Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 110.09 kDa 
• Atom Count: 8720 
• Modelled Residue Count: 945 
• Deposited Residue Count: 945 
• Unique protein chains: 2

5F0E

Murine endoplasmic reticulum alpha-glucosidase II

• PDB DOI: 10.2210/pdb5F0E/pdb

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2015-11-27 Released: 2016-07-27 
• Deposition Author(s): Caputo, A.T., Roversi, P., Alonzi, D.S., Kiappes, J.L., Zitzmann, N.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.169 
• R-Value Work: 0.141 
• R-Value Observed: 0.143 

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 U S A 113: E4630-E4638

• PubMed: 27462106 
• DOI: 10.1073/pnas.1604463113
• Primary Citation of Related Structures:  
  5F0E, 5H9O, 5HJO, 5HJR, 5IED, 5IEE, 5IEF, 5IEG


• 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 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.

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Organizational Affiliation: 

Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom; [e-mail] [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neutral alpha-glucosidase AB	A	857	Mus musculus	Mutation(s): 0  Gene Names: Ganab, G2an, Kiaa0088 EC: 3.2.1.84 (PDB Primary Data), 3.2.1.207 (UniProt)
UniProt
Find proteins for Q8BHN3 (Mus musculus) Explore Q8BHN3  Go to UniProtKB:  Q8BHN3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosidase 2 subunit beta	B	88	Mus musculus	Mutation(s): 0  Gene Names: Prkcsh
UniProt & NIH Common Fund Data Resources
Find proteins for O08795 (Mus musculus) Explore O08795  Go to UniProtKB:  O08795
IMPC:  MGI:107877

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
P6G	G [auth A], H [auth A], I [auth A]	HEXAETHYLENE GLYCOL C12 H26 O7 IIRDTKBZINWQAW-UHFFFAOYSA-N
PG4	D [auth A], E [auth A], F [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
EDO	J [auth A], K [auth A], L [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT	M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N
CA	X [auth B], Y [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.74 Å
• R-Value Free: 0.169 
• R-Value Work: 0.141 
• R-Value Observed: 0.143 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.144	α = 90
b = 173.773	β = 90
c = 62.836	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2015-11-27 
• Released Date: 2016-07-27 
Deposition Author(s): Caputo, A.T., Roversi, P., Alonzi, D.S., Kiappes, J.L., Zitzmann, N.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	097300/Z/11/Z

Revision History  

• Version 1.0: 2016-07-27
  Type: Initial release
  
• Version 1.1: 2016-08-03
  Changes: Database references
• Version 1.2: 2016-08-24
  Changes: Database references
• Version 1.3: 2017-08-16
  Changes: Data collection
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary