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 Microscopy	resolution	19.80 Å
ligand	CMP BindingDB	enzyme	Transferase E.C.2.7.7.6 BRENDA
Gene Ontology	Chain Function Process Component A, B C D E F bacterial sigma factor activ... H, G
Primary reference	Three-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] (598 Kb) [Save to disk] Biological Unit Coordinates (3iyd.pdb1.gz) 591 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

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 3IYD, from MSDmotif at EBI

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)

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