2I9T Transcription Dna date Sep 06, 2006
title Structure Of Nf-Kb P65-P50 Heterodimer Bound To Prdii Elemen Interferon Promoter
authors C.R.Escalante, L.Shen, D.Thanos, A.K.Aggarwal
compound source
Molecule: 5'-D(Apgptpgpgpgpapapaptptpcpcptpc 3';
Chain: C
Engineered: Yes
Other_details: Prdii Dna Element
Synthetic: Yes

Molecule: 5'-D(Cpapgpapgpgpapaptptptpcpcpcpa 3';
Chain: D
Engineered: Yes

Synthetic: Yes

Molecule: Transcription Factor P65
Chain: A
Fragment: Residues 19-291
Synonym: Nuclear Factor Nf-Kappa-B P65 Subunit
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Gene: Rela, Nfkb3
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-15b

Molecule: Nuclear Factor Nf-Kappa-B P105 Subunit
Chain: B
Fragment: Residues 39-350
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Gene: Nfkb1
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-9a
symmetry Space Group: P 21 21 2
R_factor 0.233 R_Free 0.288
crystal
cell
length a length b length c angle alpha angle beta angle gamma
97.620 166.110 60.050 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.80 Å
Gene
Ontology
ChainFunctionProcessComponent
A


B


Primary referenceStructure of NF-kappaB p50/p65 heterodimer bound to the PRDII DNA element from the interferon-beta promoter., Escalante CR, Shen L, Thanos D, Aggarwal AK, Structure. 2002 Mar;10(3):383-91. PMID:12005436
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (113 Kb) [Save to disk]
  • Biological Unit Coordinates (2i9t.pdb1.gz) 107 Kb
  • CSU: Contacts of Structural Units for 2I9T
  • Likely Quarternary Molecular Structure file(s) for 2I9T
  • Structure Factors (179 Kb)
  • Retrieve 2I9T in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2I9T from S2C, [Save to disk]
  • Re-refined 2i9t structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2I9T 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 2I9T
  • 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 2I9T, from MSDmotif at EBI
  • Fold representative 2i9t from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2i9t_D] [2i9t] [2i9t_B] [2i9t_A] [2i9t_C]
  • SWISS-PROT database: [P25799] [Q04207]
  • Domain organization of [NFKB1_MOUSE] [TF65_MOUSE] by SWISSPFAM
  • Domain found in 2I9T: [IPT ] by SMART
  • Other resources with information on 2I9T
  • Community annotation for 2I9T 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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