7KDV | pdb_00007kdv

Murine core lysosomal multienzyme complex (LMC) composed of acid beta-galactosidase (GLB1) and protective protein cathepsin A (PPCA, CTSA)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history. 

Literature

Structure of the murine lysosomal multienzyme complex core.

Gorelik, A., Illes, K., Hasan, S.M.N., Nagar, B., Mazhab-Jafari, M.T.

(2021) Sci Adv 7

  • DOI: https://doi.org/10.1126/sciadv.abf4155

  • PubMed Abstract: 

    The enzymes β-galactosidase (GLB1) and neuraminidase 1 (NEU1; sialidase 1) participate in the degradation of glycoproteins and glycolipids in the lysosome. To remain active and stable, they associate with PPCA [protective protein cathepsin A (CTSA)] into a high-molecular weight lysosomal multienzyme complex (LMC), of which several forms exist. Genetic defects in these three proteins cause the lysosomal storage diseases GM1-gangliosidosis/mucopolysaccharidosis IV type B, sialidosis, and galactosialidosis, respectively. To better understand the interactions between these enzymes, we determined the three-dimensional structure of the murine LMC core. This 0.8-MDa complex is composed of three GLB1 dimers and three CTSA dimers, adopting a triangular architecture maintained through six copies of a unique GLB1-CTSA polar interface. Mutations in this contact surface that occur in GM1-gangliosidosis prevent formation of the LMC in vitro. These findings may facilitate development of therapies for lysosomal storage disorders.

    • Organizational Affiliation: 
    • Department of Biochemistry, McGill University, Montreal, Quebec, Canada.

Macromolecule Content 

  • Total Structure Weight: 759.89 kDa 
  • Atom Count: 51,696 
  • Modeled Residue Count: 6,312 
  • Deposited Residue Count: 6,546 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Beta-galactosidase
A, C, E, G, I
A, C, E, G, I, K
630Mus musculusMutation(s): 3 
Gene Names: Glb1, Bgl, Glb-1
EC: 3.2.1.23
UniProt
Find proteins for P23780 (Mus musculus)
Explore P23780 
Go to UniProtKB:  P23780
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP23780
Glycosylation
Glycosylation Sites: 6
Go to GlyGen: P23780-1
Sequence Annotations
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Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Lysosomal protective protein
B, D, F, H, J
B, D, F, H, J, L
461Mus musculusMutation(s): 1 
Gene Names: Ctsa, Ppgb
EC: 3.4.16.5
UniProt & NIH Common Fund Data Resources
Find proteins for P16675 (Mus musculus)
Explore P16675 
Go to UniProtKB:  P16675
IMPC:  MGI:97748
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16675
Glycosylation
Glycosylation Sites: 2
Go to GlyGen: P16675-1
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
BA [auth b],
CA [auth c],
M,
N,
P,
BA [auth b],
CA [auth c],
M,
N,
P,
Q,
S,
T,
V,
W,
Y,
Z
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT
Entity ID: 4
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
AA [auth a],
DA [auth d],
O,
R,
U,
AA [auth a],
DA [auth d],
O,
R,
U,
X
3N-Glycosylation
Glycosylation Resources
GlyTouCan: G15407YE
GlyCosmos: G15407YE
GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG


Download:Ideal Coordinates CCD File
AB [auth I]
BB [auth I]
CB [auth J]
DB [auth K]
EA [auth A]
AB [auth I],
BB [auth I],
CB [auth J],
DB [auth K],
EA [auth A],
EB [auth K],
FA [auth A],
FB [auth K],
GA [auth A],
GB [auth K],
HA [auth A],
HB [auth L],
IA [auth B],
JA [auth C],
KA [auth C],
LA [auth C],
MA [auth C],
NA [auth D],
OA [auth E],
PA [auth E],
QA [auth E],
RA [auth E],
SA [auth F],
TA [auth G],
UA [auth G],
VA [auth G],
WA [auth G],
XA [auth H],
YA [auth I],
ZA [auth I]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.59 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

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View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaMFE-164773
Canadian Institutes of Health Research (CIHR)CanadaMOP-133535
Canadian Institutes of Health Research (CIHR)Canada419240

Revision History  (Full details and data files)

  • Version 1.0: 2021-03-17
    Type: Initial release
  • Version 1.1: 2021-05-26
    Changes: Database references
  • Version 1.2: 2024-11-13
    Changes: Data collection, Database references, Refinement description, Structure summary