1TWF Transcription date Jun 30, 2004
title Rna Polymerase II Complexed With Utp At 2.3 A Resolution
authors K.D.Westover, D.A.Bushnell, R.D.Kornberg
compound source
Molecule: Dna-Directed Rna Polymerase II Largest Subunit
Chain: A
Synonym: B220
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
Synonym: B150, Rna Polymerase II Subunit 2
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
Synonym: B44.5
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
Synonym: Abc27
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
Synonym: Abc23
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
Synonym: Abc14.4
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
Synonym: B12.6
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
Synonym: Abc10-Beta, Abc8
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
Synonym: B13.6
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
Synonym: Abc10-Alpha
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Delta-Rpb4
symmetry Space Group: I 2 2 2
R_factor 0.247 R_Free 0.294
crystal
cell
length a length b length c angle alpha angle beta angle gamma
123.000 223.000 374.000 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.30 Å
ligand MN, UTP, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
note 1TWF is a representative structure
related structures by homologous chain: 1DZF, 1I50, 1K83
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] (586 Kb) [Save to disk]
  • Biological Unit Coordinates (1twf.pdb1.gz) 576 Kb
  • Biological Unit Coordinates (1twf.pdb2.gz) 1142 Kb
  • LPC: Ligand-Protein Contacts for 1TWF
  • CSU: Contacts of Structural Units for 1TWF
  • Likely Quarternary Molecular Structure file(s) for 1TWF
  • Structure Factors (2123 Kb)
  • Retrieve 1TWF in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1TWF from S2C, [Save to disk]
  • Re-refined 1twf structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1TWF 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 1TWF
  • 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 1TWF, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1twfa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1twfb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1twfc1, region C:3-41,C:173-268 [Jmol] [rasmolscript] [script source]
        - Domain d1twfc2, region C:42-172 [Jmol] [rasmolscript] [script source]
        - Domain d1twfe1, region E:1-143 [Jmol] [rasmolscript] [script source]
        - Domain d1twfe2, region E:144-215 [Jmol] [rasmolscript] [script source]
        - Domain d1twff_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1twfh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1twfi1, region I:1-49 [Jmol] [rasmolscript] [script source]
        - Domain d1twfi2, region I:50-121 [Jmol] [rasmolscript] [script source]
        - Domain d1twfj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1twfk_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1twfl_, region L [Jmol] [rasmolscript] [script source]
  • Fold representative 1twf from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1twf_H] [1twf_L] [1twf_B] [1twf_E] [1twf_A] [1twf] [1twf_F] [1twf_C] [1twf_K] [1twf_J] [1twf_I]
  • 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 1TWF: [RNA_pol_Rpb6] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [ZnF_C2C2 ] by SMART
  • Other resources with information on 1TWF
  • Community annotation for 1TWF at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

  • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014
    Bioinformatics Unit
    Weizmann Institute of Science