2YPA Immune System date Oct 30, 2012
title Structure Of The Scl:E47:Lmo2:Ldb1 Complex Bound To Dna
authors K.El Omari, S.J.Hoosdally, K.Tuladhar, D.Karia, E.Ponsele, O.Plat P.Vyas, R.Patient, C.Porcher, E.J.Mancini
compound source
Molecule: T-Cell Acute Lymphocytic Leukemia Protein 1
Chain: A
Fragment: Bhlh, Residues 180-253
Synonym: Tal-1, Class A Basic Helix-Loop-Helix Protein 17, Stem Cell Protein, T-Cell Leukemialymphoma Protein 5, Scl
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Transcription Factor E2-Alpha
Chain: B
Fragment: Residues 535-613
Synonym: Class B Basic Helix-Loop-Helix Protein 21, Bhlhb21 Immunoglobulin Enhancer-Binding Factor E12e47, Immunoglob Transcript Ion Factor 1, Kappa-E2-Binding Factor, Transcri Factor 3, Tcf-3, Transcription Factor Itf-1, E47;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Rhombotin-2
Chain: C
Fragment: Lim, Residues 25-156
Synonym: Cysteine-Rich Protein Ttg-2, Lim Domain Only Prote Lmo-2, T-Cell Translocation Protein 2, Lmo2;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Lim Domain-Binding Protein 1
Chain: D
Fragment: Lid, Residues 336-375
Synonym: Ldb-1, Carboxyl-Terminal Lim Domain-Binding Protei Clim-2, Lim Domain-Binding Factor Clim2, Hldb1, Nuclear Li Interactor, Ldb1;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Ebox Forward
Chain: E

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606

Molecule: Ebox Reverse
Chain: F

Synthetic: Yes
Organism_scientific: Homo Sapiens
Organism_taxid: 9606
symmetry Space Group: F 2 2 2
R_factor 0.22401 R_Free 0.26945
crystal
cell
length a length b length c angle alpha angle beta angle gamma
102.966 141.044 148.793 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
ligand ZN enzyme
Primary referenceStructural Basis for LMO2-Driven Recruitment of the SCL:E47bHLH Heterodimer to Hematopoietic-Specific Transcriptional Targets., El Omari K, Hoosdally SJ, Tuladhar K, Karia D, Hall-Ponsele E, Platonova O, Vyas P, Patient R, Porcher C, Mancini EJ, Cell Rep. 2013 Jul 11;4(1):135-47. doi: 10.1016/j.celrep.2013.06.008. Epub 2013, Jul 3. PMID:23831025
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (130 Kb) [Save to disk]
  • Biological Unit Coordinates (2ypa.pdb1.gz) 123 Kb
  • LPC: Ligand-Protein Contacts for 2YPA
  • CSU: Contacts of Structural Units for 2YPA
  • Structure Factors (219 Kb)
  • Retrieve 2YPA in mmCIF format [Save to disk]
  • Re-refined 2ypa structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2YPA 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 2YPA
  • 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
  • 3D motif for 2YPA, from MSDmotif at EBI
  • Fold representative 2ypa from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ypa_C] [2ypa] [2ypa_B] [2ypa_A] [2ypa_F] [2ypa_D] [2ypa_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 2YPA: [HLH] [LIM ] by SMART
  • Other resources with information on 2YPA
  • Community annotation for 2YPA at PDBWiki (http://pdbwiki.org)

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