5EGO Transcription date Oct 27, 2015
title Hoxb13-Meis1 Heterodimer Bound To Methylated Dna
authors E.Morgunova, Y.Yin, A.Jolma, A.Popov, J.Taipale
compound source
Molecule: Homeobox Protein Meis1
Chain: A
Fragment: Unp Residues 279-333
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Meis1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_variant: Rosetta
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Petg20a

Molecule: Dna (5'-D(Pgptptpgpapcpapgptptptptpa Pgpapgpg)-3');
Chain: D
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'-D(Cpcptp(5cm) Pgptpapapapapcptpgptpcpapapc)-3');
Chain: E
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Homeobox Protein Hox-B13
Chain: B
Fragment: Unp Residues 217-277
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_vector_type: Plasmid
Expression_system_plasmid: Petg20a
symmetry Space Group: P 21 21 21
R_factor 0.228 R_Free 0.265
crystal
cell
length a length b length c angle alpha angle beta angle gamma
40.976 51.480 113.575 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.54 Å
ligand 5CM enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


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] (41 Kb) [Save to disk]
  • Biological Unit Coordinates (5ego.pdb1.gz) 36 Kb
  • LPC: Ligand-Protein Contacts for 5EGO
  • CSU: Contacts of Structural Units for 5EGO
  • Structure Factors (183 Kb)
  • Retrieve 5EGO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5EGO from S2C, [Save to disk]
  • Re-refined 5ego structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5EGO 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 5EGO
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5ego from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5ego] [5ego_A] [5ego_D] [5ego_E] [5ego_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5EGO: [HOX ] by SMART
  • Other resources with information on 5EGO
  • Community annotation for 5EGO at PDBWiki (http://pdbwiki.org)

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