Movatterモバイル変換


[0]ホーム

URL:


RCSB PDB
249,906
Structures from the PDB archive
1,068,577
Computed Structure Models (CSM)
  • PDB-101
  • wwPDB
  • EMDataResource
  • NAKB: Nucleic Acid Knowledgebase
  • wwPDB Foundation
  • PDB-IHM Logo

 6D48|pdb_00006d48

Cell Surface Receptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 
    0.212 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.176 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 
    0.177 (Depositor) 

Starting Model:experimental
View more details

wwPDB Validation  3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Small Molecule Binding to Alzheimer Risk Factor CD33 Promotes A beta Phagocytosis.

Miles, L.A.Hermans, S.J.Crespi, G.A.N.Gooi, J.H.Doughty, L.Nero, T.L.Markulic, J.Ebneth, A.Wroblowski, B.Oehlrich, D.Trabanco, A.A.Rives, M.L.Royaux, I.Hancock, N.C.Parker, M.W.

(2019) iScience 19: 110-118

  • PubMed31369984 Search on PubMedSearch on PubMed Central
  • DOI: https://doi.org/10.1016/j.isci.2019.07.023
  • Primary Citation of Related Structures:  
    6D48,6D49,6D4A

  • PubMed Abstract: 

    Polymorphism in the microglial receptor CD33 gene has been linked to late-onset Alzheimer disease (AD), and reduced expression of the CD33 sialic acid-binding domain confers protection. Thus, CD33 inhibition might be an effective therapy against disease progression. Progress toward discovery of selective CD33 inhibitors has been hampered by the absence of an atomic resolution structure. We report here the crystal structures of CD33 alone and bound to a subtype-selective sialic acid mimetic called P22 and use them to identify key binding residues by site-directed mutagenesis and binding assays to reveal the molecular basis for its selectivity toward sialylated glycoproteins and glycolipids. We show that P22, when presented on microparticles, increases uptake of the toxic AD peptide, amyloid-β (Aβ), into microglial cells. Thus, the sialic acid-binding site on CD33 is a promising pharmacophore for developing therapeutics that promote clearance of the Aβ peptide that is thought to cause AD.


  • Organizational Affiliation
    • ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3056, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia. Electronic address: lmiles@svi.edu.au.
    • ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3056, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia.
    • Janssen Research & Development, a Division of Janssen Pharmaceutica N.V, 2340 Beerse, Belgium.
    • Neuroscience Medicinal Chemistry, Janssen Research & Development, 45007 Toledo, Spain.
    • Molecular and Cellular Pharmacology, Janssen Research & Development, LLC, La Jolla, CA 92121, USA.
    • ACRF Rational Drug Discovery Centre, St. Vincent's Institute of Medical Research, Fitzroy, VIC 3056, Australia; Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC 3010, Australia. Electronic address: mparker@svi.edu.au.
Biological Assembly 1  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report


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


Find Similar Assemblies

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


Biological Assembly Evidence: gel filtration
Biological Assembly 2  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report


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


Find Similar Assemblies

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report


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


Find Similar Assemblies

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

 Explore in 3DStructure |Sequence Annotations |Electron Density |Validation Report


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


Find Similar Assemblies

Biological assembly 4 assigned by authors and generated by PISA (software)

PreviousNext

Macromolecule Content 

  • Total Structure Weight: 58.59 kDa 
  • Atom Count: 4,546 
  • Modeled Residue Count: 498 
  • Deposited Residue Count: 508 
  • Unique protein chains: 1

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Myeloid cell surface antigen CD33A [auth E],
B [auth F],
C [auth G],
D [auth H]
127Homo sapiensMutation(s): 0 
Gene Names: CD33SIGLEC3
UniProt & NIH Common Fund Data Resources
Find proteins for P20138 (Homo sapiens)
Explore P20138 
Go to UniProtKB:  P20138
PHAROS:  P20138
GTEx:  ENSG00000105383 
Entity Groups 
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20138
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.78 Å
  • R-Value Free: 0.212 (Depositor), 0.210 (DCC) 
  • R-Value Work: 0.176 (Depositor), 0.180 (DCC) 
  • R-Value Observed: 0.177 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.801α = 90
b = 41.543β = 96.55
c = 107.498γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-17
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection, Database references
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.3: 2024-10-30
    Changes: Structure summary
  • RCSB PDB is hosted by

  • The Rutgers Artificial Intelligence and Data Science Collaboratory logo
    Uiversity of California San Diego logoSan Diego Supercomputer Center logo
    University of California San Francisco Logo

RCSB PDB Core Operations are funded by theU.S. National Science Foundation (DBI-2321666), theUS Department of Energy (DE-SC0019749), and theNational Cancer Institute,National Institute of Allergy and Infectious Diseases, andNational Institute of General Medical Sciences of theNational Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.


[8]ページ先頭

©2009-2026 Movatter.jp