6LAF

Crystal structure of the core domain of Amuc_1100 from Akkermansia muciniphila


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.259 

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This is version 1.4 of the entry. See complete history


Literature

The variable oligomeric state of Amuc_1100 from Akkermansia muciniphila.

Wang, J.Xiang, R.Wang, R.Zhang, B.Gong, W.Zhang, J.Zhang, M.Wang, M.

(2020) J Struct Biol 212: 107593-107593

  • DOI: https://doi.org/10.1016/j.jsb.2020.107593
  • Primary Citation of Related Structures:  
    6LAD, 6LAF

  • PubMed Abstract: 

    Akkermansia muciniphila is a beneficial microorganism colonized in the human gut that can reverse many intestinal metabolic-related diseases. Amuc_1100 is an outer-membrane protein of A. muciniphila. Oral administration of Amuc_1100 can reduce fat mass development, insulin resistance, and dyslipidemia in mice and activated the toll-like receptor 2 (TLR2) to regulate the immune response of the host, but the molecular mechanism remains unclear. Here we report the crystal structure of the extramembranous domain of Amuc_1100, which consists of a four-stranded antiparallel β-sheet and four α-helices. Two C-terminal helices and the four-stranded antiparallel β-sheet formed two "αββ" motifs and constituted the core domain, which shared a similar fold with type IV pili and type II Secretion system protein. Although the full-length of the extramembranous domain of Amuc_1100 existed as a monomer in solution, they formed trimer in the crystal. Elimination of the N-terminal coiled-coil helix α1 led to dimerization of Amuc_1100 both in solution and in crystal, indicating that the oligomeric state of Amuc_1100 was variable and could be influenced by α1. In addition, we identified that Amuc_1100 could directly bind human TLR2 (hTRL2) in vitro, suggesting that Amuc_1100 may serve as a new ligand for hTLR2. Dimerization of Amuc_1100 improved its hTLR2-binding affinity, suggesting that the α1-truncated Amuc_1100 could be a beneficial candidate for the development of A. muciniphila related drugs.


  • Organizational Affiliation

    School of Life Sciences, Anhui University, Hefei 230601, Anhui, China; Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, Anhui, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei 230601, Anhui, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Amuc_1100
A, B
246Akkermansia muciniphila ATCC BAA-835Mutation(s): 0 
Gene Names: Amuc_1100
UniProt
Find proteins for B2UR41 (Akkermansia muciniphila (strain ATCC BAA-835 / DSM 22959 / JCM 33894 / BCRC 81048 / CCUG 64013 / CIP 107961 / Muc))
Explore B2UR41 
Go to UniProtKB:  B2UR41
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB2UR41
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.259 
  • Space Group: P 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.746α = 90
b = 85.538β = 90
c = 86.413γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RESOLVEphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other governmentChina--

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-05
    Type: Initial release
  • Version 1.1: 2020-08-19
    Changes: Database references
  • Version 1.2: 2020-10-07
    Changes: Database references
  • Version 1.3: 2021-03-03
    Changes: Structure summary
  • Version 1.4: 2024-03-27
    Changes: Data collection, Database references, Refinement description