8PXV

Targeting extended blood antigens by Akkermansia muciniphila enzymes unveils a missing link for generating universal donor blood

• PDB DOI: https://doi.org/10.2210/pdb8PXV/pdb

• Classification: HYDROLASE
• Organism(s): Akkermansia muciniphila
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-07-24 Released: 2024-02-28 
• Deposition Author(s): Weikum, J., Jensen, M., Abou Hachem, M., Morth, J.P.
• Funding Organization(s): Independent Research Fund Denmark - Technology and Production Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.212 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 

Literature

Akkermansia muciniphila exoglycosidases target extended blood group antigens to generate ABO-universal blood

Jensen, M., Stenfelt, L., Hagman, J.R., Pichler, M.J., Weikum, J., Nielsen, T.S., Hult, A., Morth, J.P., Olsson, M.L., Abou Hachem, M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 220.73 kDa 
• Atom Count: 15,590 
• Modelled Residue Count: 1,912 
• Deposited Residue Count: 1,965 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-N-acetylhexosaminidase	A, B, C	655	Akkermansia muciniphila	Mutation(s): 0  Gene Names: Amuc_0369
UniProt
Find proteins for B2UN02 (Akkermansia muciniphila (strain ATCC BAA-835 / DSM 22959 / JCM 33894 / BCRC 81048 / CCUG 64013 / CIP 107961 / Muc)) Explore B2UN02  Go to UniProtKB:  B2UN02

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-4)-beta-D-glucopyranose	D [auth E], E [auth F]	2		N/A
Glycosylation Resources
GlyTouCan:  G84224TW GlyCosmos:  G84224TW GlyGen:  G84224TW

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	G [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900004	D [auth E], E [auth F]	beta-lactose	Oligosaccharide / Nutrient

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.212 
• R-Value Work: 0.178 
• R-Value Observed: 0.180 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.26	α = 90
b = 170.42	β = 90
c = 171.94	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
xia2	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-02-28 
Deposition Author(s): Weikum, J., Jensen, M., Abou Hachem, M., Morth, J.P.

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Funding Organization	Location	Grant Number
Independent Research Fund Denmark - Technology and Production Sciences	Denmark	0136-00086A

Revision History  

• Version 1.0: 2024-02-28
  Type: Initial release
  
• Version 1.1: 2024-03-06
  Changes: Database references