5D4D Transcription Dna date Aug 07, 2015
title Crystal Structure Of Thermus Thermophilus Product Complex Fo Transcription Initiation With Nad And Ctp
authors Y.Zhang, R.H.Ebright
compound source
Molecule: Dna-Directed Rna Polymerase Subunit Alpha
Chain: A, B, K, L
Synonym: Rnap Subunit Alpha,Rna Polymerase Subunit Alpha, Transcriptase Subunit Alpha;
Ec: 2.7.7.6
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Dna-Directed Rna Polymerase Subunit Beta
Chain: C, M
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, N
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, O
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, P
Engineered: Yes

Organism_scientific: Thermus Thermophilus (Strain Hb27 At 163 Dsm 7039);
Organism_taxid: 262724
Strain: Hb27 Atcc Baa-163 Dsm 7039
Gene: Siga, Rpod, Tt_c0164
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plsamid
Expression_system_plasmid: Pet28a

Molecule: Dna (5'- D(Cpctpgpcpaptpcpcpgptpgpapgptpapgpapg)-
Chain: G, R
Engineered: Yes

Synthetic: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274

Molecule: Dna (27-Mer)
Chain: H, S
Engineered: Yes

Synthetic: Yes
Organism_scientific: Thermus Thermophilus
Organism_taxid: 274
symmetry Space Group: P 1 21 1
R_factor 0.201 R_Free 0.254
crystal
cell
length a length b length c angle alpha angle beta angle gamma
185.000 103.510 296.300 90.00 98.27 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand A, C, CTP, MG, NAD, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene TT
Gene
Ontology
ChainFunctionProcessComponent
A, K, B, L


F, P
  • bacterial sigma factor activ...


  • M, C


    N, D


    O, E


    Primary referenceThe mechanism of RNA 5' capping with NAD+, NADH and desphospho-CoA., Bird JG, Zhang Y, Tian Y, Panova N, Barvik I, Greene L, Liu M, Buckley B, Krasny L, Lee JK, Kaplan CD, Ebright RH, Nickels BE, Nature. 2016 Jul 21;535(7612):444-7. PMID:27383794
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1172 Kb) [Save to disk]
  • Biological Unit Coordinates (5d4d.pdb1.gz) 594 Kb
  • Biological Unit Coordinates (5d4d.pdb2.gz) 584 Kb
  • LPC: Ligand-Protein Contacts for 5D4D
  • CSU: Contacts of Structural Units for 5D4D
  • Structure Factors (1982 Kb)
  • Retrieve 5D4D in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5D4D from S2C, [Save to disk]
  • Re-refined 5d4d structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 5D4D 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 5D4D
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 5d4d from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5d4d_M] [5d4d_G] [5d4d_O] [5d4d_R] [5d4d_B] [5d4d] [5d4d_C] [5d4d_S] [5d4d_N] [5d4d_F] [5d4d_A] [5d4d_L] [5d4d_D] [5d4d_P] [5d4d_H] [5d4d_K] [5d4d_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 5D4D: [HhH1] [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART
  • Other resources with information on 5D4D
  • Community annotation for 5D4D at PDBWiki (http://pdbwiki.org)

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