1TF6 Transcription Dna date Mar 02, 1998
title Co-Crystal Structure Of Xenopus Tfiiia Zinc Finger Domain Bound To The 5s Ribosomal Rna Gene Internal Control Region
authors R.T.Nolte, R.M.Conlin, S.C.Harrison, R.S.Brown
compound source
Molecule: Dna (5'- D(Apcpgpgpgpcpcptpgpgptptpapgptpapc Pcptpgpgpap Tpgpgpgpapgpapcpc)-3');
Chain: B, E
Fragment: Internal Promoter Region
Synonym: 5s Ribosomal Rna Gene
Engineered: Yes
Synthetic: Yes

Molecule: Dna (5'- D(Tpgpgptpcptpcpcpcpaptpcpcpapgpgpt Papcptpapap Cpcpapgpgpcpcpcpg)-3');
Chain: C, F
Fragment: Internal Promoter Region
Synonym: 5s Ribosomal Rna Gene
Engineered: Yes

Synthetic: Yes

Molecule: Protein (Transcription Factor Iiia)
Chain: A, D
Fragment: Nh2-Terminal Six Fingers, Residue 1-190
Synonym: Transcription Factor Iiia
Engineered: Yes

Organism_scientific: Xenopus Laevis
Organism_common: African Clawed Frog
Organism_taxid: 8355
Organ: Ovary
Cell: Oocyte
Organelle: Nucleus
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_cellular_location: Inclusion Body
Expression_system_plasmid: Prset B
Other_details: Cdna
symmetry Space Group: P 1
R_factor 0.308 R_Free 0.363
length a length b length c angle alpha angle beta angle gamma
64.180 64.712 78.035 90.07 92.98 102.95
method X-Ray Diffractionresolution 3.10 Å
ligand ZN enzyme
note 1TF6 (Molecule of the Month:pdb87)
Primary referenceDiffering roles for zinc fingers in DNA recognition: structure of a six-finger transcription factor IIIA complex., Nolte RT, Conlin RM, Harrison SC, Brown RS, Proc Natl Acad Sci U S A 1998 Mar 17;95(6):2938-43. PMID:9501194
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (118 Kb) [Save to disk]
  • Biological Unit Coordinates (1tf6.pdb1.gz) 57 Kb
  • Biological Unit Coordinates (1tf6.pdb2.gz) 57 Kb
  • LPC: Ligand-Protein Contacts for 1TF6
  • CSU: Contacts of Structural Units for 1TF6
  • Likely Quarternary Molecular Structure file(s) for 1TF6
  • Structure Factors (284 Kb)
  • Retrieve 1TF6 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1TF6 from S2C, [Save to disk]
  • Re-refined 1tf6 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1TF6 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 1TF6
  • 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 1TF6, from MSDmotif at EBI
  • Genome occurence of 1TF6's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1tf6a1, region A:10-40 [Jmol] [rasmolscript] [script source]
        - Domain d1tf6a4, region A:101-131 [Jmol] [rasmolscript] [script source]
        - Domain d1tf6a5, region A:132-160 [Jmol] [rasmolscript] [script source]
        - Domain d1tf6a6, region A:161-188 [Jmol] [rasmolscript] [script source]
        - Domain d1tf6a2, region A:41-70 [Jmol] [rasmolscript] [script source]
        - Domain d1tf6a3, region A:71-100 [Jmol] [rasmolscript] [script source]
        - Domain d1tf6d4, region D:101-131 [Jmol] [rasmolscript] [script source]
        - Domain d1tf6d5, region D:132-160 [Jmol] [rasmolscript] [script source]
        - Domain d1tf6d6, region D:161-188 [Jmol] [rasmolscript] [script source]
        - Domain d1tf6d2, region D:41-70 [Jmol] [rasmolscript] [script source]
        - Domain d1tf6d1, region D:7-40 [Jmol] [rasmolscript] [script source]
        - Domain d1tf6d3, region D:71-100 [Jmol] [rasmolscript] [script source]
  • Fold representative 1tf6 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1tf6_A] [1tf6_C] [1tf6_D] [1tf6_F] [1tf6_B] [1tf6] [1tf6_E]
  • SWISS-PROT database: [P03001]
  • Domain organization of [TF3A_XENLA] by SWISSPFAM
  • Domain found in 1TF6: [ZnF_C2H2 ] by SMART
  • Other resources with information on 1TF6
  • Community annotation for 1TF6 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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