4U68 | pdb_00004u68

Crystal structure of Rhino chromodomain in complex with H3K9me3

• PDB DOI: https://doi.org/10.2210/pdb4U68/pdb

• 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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

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

• PubMed: 25613572 
• DOI: https://doi.org/10.1038/cr.2015.10
• Primary Citation of Related Structures:  
  4U68

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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.
Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA.
1] National Laboratory of Biomacromolecules, Chinese Academy of Sciences, Beijing 100101, China [2] University of Chinese Academy of Sciences, Beijing 100049, China.
Collaborative Innovation Center of Genetics and Development, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China.
National Laboratory of Biomacromolecules, Chinese Academy of Sciences, Beijing 100101, China.
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.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content 

• Total Structure Weight: 28.95 kDa 
• Atom Count: 1,853 
• Modeled Residue Count: 203 
• Deposited Residue Count: 258 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rhino	A, B, C	75	Drosophila melanogaster	Mutation(s): 0  Gene Names: rhi, rhino, CG10683, Dmel_CG10683
UniProt
Find proteins for Q7JXA8 (Drosophila melanogaster) Explore Q7JXA8  Go to UniProtKB:  Q7JXA8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H3K9me3	D, E, F	11	Drosophila melanogaster	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431 GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M3L	D, E, F	L-PEPTIDE LINKING	C9 H21 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.206 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.946	α = 90
b = 67.679	β = 106.46
c = 79.75	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
Coot	model building
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-08-05 
Deposition Author(s): Yu, B.W., Huang, Y.

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Funding Organization	Location	Grant Number
Ministry of Science and Technology of China	China	2012CB910502
National Natural Science Foundation of China	China	31270774
Strategic Priority Research Program	China	XDB08010202

Revision History  

• 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