3IYD Transcription Dna date Aug 01, 2009
title Three-Dimensional Em Structure Of An Intact Activator-Depend Transcription Initiation Complex
authors B.P.Hudson, J.Quispe, S.Lara, Y.Kim, H.Berman, E.Arnold, R.H.Ebrig C.L.Lawson
compound source
Molecule: Dna-Directed Rna Polymerase Subunit Alpha
Chain: A, B
Synonym: Rnap Subunit Alpha, Transcriptase Subunit Alpha, R Polymerase Subunit Alpha;
Ec: 2.7.7.6
Engineered: Yes
Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12
Gene: B3295, Jw3257, Pez, Phs, Rpoa, Rpob, Rpoc, Rpod, Rpoz
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De2)
Expression_system_plasmid: Pecabc-H6, Prsfduet-Sigma, Pcdf-

Molecule: Dna-Directed Rna Polymerase Subunit Beta
Chain: C
Synonym: Rnap Subunit Beta, Transcriptase Subunit Beta, Rna Polymerase Subunit Beta;
Ec: 2.7.7.6
Engineered: Yes

Organism_scientific: Escherichia Coli
Organism_taxid: 83333
Strain: K-12
Gene: Rpob, Gron, Nitb, Rif, Ron, Stl, Stv, Tabd, B3987, Jw
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Bl21(De3)

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

Synthetic: Yes
Other_details: Purchased From Idt And Annealed

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

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Gene: Rpoz, B3649, Jw3624
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Rna Polymerase Sigma Factor Rpod
Chain: F
Synonym: Rnap Polymerase (Sigma70 Holoenzyme)
Engineered: Yes

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Gene: Rpod
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Catabolite Gene Activator
Chain: G, H
Synonym: Camp Receptor Protein, Camp Regulatory Protein, Ca Activator Protein;
Engineered: Yes

Organism_scientific: Escherichia Coli K-12
Organism_taxid: 83333
Gene: Crp, Cap, Csm, B3357, Jw5702
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna (98-Mer)
Chain: I
Synonym: Lac(Icap)Up-Uv5-Bubble
Engineered: Yes

Synthetic: Yes

Molecule: Dna (98-Mer)
Chain: J
Engineered: Yes

Synthetic: Yes
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 19.80 Å
ligand CMP BindingDB enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


C


D


E


F
  • bacterial sigma factor activ...


  • H, G


    Primary referenceThree-dimensional EM structure of an intact activator-dependent transcription initiation complex., Hudson BP, Quispe J, Lara-Gonzalez S, Kim Y, Berman HM, Arnold E, Ebright RH, Lawson CL, Proc Natl Acad Sci U S A. 2009 Nov 24;106(47):19830-5. Epub 2009 Nov 10. PMID:19903881
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (613 Kb) [Save to disk]
  • Biological Unit Coordinates (3iyd.pdb1.gz) 604 Kb
  • LPC: Ligand-Protein Contacts for 3IYD
  • CSU: Contacts of Structural Units for 3IYD
  • Retrieve 3IYD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3IYD from S2C, [Save to disk]
  • View 3IYD 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 3IYD
  • 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 3IYD, from MSDmotif at EBI
  • Fold representative 3iyd from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3iyd_H] [3iyd_F] [3iyd_I] [3iyd_J] [3iyd_E] [3iyd] [3iyd_B] [3iyd_D] [3iyd_A] [3iyd_C] [3iyd_G]
  • SWISS-PROT database: [P0ACJ8] [P0A7Z4] [P0A8V2] [P0A8T7] [P00579] [P0A800]
  • Domain organization of [CRP_ECOLI] [RPOA_ECOLI] [RPOB_ECOLI] [RPOC_ECOLI] [RPOD_ECOLI] [RPOZ_ECOLI] by SWISSPFAM
  • Domains found in 3IYD: [HTH_CRP] [RNA_pol_Rpb6] [RPOLA_N] [RPOLD] [cNMP ] by SMART
  • Other resources with information on 3IYD
  • Community annotation for 3IYD at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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