Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

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

Macromolecule Content

• Total Structure Weight: 41925.73 
• Atom Count: 2739 
• Residue Count: 352 
• 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


• 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: 2.3 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.,Sect.D 65: 212-219

• PubMed: 19237743 
• DOI: 10.1107/S0907444908041474


• 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

Find similar proteins by: Sequence  |  Structure

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)
Find proteins for Q9P016 (Homo sapiens) Go to Gene View: THYN1 Go to UniProtKB:  Q9P016

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.238 
• R-Value Work: 0.182 
• Space Group: P 3₁

Unit Cell:

Length (Å)	Angle (°)
a = 51.258	α = 90.00
b = 51.258	β = 90.00
c = 122.400	γ = 120.00

Software Package:

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

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
  Type: Version format compliance