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 Diffractionresolution 4.30 Å
ligand MG, UTP, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
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 referenceStructural 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] (591 Kb) [Save to disk]
  • Biological Unit Coordinates (2nvz.pdb1.gz) 579 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
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 2NVZ, from MSDmotif at EBI
  • Fold representative 2nvz from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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