3H3V	Transferase Dna Rna	date	Apr 17, 2009
title	Yeast Rnap II Containing Poly(A)-Signal Sequence In The Acti
authors	S.Dengl, P.Cramer
compound		source
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb1 Chain: B 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: Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb2 Chain: C 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: Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb3 Chain: D Synonym: Rna Polymerase II Subunit B3, Rna Polymerase II Su Dna-Directed Rna Polymerase II 45 Kda Polypeptide, B44.5; Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb4 Chain: E Synonym: Rna Polymerase II Subunit B4, Dna-Directed Rna Pol 32 Kda Polypeptide, B32; Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun Chain: F Synonym: Rna Polymerases I, II, And III Subunit Abc1, Dna-D Rna Polymerases I, II, And III 27 Kda Polypeptide, Abc27; Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun Chain: G Synonym: Rna Polymerases I, II, And III Subunit Abc2, Dna-D Rna Polymerases I, II, And III 23 Kda Polypeptide, Abc23; Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb7 Chain: H Synonym: Rna Polymerase II Subunit B7, B16 Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun Chain: I Synonym: Rna Polymerases I, II, And III Subunit Abc3, Dna-D Rna Polymerases I, II, And III 14.5 Kda Polypeptide, Abc14. Abc14.4; Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb9 Chain: J Synonym: Rna Polymerase II Subunit B9, Dna-Directed Rna Pol Subunit 9, Dna-Directed Rna Polymerase II 14.2 Kda Polypept B12.6; Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun Chain: K Synonym: Rna Polymerases I, II, And III Subunit Abc5, Dna-D Rna Polymerases I, II, And III 8.3 Kda Polypeptide, Abc10-B Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb11 Chain: L Synonym: Rna Polymerase II Subunit B11, Dna-Directed Rna Po II 13.6 Kda Polypeptide, B13.6; Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932
Molecule: Dna-Directed Rna Polymerases I, II, And III Subun Chain: M Synonym: Rna Polymerases I, II, And III Subunit Abc4, Abc10 Ec: 2.7.7.6		Organism_scientific: Saccharomyces Cerevisiae Organism_common: Yeast Organism_taxid: 4932
Molecule: 5'-D(Apgpcptpcpapapgptpapgpcptpgpc Aptptpgpcpaptpt)-3'; Chain: N Engineered: Yes		Synthetic: Yes
Molecule: 5'-D(Cpapgpcptpapcptptpgpapgpcpt)-3 Chain: P Engineered: Yes		Synthetic: Yes
Molecule: 5'-R(Upgpcpapupupupcpgpcpapapupapa Chain: T Engineered: Yes		Synthetic: Yes
symmetry	Space Group: C 2 2 21	R_factor 0.205 R_Free 0.241
crystal cell	length a length b length c angle alpha angle beta angle gamma 222.470 391.620 284.120 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	4.00 Å
ligand	MG, ZN	enzyme	Transferase E.C.2.7.7.6 BRENDA
Gene Ontology	Chain Function Process Component 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... K RNA-directed 5'-3' RNA polym... DNA-directed RNA polymerase ... L RNA-directed 5'-3' RNA polym... M RNA-directed 5'-3' RNA polym...
Primary reference	Torpedo Nuclease Rat1 Is Insufficient to Terminate RNA Polymerase II in Vitro., Dengl S, Cramer P, J Biol Chem. 2009 Aug 7;284(32):21270-9. Epub 2009 Jun 17. PMID:19535338

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (643 Kb) [Save to disk] Biological Unit Coordinates (3h3v.pdb1.gz) 634 Kb LPC: Ligand-Protein Contacts for 3H3V CSU: Contacts of Structural Units for 3H3V Likely Quarternary Molecular Structure file(s) for 3H3V Structure Factors (1835 Kb) Retrieve 3H3V in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 3H3V from S2C, [Save to disk] Re-refined 3h3v structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 3H3V 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 3H3V

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 3H3V, from MSDmotif at EBI

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [3h3v_T] [3h3v_M] [3h3v_L] [3h3v_D] [3h3v_E] [3h3v_N] [3h3v_K] [3h3v_I] [3h3v] [3h3v_C] [3h3v_H] [3h3v_P] [3h3v_G] [3h3v_F] [3h3v_B] [3h3v_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 3H3V: [RNA_pol_Rpb6] [RPOL4c] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [S1] [ZnF_C2C2 ] by SMART

Other resources with information on 3H3V

Community annotation for 3H3V at PDBWiki (http://pdbwiki.org) MMDB (Entrez's Structure Database)

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