Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 35.06 kDa 
• Atom Count: 2503 
• Modelled Residue Count: 292 
• Deposited Residue Count: 304 
• Unique protein chains: 1

1M6P

EXTRACYTOPLASMIC DOMAIN OF BOVINE CATION-DEPENDENT MANNOSE 6-PHOSPHATE RECEPTOR

• PDB DOI: 10.2210/pdb1M6P/pdb

• Classification: RECEPTOR
• Organism(s): Bos taurus
• Expression System: Trichoplusia ni
• Mutation(s): Yes 


• Deposited: 1998-04-19 Released: 1999-04-27 
• Deposition Author(s): Roberts, D.L., Weix, D.J., Dahms, N.M., Kim, J.J.-P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.276 
• R-Value Work: 0.224 
• R-Value Observed: 0.224 

Literature

Molecular basis of lysosomal enzyme recognition: three-dimensional structure of the cation-dependent mannose 6-phosphate receptor.

Roberts, D.L., Weix, D.J., Dahms, N.M., Kim, J.J.

(1998) Cell 93: 639-648

• PubMed: 9604938 
• DOI: 10.1016/s0092-8674(00)81192-7
• Primary Citation of Related Structures:  
  1M6P


• PubMed Abstract: 
  

Targeting of newly synthesized lysosomal hydrolases to the lysosome is mediated by the cation-dependent mannose 6-phosphate receptor (CD-MPR) and the insulin-like growth factor II/cation-independent mannose 6-phosphate receptor (IGF-II/CI-MPR). The two receptors, which share sequence similarities, constitute the P-type family of animal lectins. We now report the three-dimensional structure of a glycosylation-deficient, yet fully functional form of the extracytoplasmic domain of the bovine CD-MPR (residues 3-154) complexed with mannose 6-phosphate at 1.8 A resolution. The extracytoplasmic domain of the CD-MPR crystallizes as a dimer, and each monomer folds into a nine-stranded flattened beta barrel, which bears a striking resemblance to avidin. The distance of 40 A between the two ligand-binding sites of the dimer provides a structural basis for the observed differences in binding affinity exhibited by the CD-MPR toward various lysosomal enzymes.

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Organizational Affiliation: 

Department of Biochemistry, Medical College of Wisconsin, Milwaukee 53226, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CATION-DEPENDENT MANNOSE-6-PHOSPHATE RECEPTOR	A, B	152	Bos taurus	Mutation(s): 4  Gene Names: M6PR
UniProt
Find proteins for P11456 (Bos taurus) Explore P11456  Go to UniProtKB:  P11456

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
M6P	D [auth A], F [auth B]	6-O-phosphono-alpha-D-mannopyranose C6 H13 O9 P NBSCHQHZLSJFNQ-PQMKYFCFSA-N
MN	C [auth A], E [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
M6P	Binding MOAD:  1M6P	Kd: 8000 (nM) from 1 assay(s)
	PDBBind:  1M6P	Kd: 8000 (nM) from 1 assay(s)
	BindingDB:  1M6P	IC50: 2.30e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.276 
• R-Value Work: 0.224 
• R-Value Observed: 0.224 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.641	α = 90
b = 92.641	β = 90
c = 85.316	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASES	phasing
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-04-19 
• Released Date: 1999-04-27 
Deposition Author(s): Roberts, D.L., Weix, D.J., Dahms, N.M., Kim, J.J.-P.

Revision History  

• Version 1.0: 1999-04-27
  Type: Initial release
  
• Version 1.1: 2008-03-24
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2021-11-03
  Changes: Database references, Structure summary