5IEG

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.822 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structures of mammalian ER alpha-glucosidase II capture the binding modes of broad-spectrum iminosugar antivirals.

Caputo, A.T.Alonzi, D.S.Marti, L.Reca, I.B.Kiappes, J.L.Struwe, W.B.Cross, A.Basu, S.Lowe, E.D.Darlot, B.Santino, A.Roversi, P.Zitzmann, N.

(2016) Proc.Natl.Acad.Sci.USA 113: E4630-E4638

  • DOI: 10.1073/pnas.1604463113
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The biosynthesis of enveloped viruses depends heavily on the host cell endoplasmic reticulum (ER) glycoprotein quality control (QC) machinery. This dependency exceeds the dependency of host glycoproteins, offering a window for the targeting of ERQC f ...

    The biosynthesis of enveloped viruses depends heavily on the host cell endoplasmic reticulum (ER) glycoprotein quality control (QC) machinery. This dependency exceeds the dependency of host glycoproteins, offering a window for the targeting of ERQC for the development of broad-spectrum antivirals. We determined small-angle X-ray scattering (SAXS) and crystal structures of the main ERQC enzyme, ER α-glucosidase II (α-GluII; from mouse), alone and in complex with key ligands of its catalytic cycle and antiviral iminosugars, including two that are in clinical trials for the treatment of dengue fever. The SAXS data capture the enzyme's quaternary structure and suggest a conformational rearrangement is needed for the simultaneous binding of a monoglucosylated glycan to both subunits. The X-ray structures with key catalytic cycle intermediates highlight that an insertion between the +1 and +2 subsites contributes to the enzyme's activity and substrate specificity, and reveal that the presence of d-mannose at the +1 subsite renders the acid catalyst less efficient during the cleavage of the monoglucosylated substrate. The complexes with iminosugar antivirals suggest that inhibitors targeting a conserved ring of aromatic residues between the α-GluII +1 and +2 subsites would have increased potency and selectivity, thus providing a template for further rational drug design.


    Organizational Affiliation

    Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Neutral alpha-glucosidase AB
A
914Mus musculusMutation(s): 0 
Gene Names: Ganab (G2an, Kiaa0088)
EC: 3.2.1.207
Find proteins for Q8BHN3 (Mus musculus)
Go to UniProtKB:  Q8BHN3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Glucosidase 2 subunit beta
B
88Mus musculusMutation(s): 0 
Gene Names: Prkcsh
Find proteins for O08795 (Mus musculus)
Go to UniProtKB:  O08795
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FMT
Query on FMT

Download SDF File 
Download CCD File 
A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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Download CCD File 
A, B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
P6G
Query on P6G

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Download CCD File 
A
HEXAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
6A9
Query on 6A9

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Download CCD File 
A
N-9'-methoxynonyl-1-deoxynojirimycin
C16 H33 N O5
TYTARGBBJQKLAJ-QKPAOTATSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.822 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.175 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 104.321α = 90.00
b = 173.311β = 90.00
c = 63.032γ = 90.00
Software Package:
Software NamePurpose
AutoPROCdata reduction
BUSTERrefinement
Aimlessdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2016-07-27
    Type: Initial release
  • Version 1.1: 2016-08-03
    Type: Database references
  • Version 1.2: 2016-08-24
    Type: Database references