5MHF | pdb_00005mhf

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 (Depositor), 0.248 (DCC) 
  • R-Value Work: 
    0.188 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5MHF

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 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.

Macromolecule Content 

  • Total Structure Weight: 362.04 kDa 
  • Atom Count: 26,145 
  • Modeled Residue Count: 3,032 
  • Deposited Residue Count: 3,180 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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 GlycosylationD 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 GlycosylationD 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 (Depositor), 0.248 (DCC) 
  • R-Value Work:  0.188 (Depositor), 0.219 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
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