2VUM Transferase date May 27, 2008
title Alpha-Amanitin Inhibited Complete Rna Polymerase II Elongati
authors F.Brueckner, P.Cramer
compound source
Molecule: Dna-Directed Rna Polymerase II Subunit Rpb1
Chain: A
Synonym: Rna Polymerase II Subunit B1, Rna Polymerase II Su Dna-Directed Rna Polymerase III Largest Subunit, B220, Dna- Rna Polymerase II Largest Subunit;
Ec: 2.7.7.6
Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Bakers' Yeast
Organism_taxid: 4932

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

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Bakers' Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb3
Chain: C
Synonym: Dna-Directed Rna Polymerase II 45 Kda Polypeptide, Polymerase II Subunit B3, Rna Polymerase II Subunit 3, Dna- Rna Polymerase II 45 Kda Polypeptide, B445.;
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Bakers' Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb4
Chain: D
Synonym: Dna-Directed Rna Polymerase II 32 Kda Polypeptide, Polymerase II Subunit B4, Dna-Directed Rna Polymerase II 32 Polypeptide, B32;
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Bakers' Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: E
Synonym: Dna-Directed Rna Polymerases I, II, And III 27 Kda Polypeptide, Rna Polymerases I, II, And III Subunit Abc1, D Directed Rna Polymerases I, II, And III 27 Kda Polypeptide,
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Bakers' Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: F
Synonym: Dna-Directed Rna Polymerases I, II, And III 23 Kda Polypeptide, Rna Polymerases I, II, And III Subunit Abc2, D Directed Rna Polymerases I, II, And III 23 Kda Polypeptide,
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Bakers' Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb7
Chain: G
Synonym: Dna-Directed Rna Polymerase II 19 Kda Polypeptide, Polymerase II Subunit B7, B16;
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Bakers' Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: H
Synonym: Dna-Directed Rna Polymerases I, II, And III 14.5 K Polypeptide, Rna Polymerases I, II, And III Subunit Abc3, D Directed Rna Polymerases I, II, And III 145 Kda Polypeptide Abc145;
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Bakers' Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb9
Chain: I
Synonym: Dna-Directed Rna Polymerase II Subunit 9, Rna Poly Subunit B9, Dna-Directed Rna Polymerase II Subunit 9, Dna-D Rna Polymerase II 142 Kda Polypeptide, B126;
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Bakers' Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: J
Synonym: Dna-Directed Rna Polymerases I, II, And III Subuni Polymerases I, II, And III Subunit Abc5, Dna-Directed Rna P I, II, And III 83 Kda Polypeptide, Abc10-Beta, Abc8;
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Bakers' Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerase II Subunit Rpb11
Chain: K
Synonym: Dna-Directed Rna Polymerase II 13.6 Kda Polypeptid Polymerase II Subunit B11, Dna-Directed Rna Polymerase II 1 Polypeptide, B136;
Ec: 2.7.7.6

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Bakers' Yeast
Organism_taxid: 4932

Molecule: Dna-Directed Rna Polymerases I, II, And III Subun
Chain: L
Synonym: Dna-Directed Rna Polymerases I, II, And III 7.7 Kd Polypeptide, Rna Polymerases I, II, And III Subunit Abc4, A Alpha;

Organism_scientific: Saccharomyces Cerevisiae
Organism_common: Bakers' Yeast
Organism_taxid: 4932

Molecule: Amatoxin
Chain: M
Synonym: Alpha Amanitin, Gamma-Amanitin

Organism_scientific: Amanita Phalloides
Organism_common: Death Cap
Organism_taxid: 67723

Molecule: 5'-D(Apapapcptpapcptptpgp Apgpcpt)-
Chain: N
Synonym: Nontemplate Dna
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Synthetic Oligonucleotide

Molecule: 5'-R(Apapapgpapcpcpapgpgpc)-3'
Chain: P
Synonym: Product Rna
Engineered: Yes

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Synthetic Oligonucleotide

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

Synthetic: Yes
Organism_scientific: Synthetic Construct
Organism_taxid: 32630
Other_details: Synthetic Oligonucleotide
symmetry Space Group: C 2 2 21
R_factor 0.255 R_Free 0.288
crystal
cell
length a length b length c angle alpha angle beta angle gamma
220.619 394.234 283.966 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.40 Å
ligand BRU, CSX, HYP, ILX, MG, TRX, 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
  • RNA-directed 5'-3' RNA polym...


  • 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 referenceStructural basis of transcription inhibition by alpha-amanitin and implications for RNA polymerase II translocation., Brueckner F, Cramer P, Nat Struct Mol Biol. 2008 Aug;15(8):811-8. Epub 2008 Jun 13. PMID:18552824
    Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (665 Kb) [Save to disk]
  • Biological Unit Coordinates (2vum.pdb1.gz) 652 Kb
  • LPC: Ligand-Protein Contacts for 2VUM
  • CSU: Contacts of Structural Units for 2VUM
  • Likely Quarternary Molecular Structure file(s) for 2VUM
  • Structure Factors (3329 Kb)
  • Retrieve 2VUM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2VUM from S2C, [Save to disk]
  • Re-refined 2vum structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2VUM 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 2VUM
  • 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 2VUM, from MSDmotif at EBI
  • Fold representative 2vum from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2vum_D] [2vum_J] [2vum_T] [2vum_G] [2vum_C] [2vum_I] [2vum_P] [2vum_E] [2vum_M] [2vum_N] [2vum_B] [2vum] [2vum_F] [2vum_A] [2vum_H] [2vum_L] [2vum_K]
  • SWISS-PROT database: [P85421] [P20434] [P20435] [P20436] [P40422] [P22139] [P38902] [P04050] [P08518] [P16370] [P20433] [P34087] [P27999]
  • Domain organization of [AMATX_AMAPH] [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 2VUM: [RNA_pol_Rpb6] [RPOL4c] [RPOL8c] [RPOL9] [RPOLA_N] [RPOLCX] [RPOLD] [S1] [ZnF_C2C2 ] by SMART
  • Other resources with information on 2VUM
  • Community annotation for 2VUM 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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