1L9Z Transcription Dna date Mar 27, 2002
title Thermus Aquaticus Rna Polymerase Holoenzymefork-Junction Promoter Dna Complex At 6.5 A Resolution
authors K.S.Murakami, S.Masuda, E.A.Campbell, O.Muzzin, S.A.Darst
compound source
Molecule: Nontemplate Dna Strand
Chain: U
Engineered: Yes
Synthetic: Yes

Molecule: Template Dna Strand
Chain: T
Engineered: Yes

Synthetic: Yes

Molecule: Rna Polymerase, Alpha Subunit
Chain: A, B

Organism_scientific: Thermus Aquaticus
Organism_taxid: 271

Molecule: Rna Polymerase, Beta Subunit
Chain: C

Organism_scientific: Thermus Aquaticus
Organism_taxid: 271

Molecule: Rna Polymerase, Beta-Prime Subunit
Chain: D

Organism_scientific: Thermus Aquaticus
Organism_taxid: 271

Molecule: Rna Polymerase, Omega Subunit
Chain: E

Organism_scientific: Thermus Aquaticus
Organism_taxid: 271

Molecule: Sigma Factor Siga
Chain: H
Engineered: Yes

Organism_scientific: Thermus Aquaticus
Organism_taxid: 271
Gene: Rpod
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21 (De3)
Expression_system_vector_type: Plasmid
symmetry Space Group: P 43 2 2
length a length b length c angle alpha angle beta angle gamma
180.947 180.947 523.461 90.00 90.00 90.00
method X-Ray Diffractionresolution 6.50 Å
ligand MG, ZN enzyme Transferase E.C. BRENDA
A, B




  • bacterial sigma factor activ...

  • Primary referenceStructural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex., Murakami KS, Masuda S, Campbell EA, Muzzin O, Darst SA, Science 2002 May 17;296(5571):1285-90. PMID:12016307
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (193 Kb) [Save to disk]
  • Biological Unit Coordinates (1l9z.pdb1.gz) 176 Kb
  • LPC: Ligand-Protein Contacts for 1L9Z
  • CSU: Contacts of Structural Units for 1L9Z
  • Likely Quarternary Molecular Structure file(s) for 1L9Z
  • Retrieve 1L9Z in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1L9Z from S2C, [Save to disk]
  • View 1L9Z 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 1L9Z
  • 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 1L9Z, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1l9za_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1l9zb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1l9zc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1l9zd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1l9ze_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1l9zh_, region H [Jmol] [rasmolscript] [script source]
  • Fold representative 1l9z from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1l9z] [1l9z_B] [1l9z_A] [1l9z_C] [1l9z_H] [1l9z_E] [1l9z_U] [1l9z_T] [1l9z_D]
  • SWISS-PROT database: [Q9EZJ8] [Q9KWU8] [Q9KWU7] [Q9KWU6] [Q9EVV4]
  • Domains found in 1L9Z: [HhH1] [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
  • Other resources with information on 1L9Z
  • Community annotation for 1L9Z at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science