6X3Q | pdb_00006x3q

Hsa Siglec and Unique domains in complex with 3'sialyl-N-acetyllactosamine trisaccharide

• PDB DOI: https://doi.org/10.2210/pdb6X3Q/pdb

• Classification: CELL ADHESION
• Organism(s): Streptococcus gordonii str. Challis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-05-21 Released: 2021-11-17 
• Deposition Author(s): Stubbs, H.E., Iverson, T.M.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), American Heart Association, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.233 (Depositor), 0.252 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.207 (Depositor) 

Starting Model: experimental

Literature

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

• PubMed: 35585145 
• DOI: https://doi.org/10.1038/s41467-022-30509-y
• Primary Citation 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.

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Organizational Affiliation: 
• Division of Infectious Diseases, Veterans Affairs Medical Center, Department of Medicine, University of California, San Francisco, CA, USA.
the Northern California Institute for Research and Education, San Francisco, CA, 94121, USA.
Graduate Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN, 37232, USA.
University of Tennessee/Oak Ridge National Laboratory, Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6309, USA.
Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA.
Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA.
School of Nursing, Belmont University, Nashville, TN, 37212, USA.
Department of Chemistry, Erzincan Binali Yildirim University, Erzincan, 24100, Turkey.
Department of Chemistry, University of California, Davis, CA, 95616, USA.
Department of Microbiology, Pathology, and Immunology, Vanderbilt University, Nashville, TN, 37232, USA.
Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA.
College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA.
Department of Pharmacology, School of Graduate Studies and Research, Meharry Medical College, Nashville, TN, 37208, USA.
LS-CAT Synchrotron Research Center, Northwestern University, Argonne, IL, 60439, USA.
Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, 35899, USA.
Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA. [e-mail].
Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 26.56 kDa 
• Atom Count: 1,728 
• Modeled Residue Count: 205 
• Deposited Residue Count: 234 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptococcal hemagglutinin	A	234	Streptococcus gordonii str. Challis	Mutation(s): 0  Gene Names: hsa, SGO_0966
UniProt
Find proteins for A8AWU7 (Streptococcus gordonii (strain Challis / ATCC 35105 / BCRC 15272 / CH1 / DL1 / V288)) Explore A8AWU7  Go to UniProtKB:  A8AWU7

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N/A
Glycosylation Resources
GlyTouCan: G00065MO GlyCosmos: G00065MO GlyGen: G00065MO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA	C [auth A], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.233 (Depositor), 0.252 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.207 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.743	α = 90
b = 57.738	β = 90
c = 75.86	γ = 90

Software Package:

Software Name	Purpose
Coot	model building
PHENIX	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-11-17 
Deposition Author(s): Stubbs, H.E., Iverson, T.M.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)		--
American Heart Association		--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)		--

Revision History  

• Version 1.0: 2021-11-17
  Type: Initial release
  
• Version 1.1: 2022-06-01
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description