5I2D Transcription Dna Rna date Feb 08, 2016
title Crystal Structure Of T. Thermophilus Tthb099 Class II Transc Activation Complex: Tap-Rpo
authors Y.Feng, Y.Zhang, R.H.Ebright
compound source
Molecule: Dna-Directed Rna Polymerase Subunit Alpha
Chain: A, B, L, M
Synonym: Rnap Subunit Alpha,Rna Polymerase Subunit Alpha, Transcriptase Subunit Alpha;
Ec: 2.7.7.6
Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: Dna-Directed Rna Polymerase Subunit Beta
Chain: C, N
Synonym: Rnap Subunit Beta,Rna Polymerase Subunit Beta,Tran Subunit Beta;
Ec: 2.7.7.6

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: Dna-Directed Rna Polymerase Subunit Beta'
Chain: D, O
Synonym: Rnap Subunit Beta',Rna Polymerase Subunit Beta', Transcriptase Subunit Beta';
Ec: 2.7.7.6

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: Dna-Directed Rna Polymerase Subunit Omega
Chain: E, P
Synonym: Rnap Omega Subunit,Rna Polymerase Omega Subunit, Transcriptase Subunit Omega;
Ec: 2.7.7.6

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579

Molecule: Rna Polymerase Sigma Factor Siga
Chain: F, Q
Engineered: Yes

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579
Gene: Siga, Ttha0532
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Transcriptional Regulator, Crp Family
Chain: G, H, R, S
Engineered: Yes

Organism_scientific: Thermus Thermophilus (Strain Hb8 Atc Dsm 579);
Organism_taxid: 300852
Strain: Hb8 Atcc 27634 Dsm 579
Gene: Tthb099
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (72-Mer)
Chain: I, T
Engineered: Yes

Synthetic: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Dna (72-Mer)
Chain: J, U
Engineered: Yes

Synthetic: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Rna (5'-R(Upcpgpa)-3')
Chain: K, V
Engineered: Yes

Synthetic: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
symmetry Space Group: P 1 21 1
R_factor 0.241 R_Free 0.284
crystal
cell
length a length b length c angle alpha angle beta angle gamma
171.487 105.446 374.585 90.00 102.39 90.00
method X-Ray Diffractionresolution 4.41 Å
ligand MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
E, P


F, Q
  • bacterial sigma factor activ...


  • M, L, A, B


    N, C


    O, D


    S, H, R, G


    Primary referenceStructural basis of transcription activation., Feng Y, Zhang Y, Ebright RH, Science. 2016 Jun 10;352(6291):1330-3. doi: 10.1126/science.aaf4417. PMID:27284196
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1367 Kb) [Save to disk]
  • Biological Unit Coordinates (5i2d.pdb1.gz) 689 Kb
  • Biological Unit Coordinates (5i2d.pdb2.gz) 687 Kb
  • LPC: Ligand-Protein Contacts for 5I2D
  • CSU: Contacts of Structural Units for 5I2D
  • Structure Factors (609 Kb)
  • Retrieve 5I2D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5I2D from S2C, [Save to disk]
  • Re-refined 5i2d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5I2D 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 5I2D
  • 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
  • Fold representative 5i2d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5i2d_S] [5i2d_R] [5i2d_G] [5i2d_H] [5i2d_P] [5i2d_J] [5i2d_Q] [5i2d_D] [5i2d_M] [5i2d_B] [5i2d_L] [5i2d_I] [5i2d_O] [5i2d_C] [5i2d_K] [5i2d_E] [5i2d_U] [5i2d_T] [5i2d_A] [5i2d] [5i2d_F] [5i2d_N] [5i2d_V]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5I2D: [HTH_CRP] [HhH1] [RNA_pol_Rpb6] [RPOLA_N] [RPOLD] [cNMP ] by SMART
  • Other resources with information on 5I2D
  • Community annotation for 5I2D at PDBWiki (http://pdbwiki.org)

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