1SFO Transcription Dna-Rna Hybrid date Feb 20, 2004
title Rna Polymerase II Strand Separated Elongation Complex
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 Strand
Chain: T
Engineered: Yes
Other_details: Template

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 Polypeptide;
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 Kda 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 Kda 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 Kda 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 Polypeptide;
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 Kda 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 Polypeptide;
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 Kda 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 0.315 R_Free 0.343
crystal
cell
length a length b length c angle alpha angle beta angle gamma
167.076 221.256 193.685 90.00 100.10 90.00
method X-Ray Diffractionresolution 3.61 Å
ligand MG, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
note 1SFO supersedes 1R9R
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: separation of RNA from DNA by RNA polymerase II., Westover KD, Bushnell DA, Kornberg RD, Science 2004 Feb 13;303(5660):1014-6. PMID:14963331
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (538 Kb) [Save to disk]
  • Biological Unit Coordinates (1sfo.pdb1.gz) 517 Kb
  • LPC: Ligand-Protein Contacts for 1SFO
  • CSU: Contacts of Structural Units for 1SFO
  • Likely Quarternary Molecular Structure file(s) for 1SFO
  • Structure Factors (614 Kb)
  • Retrieve 1SFO in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1SFO from S2C, [Save to disk]
  • Re-refined 1sfo structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1SFO 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 1SFO
  • 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 1SFO, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1sfoa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1sfob_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1sfoc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1sfoe_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1sfof_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1sfoh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1sfoi_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1sfoj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1sfok_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1sfol_, region L [Jmol] [rasmolscript] [script source]
        - Domain d1sfor_, region R [Jmol] [rasmolscript] [script source]
        - Domain d1sfot_, region T [Jmol] [rasmolscript] [script source]
  • Fold representative 1sfo from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1sfo_B] [1sfo_H] [1sfo_J] [1sfo_C] [1sfo_F] [1sfo_L] [1sfo_A] [1sfo_E] [1sfo_R] [1sfo_K] [1sfo_I] [1sfo] [1sfo_T]
  • 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 1SFO: [RNA_pol_Rpb6] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [ZnF_C2C2 ] by SMART
  • Other resources with information on 1SFO
  • Community annotation for 1SFO 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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