3GTM	Transcription, Transferase Dna-Rna Hybri	date	Mar 27, 2009
title	Co-Complex Of Backtracked Rna Polymerase II With Tfiis
authors	D.Wang, D.A.Bushnell, X.Huang, K.D.Westover, M.Levitt, R.D.Kornbe
compound		source
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb1 Chain: A Fragment: Dna-Directed Rna Polymerase II Largest Subunit Synonym: Rna Polymerase II Subunit B1,Dna-Directed Rna Poly Largest Subunit,Rna Polymerase II Subunit B220; Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c); Organism_common: Baker'S Yeast Organism_taxid: 559292 Strain: Atcc 204508 S288c
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb2 Chain: B Fragment: Dna-Directed Rna Polymerase II 140 Kda Polypeptid Synonym: Rna Polymerase II Subunit 2,B150,Dna-Directed Rna II 140 Kda Polypeptide; Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c); Organism_common: Baker'S Yeast Organism_taxid: 559292 Strain: Atcc 204508 S288c
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb3 Chain: C Fragment: Dna-Directed Rna Polymerase II 45 Kda Polypeptide		Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c); Organism_common: Baker'S Yeast Organism_taxid: 559292 Strain: Atcc 204508 S288c
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun Chain: E Fragment: Dna-Directed Rna Polymerases I, II, And III 27 Kd Polypeptide;		Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c); Organism_common: Baker'S Yeast Organism_taxid: 559292 Strain: Atcc 204508 S288c
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun Chain: F Fragment: Dna-Directed Rna Polymerases I, II, And III 23 Kd Polypeptide;		Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c); Organism_common: Baker'S Yeast Organism_taxid: 559292 Strain: Atcc 204508 S288c
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun Chain: H Fragment: Dna-Directed Rna Polymerases I, II, And III 14.5 Polypeptide; Synonym: Rna Polymerases I,II,And III Subunit Abc3,Abc14.4, Dna-Directed Rna Polymerases I,And III 14.5 Kda Polypeptide		Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c); Organism_common: Baker'S Yeast Organism_taxid: 559292 Strain: Atcc 204508 S288c
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb9 Chain: I Fragment: Dna-Directed Rna Polymerase II Subunit 9 Synonym: Rna Polymerase II Subunit B9,B12.6,Dna-Directed Rn Polymerase II 14.2 Kda Polypeptide,Dna-Directed Rna Polymer Subunit 9;		Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c); Organism_common: Baker'S Yeast Organism_taxid: 559292 Strain: Atcc 204508 S288c
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun Chain: J Fragment: Dna-Directed Rna Polymerases IIIIII Subunit 10 Synonym: Rna Polymerases I,II,And III Subunit Abc5,Abc10-Be Dna-Directed Rna Polymerases I,And III 8.3 Kda Polypeptide;		Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c); Organism_common: Baker'S Yeast Organism_taxid: 559292 Strain: Atcc 204508 S288c
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb11 Chain: K Fragment: Dna-Directed Rna Polymerase II 13.6 Kda Polypepti Synonym: Rna Polymerase II Subunit B11,B13.6,Dna-Directed R Polymerase II 13.6 Kda Polypeptide;		Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c); Organism_common: Baker'S Yeast Organism_taxid: 559292 Strain: Atcc 204508 S288c
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun Chain: L Fragment: Dna-Directed Rna Polymerases I, II, And III 7.7 K Polypeptide; Synonym: Rna Polymerases I,II,And III Subunit Abc4,Abc10-Al		Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c); Organism_common: Baker'S Yeast Organism_taxid: 559292 Strain: Atcc 204508 S288c
Molecule: Transcription Elongation Factor S-II Chain: S Fragment: Transcription Factor Iis E291h Mutation, Unp Resi 309; Synonym: Dna Strand Transfer Protein Alpha,Stp-Alpha,Dna St Transferase 1,Pyrimidine Pathway Regulatory Protein 2; Engineered: Yes Mutation: Yes		Organism_scientific: Saccharomyces Cerevisiae (Strain Atcc S288c); Organism_common: Baker'S Yeast Organism_taxid: 559292 Strain: Atcc 204508 S288c Gene: Dst1, Ppr2, Ygl043w Expression_system: Escherichia Coli Expression_system_taxid: 511693 Expression_system_strain: Bl21
Molecule: Rna (5'-R(Apupcpgpapgpapgpgpapupgpc) Chain: M Fragment: Rna Strand Engineered: Yes Other_details: Rna Strand		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630 Other_details: Synthetic Rna
Molecule: Dna (28-Mer) Chain: N Fragment: Dna Template Strand Engineered: Yes Other_details: Dna Template Strand		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630 Other_details: Synthetic Template Dna
Molecule: Dna (5'-D(Cptpgpcptptpaptpcpgpgptpap Chain: O Fragment: Dna Non-Template Strand Engineered: Yes Other_details: Dna Non-Template Strand		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630 Other_details: Synthetic Non-Template Dna
symmetry	Space Group: C 1 2 1	R_factor 0.234 R_Free 0.289
crystal cell	length a length b length c angle alpha angle beta angle gamma 172.329 218.530 193.913 90.00 100.32 90.00
method	X-Ray Diffraction	resolution	3.80 Å
ligand	MG, ZN	enzyme	Transferase E.C.2.7.7.6 BRENDA
Gene Ontology	Chain Function Process Component A RNA-directed 5'-3' RNA polym... B RNA-directed 5'-3' RNA polym... C RNA-directed 5'-3' RNA polym... E RNA-directed 5'-3' RNA polym... F RNA-directed 5'-3' RNA polym... H RNA-directed 5'-3' RNA polym... I RNA-directed 5'-3' RNA polym... J RNA-directed 5'-3' RNA polym... DNA-directed RNA polymerase ... K RNA-directed 5'-3' RNA polym... L RNA-directed 5'-3' RNA polym... S
Primary reference	Structural basis of transcription: backtracked RNA polymerase II at 3.4 angstrom resolution., Wang D, Bushnell DA, Huang X, Westover KD, Levitt M, Kornberg RD, Science. 2009 May 29;324(5931):1203-6. PMID:19478184

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1261 Kb) [Save to disk] Biological Unit Coordinates (3gtm.pdb1.gz) 1250 Kb LPC: Ligand-Protein Contacts for 3GTM CSU: Contacts of Structural Units for 3GTM Likely Quarternary Molecular Structure file(s) for 3GTM Structure Factors (1154 Kb) Retrieve 3GTM in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3GTM from S2C, [Save to disk] Re-refined 3gtm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3GTM 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 3GTM

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 3D motif for 3GTM, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3gtm_I] [3gtm_L] [3gtm_B] [3gtm_A] [3gtm] [3gtm_C] [3gtm_F] [3gtm_K] [3gtm_M] [3gtm_J] [3gtm_E] [3gtm_O] [3gtm_H] [3gtm_N] [3gtm_S] SWISS-PROT database: [P20434] [P20435] [P20436] [P40422] [P22139] [P38902] [P04050] [P08518] [P16370] [P27999] [P07273] Domain organization of [RPAB1_YEAST] [RPAB2_YEAST] [RPAB3_YEAST] [RPAB4_YEAST] [RPAB5_YEAST] [RPB11_YEAST] [RPB1_YEAST] [RPB2_YEAST] [RPB3_YEAST] [RPB9_YEAST] [TFS2_YEAST] by SWISSPFAM Domains found in 3GTM: [RNA_pol_Rpb6] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [TFS2M] [ZnF_C2C2 ] by SMART

Other resources with information on 3GTM

Community annotation for 3GTM at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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