4XLR Transcription Dna date Jan 13, 2015
title Crystal Structure Of T.Aquaticus Transcription Initiation Co Card Containing Bubble Promoter And Rna
authors B.Bae, S.A.Darst
compound source
Molecule: Dna-Directed Rna Polymerase Subunit Alpha
Chain: A, B, G, H
Synonym: Rnap Subunit Alpha,Rna Polymerase Subunit Alpha, Transcriptase Subunit Alpha;
Ec: 2.7.7.6
Organism_scientific: Thermus Aquaticus
Organism_taxid: 271
Other_details: Cell

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

Organism_scientific: Thermus Aquaticus
Organism_taxid: 271
Other_details: Cell

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

Organism_scientific: Thermus Aquaticus
Organism_taxid: 271
Other_details: Cell

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

Organism_scientific: Thermus Aquaticus
Organism_taxid: 271
Other_details: Cell

Molecule: Rna Polymerase Sigma Factor Siga
Chain: F, L
Fragment: Unp Residues 92-438
Engineered: Yes

Organism_scientific: Thermus Aquaticus
Organism_taxid: 271
Gene: Siga
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid

Molecule: Card-Like Transcriptional Regulator
Chain: M, N
Engineered: Yes

Organism_scientific: Thermus Thermophilus Jl-18
Organism_taxid: 798128
Gene: Ttjl18_0238
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-Sumo

Molecule: Dna (48-Mer)
Chain: O, R
Engineered: Yes
Other_details: Dna Non-Template Strand

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Dna (48-Mer)
Chain: P, S
Engineered: Yes
Other_details: Dna Template Strand

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: Rna (5'-R(Pupcpgpa)-3')
Chain: Q, T
Engineered: Yes
Other_details: Rna Transcript

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 43 21 2
R_factor 0.275 R_Free 0.310
crystal
cell
length a length b length c angle alpha angle beta angle gamma
289.840 289.840 536.340 90.00 90.00 90.00
method X-Ray Diffractionresolution 4.30 Å
ligand MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B, H, G


C, I


F, L


J, D


K, E


Primary referenceCarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex., Bae B, Chen J, Davis E, Leon K, Darst SA, Campbell EA, Elife. 2015 Sep 8;4. doi: 10.7554/eLife.08505. PMID:26349034
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1234 Kb) [Save to disk]
  • Biological Unit Coordinates (4xlr.pdb1.gz) 626 Kb
  • Biological Unit Coordinates (4xlr.pdb2.gz) 614 Kb
  • LPC: Ligand-Protein Contacts for 4XLR
  • CSU: Contacts of Structural Units for 4XLR
  • Structure Factors (2738 Kb)
  • Retrieve 4XLR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4XLR from S2C, [Save to disk]
  • Re-refined 4xlr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4XLR 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 4XLR
  • 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 4xlr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4xlr_P] [4xlr_J] [4xlr_D] [4xlr_T] [4xlr_S] [4xlr_N] [4xlr_G] [4xlr_L] [4xlr_K] [4xlr_H] [4xlr_R] [4xlr_O] [4xlr_M] [4xlr_A] [4xlr_C] [4xlr_B] [4xlr] [4xlr_E] [4xlr_F] [4xlr_I] [4xlr_Q]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4XLR: [CarD_TRCF] [HhH1] [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
  • Other resources with information on 4XLR
  • Community annotation for 4XLR at PDBWiki (http://pdbwiki.org)

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