5UHD Transcription Dna Rna date Jan 11, 2017
title Crystal Structure Of Mycobacterium Tuberculosis Transcriptio Initiation Complex Containing 4nt Rna In Complex With Rifam
authors W.Lin, K.Das, Y.Feng, R.H.Ebright
compound source
Molecule: Dna-Directed Rna Polymerase Subunit Alpha
Chain: A, B
Synonym: Rnap Subunit Alpha,Rna Polymerase Subunit Alpha, Transcriptase Subunit Alpha;
Ec: 2.7.7.6
Engineered: Yes
 Organism_scientific: Mycobacterium Tuberculosis (Strain Atc H37rv);
Organism_taxid: 83332
Strain: Atcc 25618 H37rv
Gene: Rpoa, Rv3457c, Mtcy13e12.10c
Expression_system: Escherichia Coli 'Bl21-Gold(De3)Plyss Ag
Expression_system_taxid: 866768

Molecule: Dna-Directed Rna Polymerase Subunit Beta
Chain: C
Synonym: Rnap Subunit Beta,Rna Polymerase Subunit Beta,Tran Subunit Beta;
Ec: 2.7.7.6
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis (Strain Atc H37rv);
Organism_taxid: 83332
Strain: Atcc 25618 H37rv
Gene: Rpob, Rv0667, Mtci376.08c
Expression_system: Escherichia Coli 'Bl21-Gold(De3)Plyss Ag
Expression_system_taxid: 866768

Molecule: Dna-Directed Rna Polymerase Subunit Beta'
Chain: D
Synonym: Rnap Subunit Beta',Rna Polymerase Subunit Beta', Transcriptase Subunit Beta';
Ec: 2.7.7.6
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis (Strain Atc H37rv);
Organism_taxid: 83332
Strain: Atcc 25618 H37rv
Gene: Rpoc, Rv0668, Mtci376.07c
Expression_system: Escherichia Coli 'Bl21-Gold(De3)Plyss Ag
Expression_system_taxid: 866768

Molecule: Dna-Directed Rna Polymerase Subunit Omega
Chain: E
Synonym: Rnap Omega Subunit,Rna Polymerase Omega Subunit, Transcriptase Subunit Omega;
Ec: 2.7.7.6
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis (Strain Atc H37rv);
Organism_taxid: 83332
Strain: Atcc 25618 H37rv
Gene: Rpoz, Rv1390, Mtcy21b4.07
Expression_system: Escherichia Coli 'Bl21-Gold(De3)Plyss Ag
Expression_system_taxid: 866768

Molecule: Rna Polymerase Sigma Factor Siga
Chain: F
Synonym: Sigma-A
Engineered: Yes
Organism_scientific: Mycobacterium Tuberculosis (Strain Atc H37rv);
Organism_taxid: 83332
Strain: Atcc 25618 H37rv
Gene: Siga, Mysa, Rpod, Rpov, Rv2703, Mtcy05a6.24
Expression_system: Escherichia Coli 'Bl21-Gold(De3)Plyss Ag
Expression_system_taxid: 866768

Molecule: Dna (5'- D(Tpaptpapaptpgpgpgpapgpcptpgptpcpapcpgp G)-3');
Chain: H
Engineered: Yes
Synthetic: Yes
Organism_scientific: Mycobacterium Tuberculosis (Strain Atc H37rv);
Organism_taxid: 83332

Molecule: Dna (5'-D(Cpaptpcpcpgptpgpapgptpcpgp 3');
Chain: G
Engineered: Yes
Synthetic: Yes
Organism_scientific: Mycobacterium Tuberculosis (Strain Atc H37rv);
Organism_taxid: 83332
symmetry Space Group: P 21 21 21
R_factor 0.211 R_Free 0.264
crystal
cell
length a length b length c angle alpha angle beta angle gamma
152.079 163.099 197.904 90.00 90.00 90.00
method X-Ray Diffractionresolution 4.01 Å
ligand MG, RFP, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


C


D


E


F
  • bacterial sigma factor activ...


    • Primary referenceStructural Basis of Mycobacterium tuberculosis Transcription and Transcription Inhibition., Lin W, Mandal S, Degen D, Liu Y, Ebright YW, Li S, Feng Y, Zhang Y, Mandal S, Jiang Y, Liu S, Gigliotti M, Talaue M, Connell N, Das K, Arnold E, Ebright RH, Mol Cell. 2017 Apr 20;66(2):169-179.e8. doi: 10.1016/j.molcel.2017.03.001. Epub, 2017 Apr 6. PMID:28392175
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (543 Kb) [Save to disk]
  • Biological Unit Coordinates (5uhd.pdb1.gz) 533 Kb
  • LPC: Ligand-Protein Contacts for 5UHD
  • CSU: Contacts of Structural Units for 5UHD
  • Structure Factors (282 Kb)
  • Retrieve 5UHD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5UHD from S2C, [Save to disk]
  • Re-refined 5uhd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 5UHD 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 5UHD
  • 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 5uhd from FSSP and Dali (Families of Structurally Similar Proteins)
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5uhd] [5uhd_G] [5uhd_B] [5uhd_D] [5uhd_H] [5uhd_F] [5uhd_E] [5uhd_A] [5uhd_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 5UHD
  • Community annotation for 5UHD at PDBWiki (http://pdbwiki.org)

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