1WCM Transcription date Nov 17, 2004
title Complete 12-Subunit Rna Polymerase II At 3.8 Ang
authors K.J.Armache, S.Mitterweger, A.Meinhart, P.Cramer
compound source
Molecule: Dna-Directed Rna Polymerase II Largest Subunit
Chain: A
Synonym: Rpb1, B220
Ec: 2.7.7.6
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932

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

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II 45 Kda Polypeptide;
Chain: C
Synonym: Rpb3, B44.5
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II 32 Kda Polypeptide;
Chain: D
Synonym: Rpb4, B32, Yeast Dna-Directed Rna Polymerase II 32 Kd Polypeptide;
Ec: 2.7.7.6
Engineered: Yes
Other_details: Numbering Of Resiudes D10-D24 Is Arbitrary

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Dna-Directed Rna Polymerases I, II, And III 27 Kda Polypeptide;
Chain: E
Synonym: Rpb5, Abc27
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III 23 Kda Polypeptide;
Chain: F
Synonym: Rpb6, Abc23, Rna Polymerase II Sixth Subunit
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II 19 Kd Polypeptide
Chain: G
Synonym: Rpb7, B16, Rpb7p
Ec: 2.7.7.6
Engineered: Yes

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)

Molecule: Dna-Directed Rna Polymerases I, II, And III 14.5 Kda Polypeptide;
Chain: H
Synonym: Rpb8,Abc14.4,6-Kda Rna Polymerase Subunit
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II 14.2 Kda Polypeptide;
Chain: I
Synonym: Rpb9, B12.6, Rpb9p, Dna-Directed Rna Polymerase II Subunit 9 Dna-Directed Rna Polymerase II 14.2 Kda Polypeptide;
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II And III 8.3 Kda Polypeptide;
Chain: J
Synonym: Rpb10, Abc10-, Abc8, Abc10-Beta, Rpb10p, Dna-Directed Rna Polymerases IIIIII Subunit 10;
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II 13.6 Kda Polypeptide;
Chain: K
Synonym: Rpb11, B13.6
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III 7.7 Kda Polypeptide;
Chain: L
Synonym: Rpb12, Abc10-, Rpc10p, Abc10-Alpha
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Yeast
Organism_taxid: 4932
symmetry Space Group: C 2 2 21
R_factor 0.2569 R_Free 0.2854
crystal
cell
length a length b length c angle alpha angle beta angle gamma
222.718 395.135 284.300 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.80 Å
ligand 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


    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 referenceStructures of complete RNA polymerase II and its subcomplex, Rpb4/7., Armache KJ, Mitterweger S, Meinhart A, Cramer P, J Biol Chem. 2005 Feb 25;280(8):7131-4. Epub 2004 Dec 9. PMID:15591044
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (651 Kb) [Save to disk]
  • Biological Unit Coordinates (1wcm.pdb1.gz) 631 Kb
  • LPC: Ligand-Protein Contacts for 1WCM
  • CSU: Contacts of Structural Units for 1WCM
  • Likely Quarternary Molecular Structure file(s) for 1WCM
  • Structure Factors (1079 Kb)
  • Retrieve 1WCM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1WCM from S2C, [Save to disk]
  • Re-refined 1wcm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1WCM 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 1WCM
  • 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 1WCM, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1wcma_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1wcmb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1wcmc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1wcmd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1wcme_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1wcmf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1wcmg_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1wcmh_, region H [Jmol] [rasmolscript] [script source]
        - Domain d1wcmi_, region I [Jmol] [rasmolscript] [script source]
        - Domain d1wcmj_, region J [Jmol] [rasmolscript] [script source]
        - Domain d1wcmk_, region K [Jmol] [rasmolscript] [script source]
        - Domain d1wcml_, region L [Jmol] [rasmolscript] [script source]
  • Fold representative 1wcm from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1wcm_A] [1wcm] [1wcm_J] [1wcm_G] [1wcm_I] [1wcm_B] [1wcm_E] [1wcm_K] [1wcm_C] [1wcm_D] [1wcm_F] [1wcm_H] [1wcm_L]
  • 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 1WCM: [RNA_pol_Rpb6] [RPOL4c] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [S1] [ZnF_C2C2 ] by SMART
  • Other resources with information on 1WCM
  • Community annotation for 1WCM 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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