5EF6 Transcription date Oct 23, 2015
title Structure Of Hoxb13 Complex With Methylated Dna
authors E.Morgunova, Y.Yin, A.Jolma, A.Popov, J.Taipale
compound source
Molecule: Homeobox Protein Hox-B13
Chain: A, B, G, J
Fragment: Unp Residues 217-278
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Hoxb13
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Rosetta
Expression_system_plasmid: Petg20a

Molecule: Dna (5'-D(Ptptpgptpgptptptptpap(5cm) Pgpapgpgptpcpc)-3');
Chain: C, D, H, K
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Pgpgpapcpcptp(5cm) Pgptpapapapapcpapcpapa)-3');
Chain: F, E, I, L
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1 2 1
R_factor 0.291 R_Free 0.320
length a length b length c angle alpha angle beta angle gamma
77.969 55.557 102.010 90.00 102.24 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand 5CM enzyme
A, J, G, B

Primary referenceImpact 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 PK, Kivioja T, Dave K, Zhong F, Nitta KR, Taipale M, Popov A, Ginno PA, Domcke S, Yan J, Schubeler D, Vinson C, Taipale J, Science. 2017 May 5;356(6337). pii: eaaj2239. doi: 10.1126/science.aaj2239. PMID:28473536
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (111 Kb) [Save to disk]
  • Biological Unit Coordinates (5ef6.pdb1.gz) 27 Kb
  • Biological Unit Coordinates (5ef6.pdb2.gz) 27 Kb
  • Biological Unit Coordinates (5ef6.pdb3.gz) 27 Kb
  • Biological Unit Coordinates (5ef6.pdb4.gz) 27 Kb
  • LPC: Ligand-Protein Contacts for 5EF6
  • CSU: Contacts of Structural Units for 5EF6
  • Structure Factors (1128 Kb)
  • Retrieve 5EF6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5EF6 from S2C, [Save to disk]
  • Re-refined 5ef6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5EF6 in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 5EF6
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5ef6 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ef6_A] [5ef6_B] [5ef6_G] [5ef6_F] [5ef6_L] [5ef6] [5ef6_D] [5ef6_I] [5ef6_K] [5ef6_E] [5ef6_H] [5ef6_J] [5ef6_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5EF6
  • Community annotation for 5EF6 at PDBWiki (http://pdbwiki.org)

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