5MHF

Murine endoplasmic reticulum alpha-glucosidase I with N-9'-methoxynonyl-1-deoxynojirimycin.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Targeting Endoplasmic Reticulum alpha-Glucosidase I with a Single-Dose Iminosugar Treatment Protects against Lethal Influenza and Dengue Virus Infections.

Warfield, K.L.Alonzi, D.S.Hill, J.C.Caputo, A.T.Roversi, P.Kiappes, J.L.Sheets, N.Duchars, M.Dwek, R.A.Biggins, J.Barnard, D.Shresta, S.Treston, A.M.Zitzmann, N.

(2020) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.0c00067
  • Primary Citation of Related Structures:  
    5MHF

  • PubMed Abstract: 

    Influenza and dengue viruses present a growing global threat to public health. Both viruses depend on the host endoplasmic reticulum (ER) glycoprotein folding pathway. In 2014, Sadat et al. reported two siblings with a rare genetic defect in ER α-glucosidase I (ER Glu I) who showed resistance to viral infections, identifying ER Glu I as a key antiviral target. Here, we show that a single dose of UV-4B (the hydrochloride salt form of N -(9'-methoxynonyl)-1-deoxynojirimycin; MON-DNJ) capable of inhibiting Glu I in vivo is sufficient to prevent death in mice infected with lethal viral doses, even when treatment is started as late as 48 h post infection. The first crystal structure of mammalian ER Glu I will constitute the basis for the development of potent and selective inhibitors. Targeting ER Glu I with UV-4B-derived compounds may alter treatment paradigms for acute viral disease through development of a single-dose therapeutic regime.


  • Organizational Affiliation

    Emergent BioSolutions, Gaithersburg, Maryland 20879, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Mannosyl-oligosaccharide glucosidase
A, B, C, D
795Mus musculusMutation(s): 0 
Gene Names: MogsGcs1
EC: 3.2.1.106
UniProt & NIH Common Fund Data Resources
Find proteins for Q80UM7 (Mus musculus)
Explore Q80UM7 
Go to UniProtKB:  Q80UM7
IMPC:  MGI:1929872
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ80UM7
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q80UM7-1
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
E, F
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H
3N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7PG
Query on 7PG

Download Ideal Coordinates CCD File 
CA [auth D]
DA [auth D]
M [auth A]
Q [auth B]
W [auth C]
CA [auth D],
DA [auth D],
M [auth A],
Q [auth B],
W [auth C],
X [auth C]
2,5,8,11,14,17,20,23-OCTAOXAPENTACOSAN-25-OL
C17 H36 O9
SZGNWRSFHADOMY-UHFFFAOYSA-N
6A9
Query on 6A9

Download Ideal Coordinates CCD File 
BA [auth D],
K [auth A],
P [auth B],
V [auth C]
N-9'-methoxynonyl-1-deoxynojirimycin
C16 H33 N O5
TYTARGBBJQKLAJ-QKPAOTATSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth D]
I [auth A]
J [auth A]
L [auth A]
N [auth B]
AA [auth D],
I [auth A],
J [auth A],
L [auth A],
N [auth B],
O [auth B],
R [auth B],
S [auth C],
T [auth C],
U [auth C],
Y [auth D],
Z [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  2 Unique
IDChains TypeFormula2D DiagramParent
MLY
Query on MLY
A, B, C, D
L-PEPTIDE LINKINGC8 H18 N2 O2LYS
SME
Query on SME
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O3 SMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.01α = 90
b = 130.92β = 99.53
c = 135.37γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom106272/Z/14/Z
Wellcome TrustUnited Kingdom097300/Z/11/Z

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2020-04-22
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-01-17
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 2.2: 2024-04-24
    Changes: Structure summary