2NVZ	Transcription,Transferase Dna-Rna Hybrid	date	Nov 14, 2006
title	Rna Polymerase II Elongation Complex With Utp, Updated 1120
authors	D.Wang, D.A.Bushnell, K.D.Westover, C.D.Kaplan, R.D.Kornberg
compound		source
Molecule: 5'-R(Apupcpgpapgpapgpgpa)-3' Chain: R Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
Molecule: 28-Mer Dna Template Strand Chain: T Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
Molecule: 5'-D(Cptpgpcptptpaptpcpgpgptpapg)-3 Chain: N Engineered: Yes		Synthetic: Yes Organism_scientific: Synthetic Construct Organism_taxid: 32630
Molecule: Dna-Directed Rna Polymerase II Largest Subunit Chain: A Synonym: Rna Polymerase II Subunit 1, B220 Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Strain: Delta-Rpb4
Molecule: Dna-Directed Rna Polymerase II 140 Kda Polypeptid Chain: B Synonym: B150, Rna Polymerase II Subunit 2 Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Strain: Delta-Rpb4
Molecule: Dna-Directed Rna Polymerase II 45 Kda Polypeptide Chain: C Synonym: B44.5 Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Strain: Delta-Rpb4
Molecule: Dna-Directed Rna Polymerases I, II, And III 27 Kd Polypeptide; Chain: E Synonym: Abc27 Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Strain: Delta-Rpb4
Molecule: Dna-Directed Rna Polymerases I, II, And III 23 Kd Polypeptide; Chain: F Synonym: Abc23 Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Strain: Delta-Rpb4
Molecule: Dna-Directed Rna Polymerases I, II, And III 14.5 Polypeptide; Chain: H Synonym: Abc14.4 Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Strain: Delta-Rpb4
Molecule: Dna-Directed Rna Polymerase II Subunit 9 Chain: I Synonym: Dna-Directed Rna Polymerase II 14.2 Kda Polypeptid Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Strain: Delta-Rpb4
Molecule: Dna-Directed Rna Polymerases IIIIII Subunit 10 Chain: J Synonym: Dna- Directed Rna Polymerases I, II, And III 8.3 K Polypeptide, Abc10- Beta, Abc8; Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Strain: Delta-Rpb4
Molecule: Dna-Directed Rna Polymerase II 13.6 Kda Polypepti Chain: K Synonym: B13.6 Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Strain: Delta-Rpb4
Molecule: Dna-Directed Rna Polymerases I, II, And III 7.7 K Polypeptide; Chain: L Synonym: Abc10-Alpha Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Baker'S Yeast Organism_taxid: 4932 Strain: Delta-Rpb4
symmetry	Space Group: C 1 2 1	R_factor 0.270 R_Free 0.332
crystal cell	length a length b length c angle alpha angle beta angle gamma 169.647 222.338 194.316 90.00 101.67 90.00
method	X-Ray Diffraction	resolution	4.30 Å
ligand	MG, UTP, 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	Structural basis of transcription: role of the trigger loop in substrate specificity and catalysis., Wang D, Bushnell DA, Westover KD, Kaplan CD, Kornberg RD, Cell. 2006 Dec 1;127(5):941-54. PMID:17129781

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (581 Kb) [Save to disk] Biological Unit Coordinates (2nvz.pdb1.gz) 571 Kb LPC: Ligand-Protein Contacts for 2NVZ CSU: Contacts of Structural Units for 2NVZ Likely Quarternary Molecular Structure file(s) for 2NVZ Structure Factors (785 Kb) Retrieve 2NVZ in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 2NVZ from S2C, [Save to disk] Re-refined 2nvz structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 2NVZ 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 2NVZ

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 2NVZ, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [2nvz_A] [2nvz_R] [2nvz] [2nvz_T] [2nvz_E] [2nvz_J] [2nvz_K] [2nvz_B] [2nvz_L] [2nvz_C] [2nvz_H] [2nvz_N] [2nvz_F] [2nvz_I] SWISS-PROT database: [P20434] [P20435] [P20436] [P40422] [P22139] [P38902] [P04050] [P08518] [P16370] [P27999] Domain organization of [RPAB1_YEAST] [RPAB2_YEAST] [RPAB3_YEAST] [RPAB4_YEAST] [RPAB5_YEAST] [RPB11_YEAST] [RPB1_YEAST] [RPB2_YEAST] [RPB3_YEAST] [RPB9_YEAST] by SWISSPFAM Domains found in 2NVZ: [RNA_pol_Rpb6] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [ZnF_C2C2 ] by SMART

Other resources with information on 2NVZ

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

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