Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 45.23 kDa 
• Atom Count: 3740 
• Modelled Residue Count: 354 
• Deposited Residue Count: 382 
• Unique protein chains: 1

6ZFN

Structure of an inactive E404Q variant of the catalytic domain of human endo-alpha-mannosidase MANEA in complex with 1-methyl alpha-1,2-mannobiose

• PDB DOI: 10.2210/pdb6ZFN/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-06-17 Released: 2020-11-18 
• Deposition Author(s): Sobala, L.F., Fernandes, P.Z., Hakki, Z., Thompson, A.J., Howe, J.D., Hill, M., Zitzmann, N., Davies, S., Stamataki, Z., Butters, T.D., Alonzi, D.S., Williams, S.J., Davies, G.J.
• Funding Organization(s): European Research Council (ERC), Australian Research Council (ARC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.128 
• R-Value Work: 0.106 

Literature

Structure of human endo-alpha-1,2-mannosidase (MANEA), an antiviral host-glycosylation target.

Sobala, L.F., Fernandes, P.Z., Hakki, Z., Thompson, A.J., Howe, J.D., Hill, M., Zitzmann, N., Davies, S., Stamataki, Z., Butters, T.D., Alonzi, D.S., Williams, S.J., Davies, G.J.

(2020) Proc Natl Acad Sci U S A 117: 29595-29601

• PubMed: 33154157 
• DOI: 10.1073/pnas.2013620117
• Primary Citation of Related Structures:  
  6ZDC, 6ZDF, 6ZDK, 6ZDL, 6ZFA, 6ZFN, 6ZFQ, 6ZJ1, 6ZJ5, 6ZJ6


• PubMed Abstract: 
  

Mammalian protein N-linked glycosylation is critical for glycoprotein folding, quality control, trafficking, recognition, and function. N-linked glycans are synthesized from Glc ₃ Man ₉ GlcNAc ₂ precursors that are trimmed and modified in the endoplasmic reticulum (ER) and Golgi apparatus by glycoside hydrolases and glycosyltransferases. Endo-α-1,2-mannosidase (MANEA) is the sole endo -acting glycoside hydrolase involved in N-glycan trimming and is located within the Golgi, where it allows ER-escaped glycoproteins to bypass the classical N-glycosylation trimming pathway involving ER glucosidases I and II. There is considerable interest in the use of small molecules that disrupt N-linked glycosylation as therapeutic agents for diseases such as cancer and viral infection. Here we report the structure of the catalytic domain of human MANEA and complexes with substrate-derived inhibitors, which provide insight into dynamic loop movements that occur on substrate binding. We reveal structural features of the human enzyme that explain its substrate preference and the mechanistic basis for catalysis. These structures have inspired the development of new inhibitors that disrupt host protein N-glycan processing of viral glycans and reduce the infectivity of bovine viral diarrhea and dengue viruses in cellular models. These results may contribute to efforts aimed at developing broad-spectrum antiviral agents and help provide a more in-depth understanding of the biology of mammalian glycosylation.

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Organizational Affiliation: 

Department of Chemistry, University of York, York YO10 5DD, United Kingdom; [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycoprotein endo-alpha-1,2-mannosidase	A [auth AAA]	382	Homo sapiens	Mutation(s): 1  Gene Names: MANEA EC: 3.2.1.130
UniProt & NIH Common Fund Data Resources
Find proteins for Q5SRI9 (Homo sapiens) Explore Q5SRI9  Go to UniProtKB:  Q5SRI9
PHAROS:  Q5SRI9

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-2)-methyl alpha-D-mannopyranoside	B [auth A]	2		N/A
Glycosylation Resources
GlyTouCan:  G49351KY GlyCosmos:  G49351KY

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth AAA]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 0.128 
• R-Value Work: 0.106 
• Space Group: P 1 2₁ 1
• Diffraction Data DOI: 10.5281/zenodo.4288341 Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.752	α = 90
b = 81.68	β = 92.934
c = 52.994	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2020-06-17 
• Released Date: 2020-11-18 
Deposition Author(s): Sobala, L.F., Fernandes, P.Z., Hakki, Z., Thompson, A.J., Howe, J.D., Hill, M., Zitzmann, N., Davies, S., Stamataki, Z., Butters, T.D., Alonzi, D.S., Williams, S.J., Davies, G.J.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	United Kingdom	322942
Australian Research Council (ARC)	Australia	DP120101396
Australian Research Council (ARC)	Australia	FT130100103
Australian Research Council (ARC)	Australia	DP180101957

Revision History  

• Version 1.0: 2020-11-18
  Type: Initial release
  
• Version 1.1: 2020-12-02
  Changes: Database references
• Version 1.2: 2021-01-20
  Changes: Database references