1YTF Transcription Dna date Apr 05, 1996
title Yeast Tfiiatbpdna Complex
authors S.Tan, Y.Hunziker, D.F.Sargent, T.J.Richmond
compound source
Molecule: Dna (5'- D(Tpgptpaptpgptpaptpaptpapapapapc)-3');
Chain: E
Engineered: Yes
Synthetic: Yes

Molecule: Dna (5'- D(Gptptptptpaptpaptpapcpaptpapcpa)-3');
Chain: F
Engineered: Yes

Synthetic: Yes

Molecule: Protein (Tata Binding Protein (Tbp))
Chain: A
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Protein (Transcription Factor Iia - Toa1n Subunit);
Chain: B
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Other_details: Reconstituted From 3 Individually Overexpressed Polypeptides;

Molecule: Protein (Transcription Factor Iia - Toa1c Subunit);
Chain: C
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Protein (Transcription Factor Iia - Toa2 Subunit);
Chain: D
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 21 21 21
R_factor 0.235 R_Free 0.297
crystal
cell
length a length b length c angle alpha angle beta angle gamma
59.150 93.050 117.830 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.50 Å
note 1YTF (Molecule of the Month:pdb67)
related structures by homologous chain: 1NH2, 1QNC, 1TBP
Gene
Ontology
ChainFunctionProcessComponent
A


B


C


D


Primary referenceCrystal structure of a yeast TFIIA/TBP/DNA complex., Tan S, Hunziker Y, Sargent DF, Richmond TJ, Nature 1996 May 9;381(6578):127-51. PMID:8610010
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (78 Kb) [Save to disk]
  • Biological Unit Coordinates (1ytf.pdb1.gz) 73 Kb
  • CSU: Contacts of Structural Units for 1YTF
  • Likely Quarternary Molecular Structure file(s) for 1YTF
  • Retrieve 1YTF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1YTF from S2C, [Save to disk]
  • View 1YTF 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 1YTF
  • 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 1YTF, from MSDmotif at EBI
  • Genome occurence of 1YTF's fold from GeneCensus
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1ytfa2, region A:156-240 [Jmol] [rasmolscript] [script source]
        - Domain d1ytfa1, region A:61-155 [Jmol] [rasmolscript] [script source]
        - Domain d1ytfb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1ytfc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1ytfd1, region D:5-54 [Jmol] [rasmolscript] [script source]
        - Domain d1ytfd2, region D:55-119 [Jmol] [rasmolscript] [script source]
  • Fold representative 1ytf 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: [1ytf_D] [1ytf_B] [1ytf_C] [1ytf_F] [1ytf_E] [1ytf_A] [1ytf]
  • SWISS-PROT database: [P13393] [P32773] [P32774]
  • Domain organization of [TBP_YEAST] [TOA1_YEAST] [TOA2_YEAST] by SWISSPFAM
  • Other resources with information on 1YTF
  • Community annotation for 1YTF 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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