1JFI Transcription Dna date Jun 20, 2001
title Crystal Structure Of The Nc2-Tbp-Dna Ternary Complex
authors K.Kamada, F.Shu, H.Chen, S.Malik, G.Stelzer, R.G.Roeder, M.Meister S.K.Burley, New York Sgx Research Center For Structural Geno (Nysgxrc)
compound source
Molecule: 5'-D(Tptpgpgpcptpaptpapapapapgpgpg C)-3';
Chain: D
Engineered: Yes
Other_details: 19 Base-Pair Tata-Containing Oligonucleotide Strand;
 Synthetic: Yes

Molecule: 5'-D(Ggpapgpcpcpcptptptptpaptpapgp A)-3';
Chain: E
Engineered: Yes
Other_details: 19 Base-Pair Tata-Containing Oligonucleotide Strand;
Synthetic: Yes

Molecule: Transcription Regulator Nc2 Alpha Chain
Chain: A
Fragment: Residues 1-77
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nc2 Alpha (Drap1)
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11d

Molecule: Transcription Regulator Nc2 Beta Chain
Chain: B
Synonym: Dr1 Protein
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nc2 Beta (Dr1)
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet28a

Molecule: Tata-Box-Binding Protein (Tbp)
Chain: C
Fragment: Residues 359-539
Synonym: Transcription Initiation Factor Tfiid
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Tbp
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet15b
symmetry Space Group: C 2 2 21
R_factor 0.233 R_Free 0.277
crystal
cell
length a length b length c angle alpha angle beta angle gamma
76.684 119.075 155.076 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.62 Å
note 1JFI (Molecule of the Month:pdb67)is a representative structure
related structures by homologous chain: 1C9B, 1TBP
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


Primary referenceCrystal structure of negative cofactor 2 recognizing the TBP-DNA transcription complex., Kamada K, Shu F, Chen H, Malik S, Stelzer G, Roeder RG, Meisterernst M, Burley SK, Cell 2001 Jul 13;106(1):71-81. PMID:11461703
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (80 Kb) [Save to disk]
  • Biological Unit Coordinates (1jfi.pdb1.gz) 75 Kb
  • CSU: Contacts of Structural Units for 1JFI
  • Likely Quarternary Molecular Structure file(s) for 1JFI
  • Structure Factors (245 Kb)
  • Retrieve 1JFI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1JFI from S2C, [Save to disk]
  • Re-refined 1jfi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1JFI 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 1JFI
  • 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 1JFI, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1jfia_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1jfib_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1jfic1, region C:356-456 [Jmol] [rasmolscript] [script source]
        - Domain d1jfic2, region C:457-538 [Jmol] [rasmolscript] [script source]
  • 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: [1jfi_E] [1jfi_C] [1jfi_D] [1jfi_B] [1jfi_A] [1jfi]
  • SWISS-PROT database: [Q14919] [Q01658] [P20226]
  • Domain organization of [NC2A_HUMAN] [NC2B_HUMAN] [TBP_HUMAN] by SWISSPFAM
    • Other resources with information on 1JFI
  • Community annotation for 1JFI 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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