2B63 Transferase Rna date Sep 30, 2005
title Complete Rna Polymerase II-Rna Inhibitor Complex
authors H.Kettenberger, A.Eisenfuehr, F.Brueckner, M.Theis, M.Famulok, P.Cramer
compound source
Molecule: 31-Mer
Chain: R
Engineered: Yes
Synthetic: Yes
Other_details: Synthetic Oligonucleotide Containing Four 5- Bromo-Uridine (5bu) Residues;

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

Molecule: Dna-Directed Rna Polymerase II 140 Kda Polypeptide;
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

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

Molecule: Dna-Directed Rna Polymerase II 32 Kda Polypeptide;
Chain: D
Synonym: B32
Ec: 2.7.7.6
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Rpb4
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna-Directed Rna Polymerases I, II, And III 27 Kda Polypeptide;
Chain: E
Synonym: Abc27
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III 23 Kda Polypeptide;
Chain: F
Synonym: Abc23
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II 19 Kda Polypeptide;
Chain: G
Synonym: B16
Ec: 2.7.7.6
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Gene: Rpb7
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Dna-Directed Rna Polymerases I, II, And III 14.5 Kda Polypeptide;
Chain: H
Synonym: Abc14.4
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II Subunit 9
Chain: I
Synonym: Dna-Directed Rna Polymerase II 14.2 Kda Polypeptide, B12.6;
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases IIIIII Subunit 10
Chain: J
Synonym: Dna- Directed Rna Polymerases I, II, And III 8.3 Kda Polypeptide, Abc10- Beta, Abc8;
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II 13.6 Kda Polypeptide;
Chain: K
Synonym: B13.6
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III 7.7 Kda Polypeptide;
Chain: L
Synonym: Abc10-Alpha
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
symmetry Space Group: C 2 2 21
R_factor 0.252 R_Free 0.273
crystal
cell
length a length b length c angle alpha angle beta angle gamma
224.585 399.815 286.727 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.80 Å
ligand 5BU, MG, 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...


  • 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 referenceStructure of an RNA polymerase II-RNA inhibitor complex elucidates transcription regulation by noncoding RNAs., Kettenberger H, Eisenfuhr A, Brueckner F, Theis M, Famulok M, Cramer P, Nat Struct Mol Biol. 2006 Jan;13(1):44-48. Epub 2005 Dec 11. PMID:16341226
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (666 Kb) [Save to disk]
  • Biological Unit Coordinates (2b63.pdb1.gz) 645 Kb
  • LPC: Ligand-Protein Contacts for 2B63
  • CSU: Contacts of Structural Units for 2B63
  • Likely Quarternary Molecular Structure file(s) for 2B63
  • Structure Factors (2041 Kb)
  • Retrieve 2B63 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2B63 from S2C, [Save to disk]
  • Re-refined 2b63 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2B63 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 2B63
  • 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 2B63, from MSDmotif at EBI
  • Fold representative 2b63 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2b63_I] [2b63_F] [2b63_R] [2b63_K] [2b63_C] [2b63_E] [2b63_A] [2b63_H] [2b63] [2b63_J] [2b63_L] [2b63_D] [2b63_B] [2b63_G]
  • 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 2B63: [RNA_pol_Rpb6] [RPOL4c] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [S1] [ZnF_C2C2 ] by SMART
  • Other resources with information on 2B63
  • Community annotation for 2B63 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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