5CTR

Crystal structure of human SART3 HAT-C domain-human USP4 DUSP-UBL domain complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.309 
  • R-Value Observed: 0.310 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for recruiting and shuttling of the spliceosomal deubiquitinase USP4 by SART3

Park, J.K.Das, T.Song, E.J.Kim, E.E.

(2016) Nucleic Acids Res 44: 5424-5437

  • DOI: 10.1093/nar/gkw218
  • Primary Citation of Related Structures:  
    5CTQ, 5CTR, 5CTT

  • PubMed Abstract: 
  • Squamous cell carcinoma antigen recognized by T-cells 3 (SART3) is a U4/U6 recycling factor as well as a targeting factor of USP4 and USP15. However, the details of how SART3 recognizes these deubiquitinases and how they get subsequently translocated into the nucleus are not known ...

    Squamous cell carcinoma antigen recognized by T-cells 3 (SART3) is a U4/U6 recycling factor as well as a targeting factor of USP4 and USP15. However, the details of how SART3 recognizes these deubiquitinases and how they get subsequently translocated into the nucleus are not known. Here, we present the crystal structures of the SART3 half-a-tetratricopeptide (HAT) repeat domain alone and in complex with the domain present in ubiquitin-specific protease (DUSP)-ubiquitin-like (UBL) domains of ubiquitin specific protease 4 (USP4). The 12 HAT repeats of SART3 are in two sub-domains (HAT-N and HAT-C) forming a dimer through HAT-C. USP4 binds SART3 at the opposite surface of the HAT-C dimer interface utilizing the β-structured linker between the DUSP and the UBL domains. The binding affinities of USP4 and USP15 to SART3 are 0.9 μM and 0.2 μM, respectively. The complex structure of SART3 nuclear localization signal (NLS) and importin-α reveals bipartite binding, and removal of SART3 NLS prevents the entry of USP4 (and USP15) into the nucleus and abrogates the subsequent deubiquitinase activity of USP4.


    Organizational Affiliation

    Biomedical Research Institute, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul 136-791, Republic of Korea eunice@kist.re.kr.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Squamous cell carcinoma antigen recognized by T-cells 3A, B338Homo sapiensMutation(s): 0 
Gene Names: SART3KIAA0156TIP110
UniProt & NIH Common Fund Data Resources
Find proteins for Q15020 (Homo sapiens)
Explore Q15020 
Go to UniProtKB:  Q15020
PHAROS:  Q15020
GTEx:  ENSG00000075856 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15020
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin carboxyl-terminal hydrolase 4C, D233Homo sapiensMutation(s): 0 
Gene Names: USP4UNPUNPH
EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q13107 (Homo sapiens)
Explore Q13107 
Go to UniProtKB:  Q13107
PHAROS:  Q13107
GTEx:  ENSG00000114316 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13107
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.01 Å
  • R-Value Free: 0.334 
  • R-Value Work: 0.309 
  • R-Value Observed: 0.310 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 115.202α = 90
b = 115.202β = 90
c = 306.138γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2015-07-24 
  • Released Date: 2016-04-27 
  • Deposition Author(s): Park, J.K., Kim, E.E.

Funding OrganizationLocationGrant Number
National Research Foundation of KoreaKorea, Republic OfNRF-2011-0021713

Revision History  (Full details and data files)

  • Version 1.0: 2016-04-27
    Type: Initial release
  • Version 1.1: 2016-06-29
    Changes: Database references