3W5K | pdb_00003w5k

Crystal structure of Snail1 and importin beta complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.264 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.215 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural basis for the selective nuclear import of the C2H2 zinc-finger protein Snail by importin beta.

Choi, S.Yamashita, E.Yasuhara, N.Song, J.Son, S.Y.Won, Y.H.Hong, H.R.Shin, Y.S.Sekimoto, T.Park, I.Y.Yoneda, Y.Lee, S.J.

(2014) Acta Crystallogr D Biol Crystallogr 70: 1050-1060

  • DOI: https://doi.org/10.1107/S1399004714000972
  • Primary Citation Related Structures: 
    3W5K

  • PubMed Abstract: 

    Snail contributes to the epithelial-mesenchymal transition by suppressing E-cadherin in transcription processes. The Snail C2H2-type zinc-finger (ZF) domain functions both as a nuclear localization signal which binds to importin β directly and as a DNA-binding domain. Here, a 2.5 Å resolution structure of four ZF domains of Snail1 complexed with importin β is presented. The X-ray structure reveals that the four ZFs of Snail1 are required for tight binding to importin β in the nuclear import of Snail1. The shape of the ZFs in the X-ray structure is reminiscent of a round snail, where ZF1 represents the head, ZF2-ZF4 the shell, showing a novel interaction mode, and the five C-terminal residues the tail. Although there are many kinds of C2H2-type ZFs which have the same fold as Snail, nuclear import by direct recognition of importin β is observed in a limited number of C2H2-type ZF proteins such as Snail, Wt1, KLF1 and KLF8, which have the common feature of terminating in ZF domains with a short tail of amino acids.


  • Organizational Affiliation
    • College of Pharmacy, Chungbuk National University, Seungbong 410, Heungduk, Cheongju, Chungbuk 361-763, Republic of Korea.

Macromolecule Content 

  • Total Structure Weight: 126.64 kDa 
  • Atom Count: 7,588 
  • Modeled Residue Count: 969 
  • Deposited Residue Count: 1,140 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Importin subunit beta-1876Homo sapiensMutation(s): 0 
Gene Names: KPNB1NTF97
UniProt & NIH Common Fund Data Resources
Find proteins for Q14974 (Homo sapiens)
Explore Q14974 
Go to UniProtKB:  Q14974
PHAROS:  Q14974
GTEx:  ENSG00000108424 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ14974
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Zinc finger protein SNAI1264Homo sapiensMutation(s): 0 
Gene Names: SNAI1SNAH
UniProt & NIH Common Fund Data Resources
Find proteins for O95863 (Homo sapiens)
Explore O95863 
Go to UniProtKB:  O95863
PHAROS:  O95863
GTEx:  ENSG00000124216 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95863
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.264 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.215 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 228.21α = 90
b = 77.528β = 100.96
c = 72.019γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-05
    Type: Initial release
  • Version 1.1: 2014-05-07
    Changes: Database references
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations