6UM1 | pdb_00006um1

Structure of M-6-P/IGFII Receptor at pH 4.5

• PDB DOI: https://doi.org/10.2210/pdb6UM1/pdb
• EM Map EMD-20815: EMDB EMDataResource

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2019-10-08 Released: 2020-02-26 
• Deposition Author(s): Wang, R., Qi, X., Li, X.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.46 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Marked structural rearrangement of mannose 6-phosphate/IGF2 receptor at different pH environments

Wang, R., Qi, X., Schmiege, P., Coutavas, E., Li, X.

(2020) Sci Adv 6: eaaz1466

• DOI: https://doi.org/10.1126/sciadv.aaz1466

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 276.5 kDa 
• Atom Count: 17,134 
• Modeled Residue Count: 2,208 
• Deposited Residue Count: 2,499 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cation-independent mannose-6-phosphate receptor	A	2,499	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P08169 (Bos taurus) Explore P08169  Go to UniProtKB:  P08169
Glycosylation
Glycosylation Sites: 4

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth A], F [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.46 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-02-26 
Deposition Author(s): Wang, R., Qi, X., Li, X.

Revision History  

• Version 1.0: 2020-02-26
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-11-20
  Changes: Data collection, Database references, Structure summary