2YYN | pdb_00002yyn

Crystal structure of human bromodomain protein

• PDB DOI: https://doi.org/10.2210/pdb2YYN/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2007-04-30 Released: 2008-05-06 
• Deposition Author(s): Kishishita, S., Uchikubo-Kamo, T., Murayama, K., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.285 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.239 (Depositor), 0.250 (DCC) 
• R-Value Observed: 
  0.239 (Depositor) 

Literature

Crystal structure of human bromodomain protein

Kishishita, S., Uchikubo-Kamo, T., Murayama, K., Terada, T., Shirouzu, M., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 61.95 kDa 
• Atom Count: 3,896 
• Modeled Residue Count: 453 
• Deposited Residue Count: 540 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription intermediary factor 1-alpha	A, B, C, D	135	Homo sapiens	Mutation(s): 0  Gene Names: TRIM24, RNF82, TIF1, TIF1A EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for O15164 (Homo sapiens) Explore O15164  Go to UniProtKB:  O15164
PHAROS:  O15164 GTEx:  ENSG00000122779

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.285 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.239 (Depositor), 0.250 (DCC) 
• R-Value Observed: 0.239 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.855	α = 90
b = 76.16	β = 90
c = 107.599	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-05-06 
Deposition Author(s): Kishishita, S., Uchikubo-Kamo, T., Murayama, K., Terada, T., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2008-05-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2020-09-09
  Changes: Database references, Structure summary
• Version 1.3: 2022-12-21
  Changes: Database references
• Version 1.4: 2024-11-13
  Changes: Data collection, Structure summary