1OOA Transcription Rna date Mar 03, 2003
title Crystal Structure Of Nf-Kb(P50)2 Complexed To A High- Affinity Rna Aptamer
authors D.B.Huang, D.Vu, L.A.Cassiday, J.M.Zimmerman, L.J.Maher Iii, G.Ghosh
compound source
Molecule: Rna Aptamer
Chain: C, D
Fragment: 29-Nt Rna Aptamer
Engineered: Yes
Synthetic: Yes
Other_details: Synthesis Of The Rna Fragment From The T7 Promoter In Vitro Transcription;

Molecule: Nuclear Factor Nf-Kappa-B P105 Subunit
Chain: A, B
Synonym: Dna-Binding Factor Kbf1, Ebp- 1, Nf-Kappa-B1
P84nf-Kappa-B1 P98, [Contains: Nuclear Factor Nf- Kappa-B P50 Subunit];
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: House Mouse
Organism_taxid: 10090
Gene: Nfkb1
Expression_system: Escherichia Coli Bl21
Expression_system_taxid: 511693
Expression_system_strain: Bl21
Expression_system_plasmid: Pet29b
symmetry Space Group: C 1 2 1
R_factor 0.208 R_Free 0.248
crystal
cell
length a length b length c angle alpha angle beta angle gamma
76.753 151.059 95.628 90.00 105.95 90.00
method X-Ray Diffractionresolution 2.45 Å
related structures by homologous chain: 1NFK, 1SVC
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structure of NF-kappaB (p50)2 complexed to a high-affinity RNA aptamer., Huang DB, Vu D, Cassiday LA, Zimmerman JM, Maher LJ 3rd, Ghosh G, Proc Natl Acad Sci U S A 2003 Aug 5;100(16):9268-73. Epub 2003 Jul 28. PMID:12886018
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (136 Kb) [Save to disk]
  • Biological Unit Coordinates (1ooa.pdb1.gz) 68 Kb
  • Biological Unit Coordinates (1ooa.pdb2.gz) 66 Kb
  • CSU: Contacts of Structural Units for 1OOA
  • Likely Quarternary Molecular Structure file(s) for 1OOA
  • Retrieve 1OOA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1OOA from S2C, [Save to disk]
  • View 1OOA 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 1OOA
  • 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
  • 3D motif for 1OOA, from MSDmotif at EBI
  • Structure summary from SCOR (Structural Classification of RNA)
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ooaa1, region A:251-350 [Jmol] [rasmolscript] [script source]
        - Domain d1ooaa2, region A:38-250 [Jmol] [rasmolscript] [script source]
        - Domain d1ooab1, region B:251-350 [Jmol] [rasmolscript] [script source]
        - Domain d1ooab2, region B:38-250 [Jmol] [rasmolscript] [script source]
  • Fold representative 1ooa from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1ooa] [1ooa_A] [1ooa_C] [1ooa_B] [1ooa_D]
  • SWISS-PROT database: [P25799]
  • Domain organization of [NFKB1_MOUSE] by SWISSPFAM
  • Domain found in 1OOA: [IPT ] by SMART
  • Other resources with information on 1OOA
  • Community annotation for 1OOA 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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