5EQ3

Crystal structure of the SrpA adhesin from Streptococcus sanguinis with a sialyl galactose disaccharide bound

  • Classification: SUGAR BINDING PROTEIN
  • Organism(s): Streptococcus sanguinis SK36
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2015-11-12 Released: 2016-01-27 
  • Deposition Author(s): Loukachevitch, L.V., McCulloch, K.M., Vann, K.R., Wawrzak, Z., Anderson, S., Iverson, T.M.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Department of Veteran's Affairs, American Heart Association, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI), National Institutes of Health/National Center for Research Resources (NIH/NCRR), Department of Energy (DOE, United States), Michigan Economic Development Corporation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report



Literature

Structural Basis for Sialoglycan Binding by the Streptococcus sanguinis SrpA Adhesin.

Bensing, B.A.Loukachevitch, L.V.McCulloch, K.M.Yu, H.Vann, K.R.Wawrzak, Z.Anderson, S.Chen, X.Sullam, P.M.Iverson, T.M.

(2016) J Biol Chem 291: 7230-7240

  • DOI: 10.1074/jbc.M115.701425
  • Primary Citation of Related Structures:  
    5EQ2, 5EQ4, 5EQ3

  • PubMed Abstract: 
  • Streptococcus sanguinisis a leading cause of infective endocarditis, a life-threatening infection of the cardiovascular system. An important interaction in the pathogenesis of infective endocarditis is attachment of the organisms to host platelets.S. ...

    Streptococcus sanguinisis a leading cause of infective endocarditis, a life-threatening infection of the cardiovascular system. An important interaction in the pathogenesis of infective endocarditis is attachment of the organisms to host platelets.S. sanguinisexpresses a serine-rich repeat adhesin, SrpA, similar in sequence to platelet-binding adhesins associated with increased virulence in this disease. In this study, we determined the first crystal structure of the putative binding region of SrpA (SrpABR) both unliganded and in complex with a synthetic disaccharide ligand at 1.8 and 2.0 Å resolution, respectively. We identified a conserved Thr-Arg motif that orients the sialic acid moiety and is required for binding to platelet monolayers. Furthermore, we propose that sequence insertions in closely related family members contribute to the modulation of structural and functional properties, including the quaternary structure, the tertiary structure, and the ligand-binding site.


    Organizational Affiliation

    the Departments of Pharmacology and Biochemistry, Center for Structural Biology, and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37232, tina.iverson@vanderbilt.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Platelet-binding glycoproteinAB201Streptococcus sanguinis SK36Mutation(s): 0 
Gene Names: srpASSA_0829
Find proteins for A3CM52 (Streptococcus sanguinis (strain SK36))
Explore A3CM52 
Go to UniProtKB:  A3CM52
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
N-glycolyl-alpha-neuraminic acid-(2-3)-methyl beta-D-galactopyranoside
C
2 N/A Oligosaccharides Interaction
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download CCD File 
A, B
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.200 
  • Space Group: C 1 2 1
  • Diffraction Data DOI: 10.15785/SBGRID/242 SBGrid
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 174.62α = 90
b = 47.005β = 102.15
c = 64.026γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction

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
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI41513
Department of Veteran's AffairsUnited States--
American Heart AssociationUnited States14GRNT20390021
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32 GM008320
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)United StatesT32 HL007751
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesS10 RR026915
Department of Energy (DOE, United States)United StatesDE-AC02-06CH11357
Michigan Economic Development CorporationUnited States085P1000817

Revision History 

  • Version 1.0: 2016-01-27
    Type: Initial release
  • Version 1.1: 2016-02-17
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary