3RZO Transcription Rna Dna date May 12, 2011
title Rna Polymerase II Initiation Complex With A 4-Nt Rna
authors X.Liu, D.A.Bushnell, D.A.Silva, X.Huang, R.D.Kornberg
compound source
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb1
Chain: A
Synonym: Rna Polymerase II Subunit 1, Rna Polymerase II Sub Dna-Directed Rna Polymerase III Largest Subunit, Rna Polyme Subunit B220;
Ec: 2.7.7.6
Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Cb010

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

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Cb010

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb3
Chain: C
Synonym: Rna Polymerase II Subunit 3, Rna Polymerase II Sub B44.5, Dna-Directed Rna Polymerase II 45 Kda Polypeptide;

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Cb010

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: E
Synonym: Rna Polymerases I, II, And III Subunit Abc1, Abc27 Directed Rna Polymerases I, II, And III 27 Kda Polypeptide;

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Cb010

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: F
Synonym: Rna Polymerases I, II, And III Subunit Abc2, Abc23 Directed Rna Polymerases I, II, And III 23 Kda Polypeptide;

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Cb010

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: H
Synonym: Rna Polymerases I, II, And III Subunit Abc3, Abc14 Abc14.5, Dna-Directed Rna Polymerases I, II, And III 14.5 K Polypeptide;

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Cb010

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb9
Chain: I
Synonym: Rna Polymerase II Subunit B9, B12.6, Dna-Directed Polymerase II 14.2 Kda Polypeptide, Dna-Directed Rna Polyme Subunit 9;

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Cb010

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: J
Synonym: Rna Polymerases I, II, And III Subunit Abc5, Abc10 Abc8, Dna-Directed Rna Polymerases I, II, And III 8.3 Kda Polypeptide;

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Cb010

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb11
Chain: K
Synonym: Rna Polymerase II Subunit B11, B13.6, Dna-Directed Polymerase II 13.6 Kda Polypeptide;

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Cb010

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: L
Synonym: Rna Polymerases I, II, And III Subunit Abc4, Abc10

Organism_scientific: Saccharomyces Cerevisiae S288c
Organism_common: Baker'S Yeast
Organism_taxid: 559292
Strain: Cb010

Molecule: Rna (5'-R(Gpapgpg)-3')
Chain: R
Engineered: Yes
Other_details: 4-Nt Rna

Synthetic: Yes

Molecule: Dna (5'- D(Cptpapcpcpgpaptpapapgpcpapgpapcpgpaptp Cptpcpgpaptpg)-3');
Chain: T
Engineered: Yes
Other_details: Template Dna

Synthetic: Yes
symmetry Space Group: C 1 2 1
R_factor 0.188 R_Free 0.236
crystal
cell
length a length b length c angle alpha angle beta angle gamma
161.038 221.149 192.875 90.00 98.34 90.00
method X-Ray Diffractionresolution 3.00 Å
ligand 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 referenceInitiation complex structure and promoter proofreading., Liu X, Bushnell DA, Silva DA, Huang X, Kornberg RD, Science. 2011 Jul 29;333(6042):633-7. PMID:21798951
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (1244 Kb) [Save to disk]
  • Biological Unit Coordinates (3rzo.pdb1.gz) 1231 Kb
  • LPC: Ligand-Protein Contacts for 3RZO
  • CSU: Contacts of Structural Units for 3RZO
  • Structure Factors (1078 Kb)
  • Retrieve 3RZO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3RZO from S2C, [Save to disk]
  • Re-refined 3rzo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3RZO 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 3RZO
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 3RZO, from MSDmotif at EBI
  • Fold representative 3rzo from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3rzo_C] [3rzo_R] [3rzo] [3rzo_A] [3rzo_J] [3rzo_B] [3rzo_H] [3rzo_T] [3rzo_L] [3rzo_F] [3rzo_I] [3rzo_K] [3rzo_E]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 3RZO: [RNA_pol_Rpb6] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [ZnF_C2C2 ] by SMART
  • Other resources with information on 3RZO
  • Community annotation for 3RZO at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
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