6NYQ | pdb_00006nyq

Crystal structure of glycosylated lysosomal membrane protein (GLMP) luminal domain bound to a Fab fragment

• PDB DOI: https://doi.org/10.2210/pdb6NYQ/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli, Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2019-02-12 Released: 2020-01-22 
• Deposition Author(s): Huang, C.S., Boenig, G., Hymowitz, S.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.204 (Depositor), 0.211 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Literature

GLMP is essential for bone-marrow hematopoiesis and lysosomal glycolipid metabolism

Manzanillo, P., Huang, C.S., Boenig, G., Calses, P., Scherl, A., Reichelt, M., Katakam, A.K., Martin, F., Hymowitz, S.G., Ouyang, W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 92.89 kDa 
• Atom Count: 6,292 
• Modeled Residue Count: 746 
• Deposited Residue Count: 845 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
1H3 Fab light chain	A [auth L]	214	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
1H3 Fab heavy chain	B [auth H]	227	Mus musculus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycosylated lysosomal membrane protein	C	404	Mus musculus	Mutation(s): 0  Gene Names: Glmp
UniProt
Find proteins for Q9JHJ3 (Mus musculus) Explore Q9JHJ3  Go to UniProtKB:  Q9JHJ3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	H [auth C], I [auth C], J [auth C], K [auth C], L [auth C], M [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
NA	D [auth H], E [auth C], F [auth C], G [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.204 (Depositor), 0.211 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.924	α = 90
b = 55.238	β = 99.35
c = 99.639	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-01-22 
Deposition Author(s): Huang, C.S., Boenig, G., Hymowitz, S.G.

Revision History  

• Version 1.0: 2020-01-22
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Structure summary