4U68

Crystal structure of Rhino chromodomain in complex with H3K9me3

  • Classification: PROTEIN BINDING
  • Organism(s): Drosophila melanogaster
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2014-07-28 Released: 2015-08-05 
  • Deposition Author(s): Yu, B.W., Huang, Y.
  • Funding Organization(s): Ministry of Science and Technology of China, National Natural Science Foundation of China, Strategic Priority Research Program

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history. 


Literature

Structural insights into Rhino-mediated germline piRNA cluster formation

Yu, B.W., Cassani, M., Wang, M., Liu, M., Ma, J., Li, G., Zhang, Z., Huang, Y.

(2015) Cell Res 25: 525-528

  • DOI: https://doi.org/10.1038/cr.2015.10
  • Primary Citation of Related Structures:  
    4U68
    • Organizational Affiliation: 

    1] State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China [2] University of Chinese Academy of Sciences, Beijing 100049, China.


Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Rhino
A, B, C
75Drosophila melanogasterMutation(s): 0 
Gene Names: rhi, rhino, CG10683, Dmel_CG10683
UniProt
Find proteins for Q7JXA8 (Drosophila melanogaster)
Explore Q7JXA8 
Go to UniProtKB:  Q7JXA8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7JXA8
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
H3K9me3
D, E, F
11Drosophila melanogasterMutation(s): 0 
UniProt
Find proteins for P02299 (Drosophila melanogaster)
Explore P02299 
Go to UniProtKB:  P02299
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02299
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
M3L
Query on M3L
D, E, F
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.946α = 90
b = 67.679β = 106.46
c = 79.75γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
Cootmodel building
PHENIXrefinement

Structure Validation

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View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Ministry of Science and Technology of ChinaChina2012CB910502
National Natural Science Foundation of ChinaChina31270774
Strategic Priority Research ProgramChinaXDB08010202

Revision History  (Full details and data files)

  • Version 1.0: 2015-08-05
    Type: Initial release
  • Version 1.1: 2016-05-25
    Changes: Database references
  • Version 1.2: 2019-10-23
    Changes: Data collection, Derived calculations
  • Version 2.0: 2023-07-26
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 2.1: 2023-11-08
    Changes: Data collection, Refinement description