5IN1 | pdb_00005in1

Crystal Structure of the MRG701 chromodomain

• PDB DOI: https://doi.org/10.2210/pdb5IN1/pdb

• Classification: TRANSCRIPTION
• Organism(s): Oryza sativa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-03-07 Released: 2017-03-01 
• Deposition Author(s): Huang, Y., Liu, 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: 1.40 Å
• R-Value Free: 
  0.204 (Depositor), 0.204 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.184 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Structural studies on MRG701 chromodomain reveal a novel dimerization interface of MRG proteins in green plants

Liu, Y., Wu, H., Yu, Y., Huang, Y.

(2016) Protein Cell 7: 792-803

• PubMed: 27638467 
• DOI: https://doi.org/10.1007/s13238-016-0310-5
• Primary Citation Related Structures: 
  5IN1


• PubMed Abstract: 
  

  MRG proteins are conserved during evolution in fungi, flies, mammals and plants, and they can exhibit diversified functions. The animal MRGs were found to form various complexes to activate gene expression. Plant MRG1/2 and MRG702 were reported to be involved in the regulation of flowering time via binding to H3K36me3-marked flowering genes. Herein, we determined the crystal structure of MRG701 chromodomain (MRG701 ^CD ). MRG701 ^CD forms a novel dimerization fold both in crystal and in solution. Moreover, we found that the dimerization of MRG chromodomains is conserved in green plants. Our findings may provide new insights into the mechanism of MRGs in regulation of gene expression in green plants.

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Organizational Affiliation: 
• State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
University of Chinese Academy of Sciences, Beijing, 100049, China.
State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development Institute of Plant Biology, School of Life Science, Fudan University, Shanghai, 200433, China.
State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 17.85 kDa 
• Atom Count: 1,502 
• Modeled Residue Count: 142 
• Deposited Residue Count: 144 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MRG701	A, B	72	Oryza sativa	Mutation(s): 0
UniProt
Find proteins for Q2R2X7 (Oryza sativa subsp. japonica) Explore Q2R2X7  Go to UniProtKB:  Q2R2X7

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth B], D [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	E [auth B], F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.204 (Depositor), 0.204 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.184 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.786	α = 90
b = 59.801	β = 102.58
c = 40.616	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data collection
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-03-01 
Deposition Author(s): Huang, Y., Liu, 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: 2017-03-01
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Refinement description