3I4N	Transcription,Transferase Dna-Rna Hybrid	date	Jul 02, 2009
title	8-Oxoguanine Containing Rna Polymerase II Elongation Complex
authors	G.E.Damsma, P.Cramer
compound		source
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb1 Chain: A Synonym: Rna Polymerase II Subunit B1, Rna Polymerase II Su Dna-Directed Rna Polymerase III Largest Subunit, Rna Polyme Subunit B220; Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb2 Chain: B Synonym: Rna Polymerase II Subunit 2, Dna-Directed Rna Poly 140 Kda Polypeptide, B150; Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb3 Chain: C Synonym: Rna Polymerase II Subunit B3, Rna Polymerase II Su Dna-Directed Rna Polymerase II 45 Kda Polypeptide, B44.5;		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb4 Chain: D Synonym: Rna Polymerase II Subunit B4, Dna-Directed Rna Pol 32 Kda Polypeptide, B32;		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun Chain: E Synonym: Rna Polymerases I, II, And III Subunit Abc1, Dna-D Rna Polymerases I, II, And III 27 Kda Polypeptide, Abc27;		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun Chain: F Synonym: Rna Polymerases I, II, And III Subunit Abc2, Dna-D Rna Polymerases I, II, And III 23 Kda Polypeptide, Abc23;		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb7 Chain: G Synonym: Rna Polymerase II Subunit B7, B16		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun Chain: H Synonym: Rna Polymerases I, II, And III Subunit Abc3, Dna-D Rna Polymerases I, II, And III 14.5 Kda Polypeptide, Abc14. Abc14.4;		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb9 Chain: I Synonym: Rna Polymerase II Subunit B9, Dna-Directed Rna Pol Subunit 9, Dna-Directed Rna Polymerase II 14.2 Kda Polypept B12.6;		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun Chain: J Synonym: Rna Polymerases I, II, And III Subunit Abc5, Dna-D Rna Polymerases I, II, And III 8.3 Kda Polypeptide, Abc10-B		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb11 Chain: K Synonym: Rna Polymerase II Subunit B11, Dna-Directed Rna Po II 13.6 Kda Polypeptide, B13.6;		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun Chain: L Synonym: Rna Polymerases I, II, And III Subunit Abc4, Abc10		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932
Molecule: Dna (5'-D(Apgcptpcpapapgptpapcptptp Pgpcpcp(Bru)Pgpgptpcpaptpt)-3'); Chain: T Engineered: Yes		Synthetic: Yes
Molecule: Dna (5'-D(Apgptpapcptptpgpapgpcpt)-3' Chain: N Engineered: Yes		Synthetic: Yes
Molecule: Rna (5'-R(Upgpcpapupcupupcpcpapgpgp 3'); Chain: P Engineered: Yes		Synthetic: Yes
symmetry	Space Group: C 2 2 21	R_factor 0.228 R_Free 0.266
crystal cell	length a length b length c angle alpha angle beta angle gamma 221.173 394.148 282.339 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.90 Å
ligand	8OG, BRU, 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... D RNA-directed 5'-3' RNA polym... E RNA-directed 5'-3' RNA polym... F RNA-directed 5'-3' RNA polym... G 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...
Primary reference	Molecular basis of transcriptional mutagenesis at 8-oxoguanine., Damsma GE, Cramer P, J Biol Chem. 2009 Nov 13;284(46):31658-63. Epub 2009 Sep 16. PMID:19758983

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (654 Kb) [Save to disk] Biological Unit Coordinates (3i4n.pdb1.gz) 643 Kb LPC: Ligand-Protein Contacts for 3I4N CSU: Contacts of Structural Units for 3I4N Structure Factors (1940 Kb) Retrieve 3I4N in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3I4N from S2C, [Save to disk] Re-refined 3i4n structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3I4N 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 3I4N

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 3I4N, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3i4n] [3i4n_I] [3i4n_P] [3i4n_A] [3i4n_N] [3i4n_D] [3i4n_G] [3i4n_H] [3i4n_C] [3i4n_B] [3i4n_K] [3i4n_F] [3i4n_T] [3i4n_L] [3i4n_E] [3i4n_J] SWISS-PROT database: [P20434] [P20435] [P20436] [P40422] [P22139] [P38902] [P04050] [P08518] [P16370] [P20433] [P34087] [P27999] Domain organization of [RPAB1_YEAST] [RPAB2_YEAST] [RPAB3_YEAST] [RPAB4_YEAST] [RPAB5_YEAST] [RPB11_YEAST] [RPB1_YEAST] [RPB2_YEAST] [RPB3_YEAST] [RPB4_YEAST] [RPB7_YEAST] [RPB9_YEAST] by SWISSPFAM Domains found in 3I4N: [RNA_pol_Rpb6] [RPOL4c] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [S1] [ZnF_C2C2 ] by SMART

Other resources with information on 3I4N

Community annotation for 3I4N at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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