Crystal Structure of the DUF55 domain of human thymocyte nuclear protein 1

Experimental Data Snapshot

  • Resolution: 2.30 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.182 

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Determining the DUF55-domain structure of human thymocyte nuclear protein 1 from crystals partially twinned by tetartohedry

Yu, F.Song, A.Xu, C.Sun, L.Li, J.Tang, L.Yu, M.Yeates, T.O.Hu, H.He, J.

(2009) Acta Crystallogr D Biol Crystallogr 65: 212-219

  • DOI: https://doi.org/10.1107/S0907444908041474
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Human thymocyte nuclear protein 1 contains a unique DUF55 domain consisting of 167 residues (55-221), but its cellular function remains unclear. Crystals of DUF55 belonged to the trigonal space group P3(1), but twinning caused the data to approach apparent 622 symmetry. Two data sets were collected to 2.3 A resolution. Statistical analysis confirmed that both data sets were partially twinned by tetartohedry. Tetartohedral twin fractions were estimated. After the structure had been determined, only one twofold axis of rotational pseudosymmetry was found in the crystal structure. Using the DALI program, a YTH domain, which is a potential RNA-binding domain from human YTH-domain-containing protein 2, was identified as having the most similar three-dimensional fold to that of DUF55. It is thus implied that DUF55 might be a potential RNA-related domain.

  • Organizational Affiliation

    Shanghai Institute of Applied Physics, Chinese Academy of Sciences, People's Republic of China.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thymocyte nuclear protein 1
A, B
176Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9P016 (Homo sapiens)
Explore Q9P016 
Go to UniProtKB:  Q9P016
GTEx:  ENSG00000151500 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9P016
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.30 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.182 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.258α = 90
b = 51.258β = 90
c = 122.4γ = 120
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
MAR345dtbdata collection

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description