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 Diffraction	resolution	3.40 Å
ligand	BRU, CSX, HYP, ILX, MG, TRX, ZN	enzyme	Transferase E.C.2.7.7.6 BRENDA
Gene Ontology	Chain Function Process Component 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 reference	Structural 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] (654 Kb) [Save to disk] Biological Unit Coordinates (2vum.pdb1.gz) 643 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

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 3D motif for 2VUM, from MSDmotif at EBI

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)

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