5LTY | pdb_00005lty

Homeobox transcription factor CDX2 bound to methylated DNA

• PDB DOI: https://doi.org/10.2210/pdb5LTY/pdb
• NAKB: 5LTY

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-09-07 Released: 2017-05-31 
• Deposition Author(s): Morgunova, E., Popov, A., Taipale, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 
  0.242 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.205 (DCC) 
• R-Value Observed: 
  0.204 (Depositor) 

Starting Model: experimental

Literature

Impact of cytosine methylation on DNA binding specificities of human transcription factors.

Yin, Y., Morgunova, E., Jolma, A., Kaasinen, E., Sahu, B., Khund-Sayeed, S., Das, P.K., Kivioja, T., Dave, K., Zhong, F., Nitta, K.R., Taipale, M., Popov, A., Ginno, P.A., Domcke, S., Yan, J., Schubeler, D., Vinson, C., Taipale, J.

(2017) Science 356

• PubMed: 28473536 
• DOI: https://doi.org/10.1126/science.aaj2239
• Primary Citation Related Structures: 
  5EF6, 5EGO, 5HOD, 5LTY, 5LUX


• PubMed Abstract: 
  

  The majority of CpG dinucleotides in the human genome are methylated at cytosine bases. However, active gene regulatory elements are generally hypomethylated relative to their flanking regions, and the binding of some transcription factors (TFs) is diminished by methylation of their target sequences. By analysis of 542 human TFs with methylation-sensitive SELEX (systematic evolution of ligands by exponential enrichment), we found that there are also many TFs that prefer CpG-methylated sequences. Most of these are in the extended homeodomain family. Structural analysis showed that homeodomain specificity for methylcytosine depends on direct hydrophobic interactions with the methylcytosine 5-methyl group. This study provides a systematic examination of the effect of an epigenetic DNA modification on human TF binding specificity and reveals that many developmentally important proteins display preference for mCpG-containing sequences.

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Organizational Affiliation: 
• Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden.
Genome-Scale Biology Program, Post Office Box 63, FI-00014 University of Helsinki, Helsinki, Finland.
Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Room 3128, Building 37, Bethesda, MD 20892, USA.
European Synchrotron Radiation Facility, 38043 Grenoble, France.
Friedrich-Miescher-Institute for Biomedical Research (FMI), Maulbeerstrasse 66, 4058 Basel, Switzerland.
Faculty of Science, University of Basel, Petersplatz 1, 4003 Basel, Switzerland.
Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE 141 83 Stockholm, Sweden. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 39.86 kDa 
• Atom Count: 2,757 
• Modeled Residue Count: 213 
• Deposited Residue Count: 214 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Homeobox protein CDX-2	C [auth K], D [auth M]	71	Homo sapiens	Mutation(s): 0  Gene Names: CDX2, CDX3
UniProt & NIH Common Fund Data Resources
Find proteins for Q99626 (Homo sapiens) Explore Q99626  Go to UniProtKB:  Q99626
PHAROS:  Q99626 GTEx:  ENSG00000165556

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*TP*GP*TP*GP*TP*TP*TP*TP*AP*(5CM)P*GP*AP*CP*CP*TP*CP*C)-3')	A, B	18	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*GP*AP*GP*GP*TP*(5CM)P*GP*TP*AP*AP*AP*AP*CP*AP*CP*AP*A)-3')	E [auth F], F [auth E]	18	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free:  0.242 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.205 (DCC) 
• R-Value Observed: 0.204 (Depositor) 

Space Group: I 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.882	α = 90
b = 46.613	β = 98.46
c = 120.428	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-31 
Deposition Author(s): Morgunova, E., Popov, A., Taipale, J.

Revision History  

• Version 1.0: 2017-05-31
  Type: Initial release
  
• Version 1.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description