Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  (To be retired June 1st  )
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 41.93 kDa 
• Atom Count: 2776 
• Residue Count: 330 
• Unique protein chains: 1

3EOP

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

• DOI: 10.2210/pdb3EOP/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-29 Released: 2009-09-29 
• Deposition Author(s): Yu, F., Song, A., Xu, C., Sun, L., Li, L., Tang, L., Hu, H., He, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.238 
• R-Value Work: 0.182 

Literature

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

• PubMed: 19237743 
• DOI: 10.1107/S0907444908041474
• Structures With Same Primary Citation


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Thymocyte nuclear protein 1	A, B	176	Homo sapiens	Mutation(s): 0  Gene Names: THYN1, THY28, HSPC144, MDS012, My0054
Find proteins for Q9P016 (Homo sapiens) Go to UniProtKB:  Q9P016
NIH Common Fund Data Resources
PHAROS  Q9P016 GTEx  ENSG00000151500

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.238 
• R-Value Work: 0.182 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.258	α = 90
b = 51.258	β = 90
c = 122.4	γ = 120

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-09-29 
• Released Date: 2009-09-29 
Deposition Author(s): Yu, F., Song, A., Xu, C., Sun, L., Li, L., Tang, L., Hu, H., He, J.

Revision History 

• Version 1.0: 2009-09-29
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance