1R9T Transcription Dna-Rna Hybrid date Oct 30, 2003
title Rna Polymerase II Strand Separated Elongation Complex, Misma Nucleotide
authors K.D.Westover, D.A.Bushnell, R.D.Kornberg
compound source
Molecule: Rna Strand
Chain: R
Engineered: Yes
Other_details: Transcript
 Synthetic: Yes

Molecule: Dna Template Strand
Chain: T
Engineered: Yes
Synthetic: Yes

Molecule: Dna Nontemplate Strand
Chain: N
Engineered: Yes
Synthetic: Yes

Molecule: Dna-Directed Rna Polymerase II Largest Subunit
Chain: A
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
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
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
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
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
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 14.2 Kda Polypepti
Chain: I
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 8.3 K Polypeptide;
Chain: J
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
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
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 0.230 R_Free 0.317
crystal
cell
length a length b length c angle alpha angle beta angle gamma
168.846 222.958 193.602 90.00 101.17 90.00
method X-Ray Diffractionresolution 3.50 Å
ligand ATP, 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...


    • 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: nucleotide selection by rotation in the RNA polymerase II active center., Westover KD, Bushnell DA, Kornberg RD, Cell 2004 Nov 12;119(4):481-9. PMID:15537538
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (601 Kb) [Save to disk]
  • Biological Unit Coordinates (1r9t.pdb1.gz) 588 Kb
  • LPC: Ligand-Protein Contacts for 1R9T
  • CSU: Contacts of Structural Units for 1R9T
  • Likely Quarternary Molecular Structure file(s) for 1R9T
  • Structure Factors (1172 Kb)
  • Retrieve 1R9T in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1R9T from S2C, [Save to disk]
  • Re-refined 1r9t structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1R9T 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 1R9T
  • 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 1R9T, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1r9ta_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1r9tb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1r9tc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1r9te_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1r9tf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1r9th_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1r9ti_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1r9tj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1r9tk_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1r9tl_, region L [Jmol] [rasmolscript] [script source]
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1r9t_K] [1r9t_T] [1r9t_H] [1r9t_R] [1r9t_N] [1r9t_F] [1r9t_E] [1r9t_B] [1r9t_L] [1r9t] [1r9t_I] [1r9t_A] [1r9t_J] [1r9t_C]
  • 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 1R9T: [RNA_pol_Rpb6] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [ZnF_C2C2 ] by SMART
    • Other resources with information on 1R9T
  • Community annotation for 1R9T 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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