6Z32 | pdb_00006z32

Human cation-independent mannose 6-phosphate/IGF2 receptor domains 7-11


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.47 Å
  • R-Value Free: 
    0.300 (Depositor), 0.296 (DCC) 
  • R-Value Work: 
    0.261 (Depositor), 0.270 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

Structure of the Human Cation-Independent Mannose 6-Phosphate/IGF2 Receptor Domains 7-11 Uncovers the Mannose 6-Phosphate Binding Site of Domain 9.

Bochel, A.J.Williams, C.McCoy, A.J.Hoppe, H.J.Winter, A.J.Nicholls, R.D.Harlos, K.Jones, E.Y.Berger, I.Hassan, A.B.Crump, M.P.

(2020) Structure 28: 1300-1312.e5

  • DOI: https://doi.org/10.1016/j.str.2020.08.002
  • Primary Citation Related Structures: 
    6Z30, 6Z31, 6Z32

  • PubMed Abstract: 

    The cation-independent mannose 6-phosphate (M6P)/Insulin-like growth factor-2 receptor (CI-MPR/IGF2R) is an ∼300 kDa transmembrane protein responsible for trafficking M6P-tagged lysosomal hydrolases and internalizing IGF2. The extracellular region of the CI-MPR has 15 homologous domains, including M6P-binding domains (D) 3, 5, 9, and 15 and IGF2-binding domain 11. We have focused on solving the first structures of human D7-10 within two multi-domain constructs, D9-10 and D7-11, and provide the first high-resolution description of the high-affinity M6P-binding D9. Moreover, D9 stabilizes a well-defined hub formed by D7-11 whereby two penta-domains intertwine to form a dimeric helical-type coil via an N-glycan bridge on D9. Remarkably the D7-11 structure matches an IGF2-bound state of the receptor, suggesting this may be an intrinsically stable conformation at neutral pH. Interdomain clusters of histidine and proline residues may impart receptor rigidity and play a role in structural transitions at low pH.


  • Organizational Affiliation
    • School of Chemistry, Cantock's Close, University of Bristol, Bristol BS8 1TS, UK.

Macromolecule Content 

  • Total Structure Weight: 164.57 kDa 
  • Atom Count: 10,549 
  • Modeled Residue Count: 1,351 
  • Deposited Residue Count: 1,474 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Cation-independent mannose-6-phosphate receptor
A, B
737Homo sapiensMutation(s): 1 
Gene Names: IGF2RMPRI
UniProt & NIH Common Fund Data Resources
Find proteins for P11717 (Homo sapiens)
Explore P11717 
Go to UniProtKB:  P11717
PHAROS:  P11717
GTEx:  ENSG00000197081 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11717
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P11717-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
6N-Glycosylation
Glycosylation Resources
GlyTouCan: G01760ZU
GlyCosmos: G01760ZU
GlyGen: G01760ZU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.47 Å
  • R-Value Free:  0.300 (Depositor), 0.296 (DCC) 
  • R-Value Work:  0.261 (Depositor), 0.270 (DCC) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.204α = 90
b = 139.204β = 90
c = 234.682γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
DIALSdata scaling
PHASERphasing
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/J014400/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/M009122/1
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/L01386X/1
Cancer Research UKUnited KingdomC429/A9891

Revision History  (Full details and data files)

  • Version 1.0: 2020-08-19
    Type: Initial release
  • Version 1.1: 2020-09-16
    Changes: Database references
  • Version 1.2: 2020-12-09
    Changes: Database references
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description
  • Version 1.4: 2024-11-20
    Changes: Structure summary