Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 101.83 kDa 
• Atom Count: 7,608 
• Modelled Residue Count: 845 
• Deposited Residue Count: 872 
• Unique protein chains: 1

 5NN6

Crystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with N-hydroxyethyl-1-deoxynojirimycin

• PDB DOI: 10.2210/pdb5NN6/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2017-04-08 Released: 2017-10-25 
• Deposition Author(s): Roig-Zamboni, V., Cobucci-Ponzano, B., Iacono, R., Ferrara, M.C., Germany, S., Parenti, G., Bourne, Y., Moracci, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.184 
• R-Value Work: 0.153 
• R-Value Observed: 0.154 

Literature

Structure of human lysosomal acid alpha-glucosidase-a guide for the treatment of Pompe disease.

Roig-Zamboni, V., Cobucci-Ponzano, B., Iacono, R., Ferrara, M.C., Germany, S., Bourne, Y., Parenti, G., Moracci, M., Sulzenbacher, G.

(2017) Nat Commun 8: 1111-1111

• PubMed: 29061980 
• DOI: 10.1038/s41467-017-01263-3
• Primary Citation of Related Structures:  
  5NN3, 5NN4, 5NN5, 5NN6, 5NN8


• PubMed Abstract: 
  

Pompe disease, a rare lysosomal storage disease caused by deficiency of the lysosomal acid α-glucosidase (GAA), is characterized by glycogen accumulation, triggering severe secondary cellular damage and resulting in progressive motor handicap and premature death. Numerous disease-causing mutations in the gaa gene have been reported, but the structural effects of the pathological variants were unknown. Here we present the high-resolution crystal structures of recombinant human GAA (rhGAA), the standard care of Pompe disease. These structures portray the unbound form of rhGAA and complexes thereof with active site-directed inhibitors, providing insight into substrate recognition and the molecular framework for the rationalization of the deleterious effects of disease-causing mutations. Furthermore, we report the structure of rhGAA in complex with the allosteric pharmacological chaperone N-acetylcysteine, which reveals the stabilizing function of this chaperone at the structural level.

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Organizational Affiliation: 

Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Univ, AFMB, 163 Avenue de Luminy, 13288, Marseille, France. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lysosomal alpha-glucosidase	A	872	Homo sapiens	Mutation(s): 0  Gene Names: GAA EC: 3.2.1.20
UniProt & NIH Common Fund Data Resources
Find proteins for P10253 (Homo sapiens) Explore P10253  Go to UniProtKB:  P10253
PHAROS:  P10253

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	B	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

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, D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G86851RC GlyCosmos:  G86851RC GlyGen:  G86851RC

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MIG	G [auth A]	(2R,3R,4R,5S)-1-(2-hydroxyethyl)-2-(hydroxymethyl)piperidine-3,4,5-triol C8 H17 N O5 IBAQFPQHRJAVAV-ULAWRXDQSA-N
PGE	CA [auth A], DA [auth A], EA [auth A], FA [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
SO4	H [auth A], I [auth A], J [auth A], K [auth A], L [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	GA [auth A], HA [auth A], IA [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO	AA [auth A], BA [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], X [auth A], Y [auth A], Z [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	M [auth A], N [auth A], O [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
MIG	Binding MOAD:  5NN6	Ki: 3000 (nM) from 1 assay(s)
	BindingDB:  5NN6	Ki: 460 (nM) from 1 assay(s)
		IC50: min: 350, max: 2000 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.184 
• R-Value Work: 0.153 
• R-Value Observed: 0.154 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 96.633	α = 90
b = 102.191	β = 90
c = 128.348	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-10-25 
Deposition Author(s): Roig-Zamboni, V., Cobucci-Ponzano, B., Iacono, R., Ferrara, M.C., Germany, S., Parenti, G., Bourne, Y., Moracci, M.

Revision History  

• Version 1.0: 2017-10-25
  Type: Initial release
  
• Version 1.1: 2017-11-01
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary