2I1P | pdb_00002i1p

Solution structure of the twelfth cysteine-rich ligand-binding repeat in rat megalin


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history

Literature

Solution structure of the twelfth cysteine-rich ligand-binding repeat in rat megalin.

Wolf, C.A.Dancea, F.Shi, M.Bade-Noskova, V.Rueterjans, H.Kerjaschki, D.Luecke, C.

(2007) J Biomol NMR 37: 321-328

  • DOI: https://doi.org/10.1007/s10858-006-9129-3
  • Primary Citation Related Structures: 
    2I1P

  • PubMed Abstract: 

    Megalin, an approx. 600 kDa transmembrane glycoprotein that acts as multi-ligand transporter, is a member of the low density lipoprotein receptor gene family. Several cysteine-rich repeats, each consisting of about 40 residues, are responsible for the multispecific binding of ligands. The solution structure of the twelfth cysteine-rich ligand-binding repeat with class A motif found in megalin features two short beta-strands and two helical turns, yielding the typical fold with a I-III, II-V and IV-VI disulfide bridge connectivity pattern and a calcium coordination site at the C-terminal end. The resulting differences in electrostatic surface potential compared to other ligand-binding modules of this gene family, however, may be responsible for the functional divergence.


  • Organizational Affiliation
    • Institute of Biophysical Chemistry, Center for Biomolecular Magnetic Resonance, J.W. Goethe-University of Frankfurt, 60439 Frankfurt, Germany.

Macromolecule Content 

  • Total Structure Weight: 5.14 kDa 
  • Atom Count: 351 
  • Modeled Residue Count: 48 
  • Deposited Residue Count: 48 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Low-density lipoprotein receptor-related protein 248Rattus norvegicusMutation(s): 0 
UniProt
Find proteins for P98158 (Rattus norvegicus)
Explore P98158 
Go to UniProtKB:  P98158
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP98158
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA

Query on CA



Download:Ideal Coordinates CCD File
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-02-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-02-19
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.4: 2023-06-14
    Changes: Database references, Derived calculations, Other
  • Version 1.5: 2024-11-13
    Changes: Data collection, Database references, Structure summary