Veterans Affairs Medical Center, Department of Medicine, University of California, San Francisco, CA, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Platelet binding protein GspB - Siglec domain127Streptococcus gordoniiMutation(s): 0 
Gene Names: gspB
Find proteins for Q939N5 (Streptococcus gordonii)
Explore Q939N5 
Go to UniProtKB:  Q939N5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ939N5
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FMT

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
C H2 O2
Query on NA

Download Ideal Coordinates CCD File 
B [auth A]
C [auth A]
D [auth A]
E [auth A]
F [auth A]
B [auth A],
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A]
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 92.083α = 90
b = 92.083β = 90
c = 143.928γ = 120
Software Package:
Software NamePurpose

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 StatesAI106987

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-19
    Type: Initial release
  • Version 1.1: 2022-06-01
    Changes: Database references, Derived calculations
  • Version 1.2: 2024-05-22
    Changes: Data collection