2RL9

Crystal Structure cation-dependent mannose 6-phosphate receptor at pH 6.5 bound to trimannoside

• PDB DOI: https://doi.org/10.2210/pdb2RL9/pdb

• Classification: Protein transport, sugar binding protein
• Organism(s): Bos taurus
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 2007-10-18 Released: 2008-02-12 
• Deposition Author(s): Olson, L.J., Hindsgaul, O., Dahms, N.M., Kim, J.-J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.265 
• R-Value Work: 0.199 

Literature

Structural insights into the mechanism of pH-dependent ligand binding and release by the cation-dependent mannose 6-phosphate receptor.

Olson, L.J., Hindsgaul, O., Dahms, N.M., Kim, J.J.

(2008) J Biol Chem 283: 10124-10134

• PubMed: 18272523 
• DOI: https://doi.org/10.1074/jbc.M708994200
• Primary Citation of Related Structures:  
  2RL7, 2RL8, 2RL9, 2RLB, 3CY4


• PubMed Abstract: 
  

  The cation-dependent mannose 6-phosphate receptor (CD-MPR) is a key component of the lysosomal enzyme targeting system that binds newly synthesized mannose 6-phosphate (Man-6-P)-containing acid hydrolases and transports them to endosomal compartments. The interaction between the MPRs and its ligands is pH-dependent; the homodimeric CD-MPR binds lysosomal enzymes optimally in the pH environment of the trans Golgi network (pH approximately 6.5) and releases its cargo in acidic endosomal compartments (

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Organizational Affiliation: 

Department of Biochemistry, Medical College of Wisconsin, 8701 Watertown Plank Road, Milwaukee, WI 53226, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 36.61 kDa 
• Atom Count: 2,521 
• Modelled Residue Count: 297 
• Deposited Residue Count: 308 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation-dependent mannose-6-phosphate receptor	A, B	154	Bos taurus	Mutation(s): 4  Gene Names: M6PR
UniProt
Find proteins for P11456 (Bos taurus) Explore P11456  Go to UniProtKB:  P11456

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
6-O-phosphono-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose	C, D	3		N/A
Glycosylation Resources
GlyTouCan:  G37444JE GlyCosmos:  G37444JE GlyGen:  G37444JE

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], G [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MN	F [auth A], H [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
M6P	BindingDB:  2RL9	IC50: 2.30e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.265 
• R-Value Work: 0.199 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.628	α = 90
b = 92.628	β = 90
c = 85.594	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-02-12 
Deposition Author(s): Olson, L.J., Hindsgaul, O., Dahms, N.M., Kim, J.-J.P.

Revision History  

• Version 1.0: 2008-02-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2014-12-17
  Changes: Atomic model
• Version 1.3: 2017-10-25
  Changes: Advisory, Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2021-10-20
  Changes: Database references, Structure summary