2O5J	Transferase Dna-Rna Hybrid	date	Dec 06, 2006
title	Crystal Structure Of The T. Thermophilus Rnap Polymerase Elo Complex With The Ntp Substrate Analog
authors	D.G.Vassylyev, M.N.Vassylyeva
compound		source
Molecule: 5'-D(Pcpcpcptpgptpcptpgpgpcpgptptp Pcpgpcpcpg)-3'; Chain: G, X Engineered: Yes Other_details: Dna Template Strand		Synthetic: Yes
Molecule: 5'-R(Pgpapgpupcpupgpcpgpgpcpgpcpgp Chain: H, Y Engineered: Yes Other_details: Rna Transcript		Synthetic: Yes
Molecule: 5'-D(Apapcpgpcpcpapgpapcpapgpgpg)-3 Chain: I, Z Engineered: Yes Other_details: Dna Non-Template Strand		Synthetic: Yes
Molecule: Dna-Directed Rna Polymerase Alpha Chain Chain: A, B, K, L Synonym: Rnap Alpha Subunit, Transcriptase Alpha Chain, Rna Polymerase Subunit Alpha; Ec: 2.7.7.6		Organism_scientific: Thermus Thermophilus Organism_taxid: 300852 Strain: Hb8
Molecule: Dna-Directed Rna Polymerase Beta Chain Chain: C, M Synonym: Rnap Beta Subunit, Transcriptase Beta Chain, Rna P Subunit Beta; Ec: 2.7.7.6		Organism_scientific: Thermus Thermophilus Organism_taxid: 300852 Strain: Hb8
Molecule: Dna-Directed Rna Polymerase Beta' Chain Chain: D, N Synonym: Rnap Beta' Subunit, Transcriptase Beta' Chain, Rna Polymerase Beta' Subunit; Ec: 2.7.7.6		Organism_scientific: Thermus Thermophilus Organism_taxid: 300852 Strain: Hb8
Molecule: Dna-Directed Rna Polymerase Omega Chain Chain: E, O Synonym: Rnap Omega Subunit, Transcriptase Omega Chain, Rna Polymerase Omega Subunit; Ec: 2.7.7.6		Organism_scientific: Thermus Thermophilus Organism_taxid: 300852 Strain: Hb8
symmetry	Space Group: P 41	R_factor 0.225 R_Free 0.257
crystal cell	length a length b length c angle alpha angle beta angle gamma 152.340 152.340 524.567 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.00 Å
ligand	APC, MG, ZN	enzyme	Transferase E.C.2.7.7.6 BRENDA
Gene Ontology	Chain Function Process Component A, K, B, L M, C N, D O, E
Primary reference	Structural basis for substrate loading in bacterial RNA polymerase., Vassylyev DG, Vassylyeva MN, Zhang J, Palangat M, Artsimovitch I, Landick R, Nature. 2007 Jun 20;. PMID:17581591

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1047 Kb) [Save to disk] Biological Unit Coordinates (2o5j.pdb1.gz) 525 Kb Biological Unit Coordinates (2o5j.pdb2.gz) 524 Kb LPC: Ligand-Protein Contacts for 2O5J CSU: Contacts of Structural Units for 2O5J Likely Quarternary Molecular Structure file(s) for 2O5J Structure Factors (2169 Kb) Retrieve 2O5J in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2O5J from S2C, [Save to disk] Re-refined 2o5j structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2O5J 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 2O5J

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 3D motif for 2O5J, from MSDmotif at EBI Fold representative 2o5j from FSSP and Dali (Families of Structurally Similar Proteins)

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2o5j_Y] [2o5j_O] [2o5j_D] [2o5j_H] [2o5j_E] [2o5j_G] [2o5j_B] [2o5j_C] [2o5j_A] [2o5j_M] [2o5j_N] [2o5j_Z] [2o5j_I] [2o5j] [2o5j_L] [2o5j_X] [2o5j_K] SWISS-PROT database: [Q5SHR6] [Q8RQE9] [Q8RQE8] [Q8RQE7] Domain organization of [RPOA_THET8] [RPOB_THET8] [RPOC_THET8] [RPOZ_THET8] by SWISSPFAM Domains found in 2O5J: [HhH1] [RNA_pol_Rpb6] [RPOLA_N] [RPOLD ] by SMART

Other resources with information on 2O5J

Community annotation for 2O5J at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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