3TZD

Crystal structure of the complex of Human Chromobox Homolog 3 (CBX3)

• PDB DOI: https://doi.org/10.2210/pdb3TZD/pdb

• Classification: TRANSCRIPTION/DNA binding Protein
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2011-09-27 Released: 2012-03-07 
• Deposition Author(s): Amaya, M.F., Ravichandran, M., Loppnau, P., Kozieradzki, I., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Bountra, C., Bochkarev, A., Min, J., Ouyang, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.231 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 

Literature

Structural basis of the chromodomain of Cbx3 bound to methylated peptides from histone h1 and G9a.

Ruan, J., Ouyang, H., Amaya, M.F., Ravichandran, M., Loppnau, P., Min, J., Zang, J.

(2012) PLoS One 7: e35376-e35376

• PubMed: 22514736 
• DOI: https://doi.org/10.1371/journal.pone.0035376
• Primary Citation of Related Structures:  
  3DM1, 3TZD


• PubMed Abstract: 
  

  HP1 proteins are highly conserved heterochromatin proteins, which have been identified to be structural adapters assembling a variety of macromolecular complexes involved in regulation of gene expression, chromatin remodeling and heterochromatin formation. Much evidence shows that HP1 proteins interact with numerous proteins including methylated histones, histone methyltransferases and so on. Cbx3 is one of the paralogues of HP1 proteins, which has been reported to specifically recognize trimethylated histone H3K9 mark, and a consensus binding motif has been defined for the Cbx3 chromodomain.

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Organizational Affiliation: 

Hefei National Laboratory for Physical Sciences, Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui, People's Republic of China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 8.99 kDa 
• Atom Count: 684 
• Modelled Residue Count: 70 
• Deposited Residue Count: 77 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromobox protein homolog 3	A	58	Homo sapiens	Mutation(s): 0  Gene Names: CBX3
UniProt & NIH Common Fund Data Resources
Find proteins for Q13185 (Homo sapiens) Explore Q13185  Go to UniProtKB:  Q13185
PHAROS:  Q13185 GTEx:  ENSG00000122565

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H1.4	B [auth T]	19	Homo sapiens	Mutation(s): 0  Gene Names: HIST1H1E, H1F4
UniProt & NIH Common Fund Data Resources
Find proteins for P10412 (Homo sapiens) Explore P10412  Go to UniProtKB:  P10412
PHAROS:  P10412 GTEx:  ENSG00000168298

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	B [auth T]	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 0.231 
• R-Value Work: 0.199 
• R-Value Observed: 0.200 
• Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.209	α = 90
b = 92.209	β = 90
c = 92.209	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-07 
Deposition Author(s): Amaya, M.F., Ravichandran, M., Loppnau, P., Kozieradzki, I., Edwards, A.M., Arrowsmith, C.H., Weigelt, J., Bountra, C., Bochkarev, A., Min, J., Ouyang, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2012-03-07
  Type: Initial release
  
• Version 1.1: 2013-01-23
  Changes: Database references