4RT4

Crystal structure of Dpy30 complexed with Bre2

• PDB DOI: https://doi.org/10.2210/pdb4RT4/pdb

• Classification: PROTEIN BINDING
• Organism(s): Homo sapiens, Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-11-12 Released: 2015-10-07 
• Deposition Author(s): Zhang, H.M., Li, M., Chang, W.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.224 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

Literature

Structural implications of Dpy30 oligomerization for MLL/SET1 COMPASS H3K4 trimethylation

Zhang, H., Li, M., Gao, Y., Jia, C., Pan, X., Cao, P., Zhao, X., Zhang, J., Chang, W.

(2015) Protein Cell 6: 147-151

• PubMed: 25542209 
• DOI: https://doi.org/10.1007/s13238-014-0127-z
• Primary Citation of Related Structures:  
  4RT4, 4RTA

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Organizational Affiliation: 

Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A4B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.89 kDa 
• Atom Count: 2,097 
• Modelled Residue Count: 225 
• Deposited Residue Count: 294 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein dpy-30 homolog	A, B, C, D	66	Homo sapiens	Mutation(s): 0  Gene Names: DPY30
UniProt & NIH Common Fund Data Resources
Find proteins for Q9C005 (Homo sapiens) Explore Q9C005  Go to UniProtKB:  Q9C005
PHAROS:  Q9C005 GTEx:  ENSG00000162961

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptide from COMPASS component BRE2	E	30	Saccharomyces cerevisiae S288C	Mutation(s): 0
UniProt
Find proteins for P43132 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P43132  Go to UniProtKB:  P43132

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.224 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.229	α = 90
b = 75.229	β = 90
c = 105.758	γ = 120

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-10-07 
Deposition Author(s): Zhang, H.M., Li, M., Chang, W.R.

Revision History  

• Version 1.0: 2015-10-07
  Type: Initial release
  
• Version 1.1: 2019-10-16
  Changes: Data collection
• Version 1.2: 2019-12-25
  Changes: Data collection, Database references
• Version 1.3: 2023-11-08
  Changes: Data collection, Database references, Refinement description