4V1M Transcription date Sep 29, 2014
title Architecture Of The Rna Polymerase II-Mediator Core Transcri Initiation Complex
authors C.Plaschka, L.Lariviere, L.Wenzeck, M.Hemann, D.Tegunov, E.V.Petr C.H.Borchers, W.Baumeister, F.Herzog, E.Villa, P.Cramer
compound source
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb1
Chain: A
Synonym: Rna Polymerase II Subunit 1, Rna Polymerase II Sub Dna-Directed Rna Polymerase III Largest Subunit, Rna Polyme Subunit B220;
Ec: 2.7.7.6
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bj5464 Rpb3 His-Bio

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

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bj5464 Rpb3 His-Bio

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb3
Chain: C
Synonym: Rna Polymerase II Subunit 3, Rna Polymerase II Sub B44.5, Dna-Directed Rna Polymerase II 45 Kda Polypeptide;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bj5464 Rpb3 His-Bio

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

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bj5464 Rpb3 His-Bio

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

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bj5464 Rpb3 His-Bio

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

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bj5464 Rpb3 His-Bio

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb9
Chain: I
Synonym: Rna Polymerase II Subunit B9, B12.6, Dna-Directed II 14.2 Kda Polypeptide, Dna-Directed Rna Polymerase II Sub

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bj5464 Rpb3 His-Bio

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

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bj5464 Rpb3 His-Bio

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb11
Chain: K
Synonym: Rna Polymerase II Subunit B11, B13.6, Dna-Directed Polymerase II 13.6 Kda Polypeptide;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bj5464 Rpb3 His-Bio

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun 4;
Chain: L
Synonym: Rna Polymerases I\,II\,And III Subunit Abc4, Abc10 Dna-Directed Rna Polymerases I\,II\,And III Subunit Rpabc 4
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Baker'S Yeast
Organism_taxid: 4932
Strain: Bj5464 Rpb3 His-Bio

Molecule: 5'-D(Apapgptpapcptptpgpap)-3'
Chain: N
Synonym: Nontemplate Dna
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-D(Cpcpapgpgpap)-3'
Chain: P
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630

Molecule: 5'-D(Tpcpapapgptpapcptptptptptpcp Cpbrupgpgptpc)-3';
Chain: T
Synonym: Template Dna
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
symmetry Space Group: P 1
R_factor
R_Free
crystal
cell
length a length b length c angle alpha angle beta angle gamma
1.000 1.000 1.000 90.00 90.00 90.00
method Electron Microscopyresolution 6.60 Å
ligand BRU, 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 referenceArchitecture of the RNA polymerase II-Mediator core initiation complex., Plaschka C, Lariviere L, Wenzeck L, Seizl M, Hemann M, Tegunov D, Petrotchenko EV, Borchers CH, Baumeister W, Herzog F, Villa E, Cramer P, Nature. 2015 Feb 4. doi: 10.1038/nature14229. PMID:25652824
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (610 Kb) [Save to disk]
  • Biological Unit Coordinates (4v1m.pdb1.gz) 600 Kb
  • LPC: Ligand-Protein Contacts for 4V1M
  • CSU: Contacts of Structural Units for 4V1M
  • Retrieve 4V1M in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4V1M from S2C, [Save to disk]
  • View 4V1M 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 4V1M
  • 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 4V1M, from MSDmotif at EBI
  • Fold representative 4v1m from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4v1m_K] [4v1m_F] [4v1m_A] [4v1m_B] [4v1m_N] [4v1m_J] [4v1m_E] [4v1m_I] [4v1m_P] [4v1m_C] [4v1m_H] [4v1m] [4v1m_T] [4v1m_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4V1M: [RNA_pol_Rpb6] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [ZnF_C2C2 ] by SMART
  • Other resources with information on 4V1M
  • Community annotation for 4V1M at PDBWiki (http://pdbwiki.org)

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