5TPT | pdb_00005tpt

The Crystal Structure of Amyloid Precursor-Like Protein 2 (APLP2) E2 Domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 
    0.260 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 
    0.218 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

The crystal structure of amyloid precursor-like protein 2 E2 domain completes the amyloid precursor protein family.

Roisman, L.C.Han, S.Chuei, M.J.Connor, A.R.Cappai, R.

(2019) FASEB J 33: 5076-5081

  • DOI: https://doi.org/10.1096/fj.201802315R
  • Primary Citation Related Structures: 
    5TPT

  • PubMed Abstract: 

    The amyloid precursor-like protein 2 (APLP2) molecule is a type I transmembrane protein that is crucial for survival, cell-cell adhesion, neuronal development, myelination, cancer metastasis, modulation of metal, and glucose and insulin homeostasis. Moreover, the importance of the amyloid precursor protein (APP) family in biology and disease is very well known because of its central role in Alzheimer disease. In this study, we determined the crystal structure of the independently folded E2 domain of APLP2 and compared that with its paralogues APP and APLP2, demonstrating high overall structural similarities. The crystal structure of APLP2 E2 was solved as an antiparallel dimer, and analysis of the protein interfaces revealed a distinct mode of dimerization that differs from the previously reported dimerization of either APP or APLP1. Analysis of the APLP2 E2 metal binding sites suggested it binds zinc and copper in a similar manner to APP and APLP1. The structure of this key protein might suggest a relationship between the distinct mode of dimerization and its biologic functions.-Roisman, L. C., Han, S., Chuei, M. J., Connor, A. R., Cappai, R. The crystal structure of amyloid precursor-like protein 2 E2 domain completes the amyloid precursor protein family.


  • Organizational Affiliation
    • Department of Pathology, The University of Melbourne, Victoria, Australia; and.

Macromolecule Content 

  • Total Structure Weight: 47.06 kDa 
  • Atom Count: 3,244 
  • Modeled Residue Count: 378 
  • Deposited Residue Count: 394 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Amyloid-like protein 2
A, B
197Homo sapiensMutation(s): 0 
Gene Names: APLP2APPL2
UniProt & NIH Common Fund Data Resources
Find proteins for Q06481 (Homo sapiens)
Explore Q06481 
Go to UniProtKB:  Q06481
PHAROS:  Q06481
GTEx:  ENSG00000084234 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06481
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free:  0.260 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.217 (DCC) 
  • R-Value Observed: 0.218 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.749α = 90
b = 150.118β = 109.69
c = 39.107γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian National Health and Medical Research CouncilAustralia566575; 509040; 628946
Australian Research CouncilAustraliaDP1096225

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-06
    Type: Initial release
  • Version 1.1: 2019-05-29
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description