7LGR | pdb_00007lgr

Streptococcus mutans Collagen binding Protein CNM - N2 Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.227 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.192 (Depositor), 0.193 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Streptococcus mutans Collagen-Binding Protein Cnm Is a Multifunctional Adhesin: A Structural Investigation.

Mieher, J.L.Schormann, N.Wu, R.Patel, M.Purushotham, S.Lemos, J.Abranches, J.Wu, H.Deivanayagam, C.

(2025) Mol Oral Microbiol 40: 265-277

  • DOI: https://doi.org/10.1111/omi.70005
  • Primary Citation Related Structures: 
    7LGR

  • PubMed Abstract: 

    The collagen-binding adhesin Cnm is a known virulence factor of Streptococcus mutans. It is present in specific serotypes (mostly e, f, and k strains) of S. mutans and belongs to the LPXTG family of cell wall-anchored surface adhesins. Here, we report the crystal structure of the collagen-binding N 2 domain of S. mutans Cnm. Using the Staphylococcus aureus collagen-binding protein Cna, which shares high sequence and structural homology with Cnm, we modeled collagen binding to S. mutans Cnm. The comparative analysis identified three conserved collagen-binding residues (Y176, F192, N194) and four equivalent residues that are different in their composition (D224, T226, S232, M276). This study also discovered the multifunctional attributes of this protein, where Cnm-FL, Cnm-N 12, and the individual domains of Cnm-N 1 and Cnm-N 2 adhere with high affinity to the scavenger receptor cysteine-rich (SRCR) domains of glycoprotein 340 (Gp340). Protein-protein docking of Cnm-N 2 and SRCR 1 showed the possibility of a shared binding site at the collagen-binding interface of Cnm-N 2 . Furthermore, competition experiments using collagen and SRCR 123 with Cnm-N 2 , Cnm-N 12, and Cnm-FL constructs confirmed that collagen and SRCR 1 share a binding site. Subsequent alanine substitution mutagenesis of the predicted collagen-binding residues validated our modeling results, confirming that Y176 and F192 are important residues for collagen and SRCR/Gp340 binding.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA.

Macromolecule Content 

  • Total Structure Weight: 19.72 kDa 
  • Atom Count: 1,254 
  • Modeled Residue Count: 151 
  • Deposited Residue Count: 177 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Collagen-binding adhesin177Streptococcus mutansMutation(s): 0 
Gene Names: cnm
UniProt
Find proteins for B9A875 (Streptococcus mutans)
Explore B9A875 
Go to UniProtKB:  B9A875
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9A875
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.227 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.192 (Depositor), 0.193 (DCC) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.553α = 90
b = 48.553β = 90
c = 106.424γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)United StatesR01 DE29007

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-26
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description
  • Version 1.2: 2026-09-09
    Changes: Database references, Structure summary