3M4O	Transferase Dna-Rna Hybrid	date	Mar 11, 2010
title	Rna Polymerase II Elongation Complex B
authors	D.Wang, G.Zhu, X.Huang, S.J.Lippard
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: Brewer'S Yeast,Lager Beer Yeast,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: Brewer'S Yeast,Lager Beer Yeast,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: Brewer'S Yeast,Lager Beer Yeast,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: Brewer'S Yeast,Lager Beer Yeast,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: Brewer'S Yeast,Lager Beer Yeast,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: Brewer'S Yeast,Lager Beer Yeast,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: Brewer'S Yeast,Lager Beer Yeast,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: Brewer'S Yeast,Lager Beer Yeast,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: Brewer'S Yeast,Lager Beer Yeast,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: Brewer'S Yeast,Lager Beer Yeast,Yeast Organism_taxid: 4932
Molecule: Rna (5'-R(Apupgpgpapgpapgpgpa)-3') Chain: R Engineered: Yes		Synthetic: Yes
Molecule: Dna (28-Mer) Chain: T Engineered: Yes		Synthetic: Yes
Molecule: Dna (5'-D(Pgptpgpgptptpaptpgpgpgptpa Chain: N Engineered: Yes		Synthetic: Yes
symmetry	Space Group: C 1 2 1	R_factor 0.241 R_Free 0.292
crystal cell	length a length b length c angle alpha angle beta angle gamma 168.114 222.131 191.782 90.00 100.99 90.00
method	X-Ray Diffraction	resolution	3.57 Å
ligand	C7P, 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...
Primary reference	X-ray structure and mechanism of RNA polymerase II stalled at an antineoplastic monofunctional platinum-DNA adduct., Wang D, Zhu G, Huang X, Lippard SJ, Proc Natl Acad Sci U S A. 2010 May 6. PMID:20448203

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1224 Kb) [Save to disk] Biological Unit Coordinates (3m4o.pdb1.gz) 1212 Kb LPC: Ligand-Protein Contacts for 3M4O CSU: Contacts of Structural Units for 3M4O Structure Factors (1313 Kb) Retrieve 3M4O in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3M4O from S2C, [Save to disk] Re-refined 3m4o structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3M4O 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 3M4O

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 3M4O, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3m4o] [3m4o_A] [3m4o_R] [3m4o_C] [3m4o_E] [3m4o_T] [3m4o_F] [3m4o_L] [3m4o_K] [3m4o_B] [3m4o_H] [3m4o_N] [3m4o_I] [3m4o_J] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 3M4O: [RNA_pol_Rpb6] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [ZnF_C2C2 ] by SMART

Other resources with information on 3M4O

Community annotation for 3M4O at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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