5XHZ

Crystal Structure Analysis of CIN85-SH3B in complex with ARAP1-P2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Biochemical and Structural Studies of the Interaction between ARAP1 and CIN85.

Li, Q.Yang, W.Wang, Y.Liu, W.

(2018) Biochemistry 57: 2132-2139

  • DOI: 10.1021/acs.biochem.8b00057
  • Primary Citation of Related Structures:  
    5XHZ

  • PubMed Abstract: 
  • Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1 (ARAP1), Cbl-interacting protein of 85 kDa (CIN85), and casitas B-lineage lymphoma (Cbl) play important roles in epidermal growth factor receptor (EGFR) internalization and recycling ...

    Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1 (ARAP1), Cbl-interacting protein of 85 kDa (CIN85), and casitas B-lineage lymphoma (Cbl) play important roles in epidermal growth factor receptor (EGFR) internalization and recycling. In previous studies, ARAP1 was found to interact with CIN85, and their interaction attenuated the ubiquitination of EGFR. However, the molecular mechanism was still unclear. In this study, we first biochemically and structurally characterized the interaction between ARAP1 and CIN85, and found that the CIN85 SH3B domain bound to the ARAP1 PXPXXRX (except P) XXR/H/K motif with high affinity and specificity. Based on this binding model, we further predicted other potential CIN85 binding partners and tested their interactions biochemically. Moreover, our swapping data and structure alignment analysis suggested that the β2-β3 loops of the CIN85 SH3 domains and the H87 ARAP1 /E132 CIN85 interaction were critical for ARAP1 binding specificity. Finally, our competitive analytical gel-filtration chromatography and isothermal titration calorimetry (ITC) results showed that ARAP1 could compete with Cbl for CIN85 binding, which provides a biochemical basis for the regulatory roles of ARAP1 in the CIN85-mediated EGFR internalizing process.


    Organizational Affiliation

    Shenzhen Key Laboratory for Neuronal Structural Biology, Biomedical Research Institute , Shenzhen Peking University-The Hong Kong University of Science and Technology Medical Center , Shenzhen 518036 , China.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SH3 domain-containing kinase-binding protein 1A, B66Mus musculusMutation(s): 0 
Gene Names: Sh3kbp1RukSeta
UniProt
Find proteins for Q8R550 (Mus musculus)
Explore Q8R550 
Go to UniProtKB:  Q8R550
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 1C, D11Mus musculusMutation(s): 0 
Gene Names: Arap1Centd2Kiaa0782
UniProt & NIH Common Fund Data Resources
Find proteins for Q4LDD4 (Mus musculus)
Explore Q4LDD4 
Go to UniProtKB:  Q4LDD4
IMPC:  MGI:1916960
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download Ideal Coordinates CCD File 
E [auth D]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.187 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.162α = 90
b = 66.162β = 90
c = 34.935γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2017-04-25 
  • Released Date: 2018-04-11 
  • Deposition Author(s): Liu, W., Yang, W.

Revision History  (Full details and data files)

  • Version 1.0: 2018-04-11
    Type: Initial release
  • Version 1.1: 2018-04-25
    Changes: Data collection, Database references