4C2M Transcription date Aug 19, 2013
title Structure Of Rna Polymerase I At 2.8 A Resolution
authors C.Engel, S.Sainsbury, A.C.Cheung, D.Kostrewa, P.Cramer
compound source
Molecule: Dna-Directed Rna Polymerase I Subunit Rpa190
Chain: A, P
Synonym: A190, Dna-Directed Rna Polymerase I 190 Kda Polype Dna-Directed Rna Polymerase I Largest Subunit;
Ec: 2.7.7.6
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Cb010

Molecule: Dna-Directed Rna Polymerase I Subunit Rpa49
Chain: 2, M
Synonym: A49, Dna-Directed Rna Polymerase I 49 Kda Polypept

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Cb010

Molecule: Dna-Directed Rna Polymerases I And III Subunit Rp
Chain: K, Z
Synonym: Rna Polymerases I And III Subunit Ac2, Dna-Directe Polymerases I And III 16 Kda Polypeptide, Rpa19, Ac19;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Cb010

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun 3;
Chain: H, W
Synonym: Rna Polymerases I\,II\,And III Subunit Abc3, Abc14 Abc14.5, Dna-Directed Rna Polymerases I\,II\,And III 14.5 Polypeptide, Rpb8;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Cb010

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun 1;
Chain: E, T
Synonym: Rna Polymerases I, II, And III Subunit Abc1, Abc27 Dna-Directed Rna Polymerases I\,II\,And III 27 Kda Polypep Rpb5;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Cb010

Molecule: Dna-Directed Rna Polymerase I Subunit Rpa135
Chain: B, Q
Synonym: Dna-Directed Rna Polymerase I 135 Kda Polypeptide, Dna-Directed Rna Polymerase I Polypeptide 2, Rna Polymeras Subunit 2, A135;
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Cb010

Molecule: Dna-Directed Rna Polymerase I Subunit Rpa12
Chain: I, X
Synonym: A12, A12.2, Dna-Directed Rna Polymerase I 13.7 Kda Polypeptide, A12.2;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Cb010

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun 4;
Chain: 1, L
Synonym: Rna Polymerases I\,II\,And III Subunit Abc4, Abc10 Rpb12;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Cb010

Molecule: Dna-Directed Rna Polymerase I Subunit Rpa14
Chain: D, S
Synonym: A14, Dna-Directed Rna Polymerase I 14 Kda Polypept

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Cb010

Molecule: Dna-Directed Rna Polymerase I Subunit Rpa34
Chain: 3, N
Synonym: A34, Dna-Directed Dna-Dependent Rna Polymerase 34. Polypeptide, A34.5, A34.5;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Cb010

Molecule: Dna-Directed Rna Polymerase I Subunit Rpa43
Chain: 4, G, O, V
Synonym: A43, Dna-Directed Dna-Dependent Rna Polymerase 36 Polypeptide, A43;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Cb010

Molecule: Dna-Directed Rna Polymerases I And III Subunit Rp
Chain: C, R
Synonym: Rna Polymerases I And III Subunit Ac1, C37, Dna-Di Rn A Polymerases I And III 40 Kda Polypeptide, Ac40, C40,

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Cb010

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun 2;
Chain: F, U
Synonym: Rna Polymerases I\,II\,And III Subunit Abc2, Abc23 Dna-Directed Rna Polymerases I\,II\,And III 23 Kda Polypep Rpb6;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Cb010

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun 5;
Chain: J, Y
Synonym: Rna Polymerases I\,II\,And III Subunit Abc5, Abc10 Abc8, Dna-Directed Rna Polymerases I\,II\,And III 8.3 Kda Polypeptide, Rpb10

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Cb010
symmetry Space Group: P 1
R_factor 0.1689 R_Free 0.2099
crystal
cell
length a length b length c angle alpha angle beta angle gamma
122.740 139.020 209.550 108.06 95.40 93.85
method X-Ray Diffractionresolution 2.80 Å
ligand SO4, ZN enzyme Transferase E.C.2.7.7.6 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
1, L
  • RNA-directed 5'-3' RNA polym...


  • 2, M


    A, P


    C, R


    F, U
  • RNA-directed 5'-3' RNA polym...


  • K, Z


    N, 3


    Q, B


    S, D


    T, E
  • RNA-directed 5'-3' RNA polym...


  • V, O, 4, G


    W, H
  • RNA-directed 5'-3' RNA polym...


  • X, I


    Y, J
  • RNA-directed 5'-3' RNA polym...

  • DNA-directed RNA polymerase ...
  • Primary referenceRNA polymerase I structure and transcription regulation., Engel C, Sainsbury S, Cheung AC, Kostrewa D, Cramer P, Nature. 2013 Oct 31;502(7473):650-5. doi: 10.1038/nature12712. Epub 2013 Oct 23. PMID:24153182
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (2930 Kb) [Save to disk]
  • Biological Unit Coordinates (4c2m.pdb1.gz) 1461 Kb
  • Biological Unit Coordinates (4c2m.pdb2.gz) 1469 Kb
  • LPC: Ligand-Protein Contacts for 4C2M
  • CSU: Contacts of Structural Units for 4C2M
  • Structure Factors (5242 Kb)
  • Retrieve 4C2M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4C2M from S2C, [Save to disk]
  • Re-refined 4c2m structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4C2M 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 4C2M
  • 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 4C2M, from MSDmotif at EBI
  • Fold representative 4c2m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4c2m_W] [4c2m_4] [4c2m_Q] [4c2m_R] [4c2m_Z] [4c2m_N] [4c2m_U] [4c2m_S] [4c2m_F] [4c2m_Y] [4c2m] [4c2m_M] [4c2m_L] [4c2m_I] [4c2m_V] [4c2m_1] [4c2m_G] [4c2m_2] [4c2m_X] [4c2m_K] [4c2m_D] [4c2m_C] [4c2m_H] [4c2m_E] [4c2m_3] [4c2m_T] [4c2m_A] [4c2m_J] [4c2m_B] [4c2m_P] [4c2m_O]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4C2M: [RNA_pol_Rpb6] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [ZnF_C2C2 ] by SMART
  • Other resources with information on 4C2M
  • Community annotation for 4C2M at PDBWiki (http://pdbwiki.org)

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