3HOW Transcription,Transferase Dna Rna Hybrid date Jun 03, 2009
title Complete Rna Polymerase II Elongation Complex III With A T-U Mismatch And A Frayed Rna 3'-Uridine
authors J.F.Sydow, F.Brueckner, A.C.M.Cheung, G.E.Damsma, S.Dengl, E.Lehmann, D.Vassylyev, P.Cramer
compound source
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb1
Chain: A
Synonym: Rna Polymerase II Subunit B1, Rna Polymerase II Subunit 1, Dna-Directed Rna Polymerase III Largest Subunit, Rna Polymerase II Subunit B220;
Ec: 2.7.7.6
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb2
Chain: B
Synonym: Rna Polymerase II Subunit 2, Dna-Directed Rna Polymerase II 140 Kda Polypeptide, B150;
Ec: 2.7.7.6

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

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb3
Chain: C
Synonym: Rna Polymerase II Subunit B3, Rna Polymerase II Subunit 3, Dna-Directed Rna Polymerase II 45 Kda Polypeptide, 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 Subunit Rpb4
Chain: D
Synonym: Rna Polymerase II Subunit B4, Dna-Directed Rna Polymerase II 32 Kda Polypeptide, B32;
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 Subunit Rpabc1;
Chain: E
Synonym: Rna Polymerases I, II, And III Subunit Abc1, Dna- Directed Rna Polymerases I, II, And III 27 Kda Polypeptide, 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 Subunit Rpabc2;
Chain: F
Synonym: Rna Polymerases I, II, And III Subunit Abc2, Dna- Directed Rna Polymerases I, II, And III 23 Kda Polypeptide, Abc23;
Ec: 2.7.7.6

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

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb7
Chain: G
Synonym: Rna Polymerase II Subunit B7, B16
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 Subunit Rpabc3;
Chain: H
Synonym: Rna Polymerases I, II, And III Subunit Abc3, Dna- Directed Rna Polymerases I, II, And III 14.5 Kda Polypeptide, Abc14.5, 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 Rpb9
Chain: I
Synonym: Rna Polymerase II Subunit B9, Dna-Directed Rna Polymerase II Subunit 9, 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 I, II, And III Subunit Rpabc5;
Chain: J
Synonym: Rna Polymerases I, II, And III Subunit Abc5, 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 Subunit Rpb11
Chain: K
Synonym: Rna Polymerase II Subunit B11, Dna-Directed Rna Polymerase II 13.6 Kda Polypeptide, 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 Subunit Rpabc4;
Chain: L
Synonym: Rna Polymerases I, II, And III Subunit Abc4, Abc10-Alpha;
Ec: 2.7.7.6

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

Molecule: 5'-D(Apcptpapcptptpgpapgpcpt)-3'
Chain: 2
Synonym: Nontemplate Dna
Engineered: Yes

Synthetic: Yes

Molecule: 5'- D(Apgpcptpcapapgptpapgptptpaptpgpcpcp(Br U)Pgpgptpcpaptpt)-3';
Chain: 1
Synonym: Template Dna
Engineered: Yes

Synthetic: Yes

Molecule: 5'- R(Upgpcpapupupucpapapcpcpapgpgpcpupu)-3';
Chain: 3
Synonym: Product Rna
Engineered: Yes

Synthetic: Yes
symmetry Space Group: C 2 2 21
R_factor 0.214 R_Free 0.254
crystal
cell
length a length b length c angle alpha angle beta angle gamma
222.645 395.962 283.476 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.60 Å
ligand BRU, 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 referenceStructural basis of transcription: mismatch-specific fidelity mechanisms and paused RNA polymerase II with frayed RNA., Sydow JF, Brueckner F, Cheung AC, Damsma GE, Dengl S, Lehmann E, Vassylyev D, Cramer P, Mol Cell. 2009 Jun 26;34(6):710-21. PMID:19560423
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (658 Kb) [Save to disk]
  • Biological Unit Coordinates (3how.pdb1.gz) 647 Kb
  • LPC: Ligand-Protein Contacts for 3HOW
  • CSU: Contacts of Structural Units for 3HOW
  • Likely Quarternary Molecular Structure file(s) for 3HOW
  • Structure Factors (1482 Kb)
  • Retrieve 3HOW in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3HOW from S2C, [Save to disk]
  • Re-refined 3how structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3HOW 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 3HOW
  • 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 3HOW, from MSDmotif at EBI
  • Fold representative 3how from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3how_F] [3how_K] [3how_D] [3how_1] [3how_A] [3how_G] [3how_B] [3how_2] [3how_I] [3how] [3how_3] [3how_C] [3how_L] [3how_J] [3how_H] [3how_E]
  • 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 3HOW: [RNA_pol_Rpb6] [RPOL4c] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [S1] [ZnF_C2C2 ] by SMART
  • Other resources with information on 3HOW
  • Community annotation for 3HOW 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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