2KIG | pdb_00002kig

A PH domain within OCRL bridges clathrin mediated membrane trafficking to phosphoinositide metabolism


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

Validation slider image for 2KIG

This is version 1.3 of the entry. See complete history

Literature

A PH domain within OCRL bridges clathrin-mediated membrane trafficking to phosphoinositide metabolism.

Mao, Y.Balkin, D.M.Zoncu, R.Erdmann, K.S.Tomasini, L.Hu, F.Jin, M.M.Hodsdon, M.E.De Camilli, P.

(2009) EMBO J 28: 1831-1842

  • DOI: https://doi.org/10.1038/emboj.2009.155
  • Primary Citation Related Structures: 
    2KIE, 2KIG

  • PubMed Abstract: 

    OCRL, whose mutations are responsible for Lowe syndrome and Dent disease, and INPP5B are two similar proteins comprising a central inositol 5-phosphatase domain followed by an ASH and a RhoGAP-like domain. Their divergent NH2-terminal portions remain uncharacterized. We show that the NH2-terminal region of OCRL, but not of INPP5B, binds clathrin heavy chain. OCRL, which in contrast to INPP5B visits late stage endocytic clathrin-coated pits, was earlier shown to contain another binding site for clathrin in its COOH-terminal region. NMR structure determination further reveals that despite their primary sequence dissimilarity, the NH2-terminal portions of both OCRL and INPP5B contain a PH domain. The novel clathrin-binding site in OCRL maps to an unusual clathrin-box motif located in a loop of the PH domain, whose mutations reduce recruitment efficiency of OCRL to coated pits. These findings suggest an evolutionary pressure for a specialized function of OCRL in bridging phosphoinositide metabolism to clathrin-dependent membrane trafficking.


  • Organizational Affiliation
    • Department of Cell Biology, Howard Hughes Medical Institute, Yale University, New Haven, CT 06511, USA.

Macromolecule Content 

  • Total Structure Weight: 18.01 kDa 
  • Atom Count: 1,263 
  • Modeled Residue Count: 161 
  • Deposited Residue Count: 161 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Inositol polyphosphate 5-phosphatase II isoform161Mus musculusMutation(s): 0 
Gene Names: Inpp5b
EC: 3.1.3.56 (UniProt), 3.1.3.36 (UniProt)
UniProt
Find proteins for Q8K337 (Mus musculus)
Explore Q8K337 
Go to UniProtKB:  Q8K337
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8K337
Sequence Annotations
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Reference Sequence

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: 2009-06-30
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2022-03-16
    Changes: Data collection, Database references, Derived calculations
  • Version 1.3: 2024-05-22
    Changes: Data collection