10QG | pdb_000010qg

Crystal Structure of Treponema denticola Sialidase (TDE_0471) bound to Neu5Ac2en (DANA)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 
    0.153 (Depositor), 0.164 (DCC) 
  • R-Value Work: 
    0.138 (Depositor), 0.150 (DCC) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Bacterial exo-alpha-sialidases subvert the complement system through desialylation.

Kurniyati, K.Clark, N.D.Fu, Q.Zhang, S.Qiu, W.Malkowski, M.G.Li, C.

(2026) bioRxiv 

  • DOI: https://doi.org/10.64898/2026.02.05.703967
  • Primary Citation of Related Structures:  
    10QF, 10QG, 10QH, 10QI

  • PubMed Abstract: 

    The complement system is a central pillar of innate immunity, yet how bacterial glycan-modifying enzymes subvert complement function remains poorly understood. Bacterial sialidases remove terminal sialic acids from host sialoglycans, but their direct impact on complement immunity is unclear. Here, we investigate the impact of six sialidases from five human pathogens on complement immunity using an integrated approach combining genetics, biochemistry, glycobiology, mass spectrometry, and structural biology. We demonstrate that major complement components (IgG, C1q, C4, and C5) and regulators (Factor I, Factor H, and C4bp) are sialylated, and that bacterial sialidase-mediated desialylation suppresses complement activation and surface deposition, thereby enabling complement evasion. Despite extensive sequence diversity, biochemical and structural analyses reveal that all examined sialidases share a conserved six-bladed β-propeller catalytic domain and cleave both N-acetylneuraminic and N-glycolylneuraminic acids, the predominant mammalian sialic acids. Together, these findings uncover a conserved mechanism by which diverse bacterial pathogens disable complement immunity through desialylation.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
exo-alpha-sialidase531Treponema denticolaMutation(s): 0 
Gene Names: TDE_0471
EC: 3.2.1.18
UniProt
Find proteins for Q73QH2 (Treponema denticola (strain ATCC 35405 / DSM 14222 / CIP 103919 / JCM 8153 / KCTC 15104))
Explore Q73QH2 
Go to UniProtKB:  Q73QH2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ73QH2
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
DAN (Subject of Investigation/LOI)
Query on DAN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID
C11 H17 N O8
JINJZWSZQKHCIP-UFGQHTETSA-N
CD
Query on CD

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
CA [auth A]
DA [auth A]
EA [auth A]
AA [auth A],
BA [auth A],
CA [auth A],
DA [auth A],
EA [auth A],
FA [auth A],
GA [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
U [auth A],
V [auth A],
W [auth A],
X [auth A],
Y [auth A],
Z [auth A]
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
E [auth A],
I [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
F [auth A],
G [auth A],
H [auth A],
J [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free:  0.153 (Depositor), 0.164 (DCC) 
  • R-Value Work:  0.138 (Depositor), 0.150 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129.811α = 90
b = 65.547β = 106.148
c = 91.679γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Cootmodel building
BUCCANEERmodel building
PHASERphasing
Aimlessdata scaling
xia2data reduction
DIALSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)United StatesR01DE023080

Revision History  (Full details and data files)

  • Version 1.0: 2026-02-25
    Type: Initial release