2RLB | pdb_00002rlb

Crystal Structure cation-dependent mannose 6-phosphate receptor at pH 6.5 bound to M6P in absence of Mn

• PDB DOI: https://doi.org/10.2210/pdb2RLB/pdb

• Classification: Protein transport, sugar binding protein
• Organism(s): Bos taurus
• Expression System: Spodoptera frugiperda
• 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: 1.75 Å
• R-Value Free: 
  0.229 (Depositor), 0.231 (DCC) 
• R-Value Work: 
  0.203 (Depositor), 0.205 (DCC) 

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 Biological Chem 283: 10124-10134

• PubMed: 18272523 
• DOI: https://doi.org/10.1074/jbc.M708994200
• Primary Citation 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: 35.85 kDa 
• Atom Count: 2,726 
• Modeled Residue Count: 300 
• 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
Glycosylation
Glycosylation Sites: 1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M6D	D [auth A], F [auth B]	6-O-phosphono-beta-D-mannopyranose C6 H13 O9 P NBSCHQHZLSJFNQ-RWOPYEJCSA-N
NAG	C [auth A], E [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.229 (Depositor), 0.231 (DCC) 
• R-Value Work:  0.203 (Depositor), 0.205 (DCC) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.386	α = 90
b = 91.386	β = 90
c = 84.816	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
CNS	phasing

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: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2021-10-20
  Changes: Database references, Structure summary
• Version 1.5: 2024-11-20
  Changes: Data collection, Structure summary