5EEA Transcription date Oct 22, 2015
title Structure Of Hoxb13-Dna(Caa) Complex
authors E.Morgunova, Y.Yin, A.Jolma, A.Popov, J.Taipale
compound source
Molecule: Dna (5'- D(Ptptpgptpgptptptptpaptptpgpgpgptpcpc)-3
Chain: D, C, H, K
Engineered: Yes
Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (5'- D(Pgpgpapcpcpcpapaptpapapapapcpapcpapa)-3
Chain: E, F, I, L
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Homeobox Protein Hox-B13
Chain: B, A, G, J
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 1 2 1
R_factor 0.251 R_Free 0.297
crystal
cell
length a length b length c angle alpha angle beta angle gamma
77.356 57.918 101.278 90.00 101.57 90.00
method X-Ray Diffractionresolution 2.20 Å
Gene
Ontology
ChainFunctionProcessComponent
A, J, G, B


Primary referenceTwo distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima., Morgunova E, Yin Y, Das PK, Jolma A, Zhu F, Popov A, Xu Y, Nilsson L, Taipale J, Elife. 2018 Apr 11;7. pii: 32963. doi: 10.7554/eLife.32963. PMID:29638214
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (118 Kb) [Save to disk]
  • Biological Unit Coordinates (5eea.pdb1.gz) 29 Kb
  • Biological Unit Coordinates (5eea.pdb2.gz) 29 Kb
  • Biological Unit Coordinates (5eea.pdb3.gz) 29 Kb
  • Biological Unit Coordinates (5eea.pdb4.gz) 29 Kb
  • CSU: Contacts of Structural Units for 5EEA
  • Structure Factors (3003 Kb)
  • Retrieve 5EEA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5EEA from S2C, [Save to disk]
  • Re-refined 5eea structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5EEA 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 5EEA
  • 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 5eea from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5eea_E] [5eea_G] [5eea_F] [5eea_H] [5eea_A] [5eea_B] [5eea_K] [5eea_I] [5eea_C] [5eea_L] [5eea] [5eea_D] [5eea_J]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 5EEA: [HOX ] by SMART
  • Other resources with information on 5EEA
  • Community annotation for 5EEA at PDBWiki (http://pdbwiki.org)

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