3MLP Transcription Dna date Apr 17, 2010
title Early B-Cell Factor 1 (Ebf1) Bound To Dna
authors N.Treiber, T.Treiber, G.Zocher, R.Grosschedl
compound source
Molecule: Transcription Factor Coe1
Chain: A, B, E, F
Fragment: Dna Binding Domain
Synonym: Ebf1, Oe-1, Oe-1, Early B-Cell Factor
Engineered: Yes
Mutation: Yes
Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Gene: Ebf1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosetta
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet23d

Molecule: Dna (5'- D(Cptptptpaptptpcpcpcpaptpgpgpgpapaptpap 3');
Chain: C, D, G, H
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Synthetic Oligonucleotide
symmetry Space Group: P 1
R_factor 0.204 R_Free 0.264
crystal
cell
length a length b length c angle alpha angle beta angle gamma
70.490 78.690 103.570 88.99 90.00 77.81
method X-Ray Diffractionresolution 2.80 Å
ligand CIT, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B


Primary referenceStructure of an Ebf1:DNA complex reveals unusual DNA recognition and structural homology with Rel proteins., Treiber N, Treiber T, Zocher G, Grosschedl R, Genes Dev. 2010 Oct 15;24(20):2270-5. Epub 2010 Sep 28. PMID:20876732
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (500 Kb) [Save to disk]
  • Biological Unit Coordinates (3mlp.pdb1.gz) 257 Kb
  • Biological Unit Coordinates (3mlp.pdb2.gz) 236 Kb
  • LPC: Ligand-Protein Contacts for 3MLP
  • CSU: Contacts of Structural Units for 3MLP
  • Structure Factors (412 Kb)
  • Retrieve 3MLP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3MLP from S2C, [Save to disk]
  • Re-refined 3mlp structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3MLP 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 3MLP
  • 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
  • 3D motif for 3MLP, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3mlp_F] [3mlp_A] [3mlp_B] [3mlp_D] [3mlp] [3mlp_H] [3mlp_C] [3mlp_G] [3mlp_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3MLP: [HLH] [IPT ] by SMART
  • Other resources with information on 3MLP
  • Community annotation for 3MLP at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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