Alpha-amanitin inhibited complete RNA polymerase II elongation complex DOI:10.2210/pdb2vum/pdb   NDB ID: 2VUM

2VUM   Display Files  close FASTA Sequence PDB File PDB File (Header) mmCIF File mmCIF File (Header) PDBML/XML File PDBML/XML File (Header)   Download Files  close FASTA Sequence PDB File (Text) PDB File (gz) mmCIF File mmCIF File (gz) PDBML/XML File PDBML/XML File (gz) Structure Factor (Text) Structure Factor (gz) Biological Assembly (gz) (A+S)   Share this Page  close Facebook Twitter LinkedIn Email Link this Page

Primary Citation       Related Citations in PDB Entry (REMARK 1) Hide     Molecular Description Hide Classification: Transferase/toxin Structure Weight: 531506.25 Molecule: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 Polymer: 1 Type: protein Length: 1733 Chains: A EC#: 2.7.7.6    Organism Saccharomyces cerevisiae Gene Names RPO21 RPB1 RPB220 SUA8 YDL140C D2150 UniProtKB:   Protein Feature View | Search PDB | P04050     Molecule: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 Polymer: 2 Type: protein Length: 1224 Chains: B EC#: 2.7.7.6    Organism Saccharomyces cerevisiae Gene Names RPB2 RPB150 RPO22 YOR151C UniProtKB:   Protein Feature View | Search PDB | P08518     Molecule: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 Polymer: 3 Type: protein Length: 318 Chains: C EC#: 2.7.7.6    Organism Saccharomyces cerevisiae Gene Names RPB3 YIL021W UniProtKB:   Protein Feature View | Search PDB | P16370     Molecule: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 Polymer: 4 Type: protein Length: 221 Chains: D EC#: 2.7.7.6    Organism Saccharomyces cerevisiae Gene Names RPB4 YJL140W J0654 UniProtKB:   Protein Feature View | Search PDB | P20433     Molecule: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1 Polymer: 5 Type: protein Length: 215 Chains: E EC#: 2.7.7.6    Organism Saccharomyces cerevisiae Gene Names RPB5 RPA7 RPC9 YBR154C YBR1204 UniProtKB:   Protein Feature View | Search PDB | P20434     Molecule: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2 Polymer: 6 Type: protein Length: 155 Chains: F EC#: 2.7.7.6    Organism Saccharomyces cerevisiae Gene Names RPO26 RPB6 YPR187W P9677.8 UniProtKB:   Protein Feature View | Search PDB | P20435     Molecule: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 Polymer: 7 Type: protein Length: 171 Chains: G EC#: 2.7.7.6    Organism Saccharomyces cerevisiae Gene Names RPB7 YDR404C D9509.22 UniProtKB:   Protein Feature View | Search PDB | P34087     Molecule: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3 Polymer: 8 Type: protein Length: 146 Chains: H EC#: 2.7.7.6    Organism Saccharomyces cerevisiae Gene Names RPB8 YOR224C YOR50-14 UniProtKB:   Protein Feature View | Search PDB | P20436     Molecule: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 Polymer: 9 Type: protein Length: 122 Chains: I EC#: 2.7.7.6    Organism Saccharomyces cerevisiae Gene Names RPB9 YGL070C UniProtKB:   Protein Feature View | Search PDB | P27999     Molecule: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5 Polymer: 10 Type: protein Length: 70 Chains: J EC#: 2.7.7.6    Organism Saccharomyces cerevisiae Gene Names RPB10 YOR210W UniProtKB:   Protein Feature View | Search PDB | P22139     Molecule: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 Polymer: 11 Type: protein Length: 120 Chains: K EC#: 2.7.7.6    Organism Saccharomyces cerevisiae Gene Names RPB11 YOL005C UniProtKB:   Protein Feature View | Search PDB | P38902     Molecule: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4 Polymer: 12 Type: protein Length: 70 Chains: L Organism Saccharomyces cerevisiae Gene Names RPC10 RPB12 YHR143W-A YHR143BW UniProtKB:   Protein Feature View | Search PDB | P40422     Molecule: ALPHA-AMANITIN Polymer: 13 Type: protein Length: 8 Chains: M Organism Amanita phalloides UniProtKB:   Protein Feature View | Search PDB | P85421     Molecule: 5'-D(*AP*AP*AP*CP*TP*AP*CP*TP*TP*GP*AP*GP*CP*T)-3' Polymer: 14 Type: dna Length: 14 Chains: N Molecule: 5'-R(*AP*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3' Polymer: 15 Type: rna Length: 11 Chains: P Molecule: 5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP *GP*TP*TP*AP*CP*GP*CP*CP*BRUP*GP*GP*TP*CP*AP*TP*T)-3' Polymer: 16 Type: dna Length: 26 Chains: T     Source Hide Polymer: 1 Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Bakers' yeast   Polymer: 2 Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Bakers' yeast   Polymer: 3 Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Bakers' yeast   Polymer: 4 Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Bakers' yeast   Polymer: 5 Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Bakers' yeast   Polymer: 6 Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Bakers' yeast   Polymer: 7 Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Bakers' yeast   Polymer: 8 Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Bakers' yeast   Polymer: 9 Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Bakers' yeast   Polymer: 10 Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Bakers' yeast   Polymer: 11 Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Bakers' yeast   Polymer: 12 Scientific Name: Saccharomyces cerevisiae   Taxonomy   Common Name: Bakers' yeast   Polymer: 13 Scientific Name: Amanita phalloides   Taxonomy   Common Name: Death cap   Polymer: 14 Scientific Name: Synthetic construct   Taxonomy     Polymer: 15 Scientific Name: Synthetic construct   Taxonomy     Polymer: 16 Scientific Name: Synthetic construct   Taxonomy         Related PDB Entries Hide Identifier Details 1A1D  YEAST RIBONUCLEIC ACID POLYMERASE SUBUNIT RPB8, NMR, MINIMIZED AVERAGE STRUCTURE, ALPHA CARBONS ONLY  1DZF  RPB5 FROM S.CEREVISIAE  1I3Q  RNA POLYMERASE II CRYSTAL FORM I AT 3.1 A RESOLUTION  1I50  RNA POLYMERASE II CRYSTAL FORM II AT 2.8 A RESOLUTION  1I6H  RNA POLYMERASE II ELONGATION COMPLEX  1K83  CRYSTAL STRUCTURE OF YEAST RNA POLYMERASE II COMPLEXED WITH THE INHIBITOR ALPHA-AMANITIN  1NIK  WILD TYPE RNA POLYMERASE II  1NT9  COMPLETE 12-SUBUNIT RNA POLYMERASE II  1PQV  RNA POLYMERASE II-TFIIS COMPLEX  1R5U  RNA POLYMERASE II TFIIB COMPLEX  1R9S  RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX,MATCHED NUCLEOTIDE  1R9T  RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX, MISMATCHED NUCLEOTIDE  1SFO  RNA POLYMERASE II STRAND SEPARATED ELONGATION COMPLEX  1TWA  RNA POLYMERASE II COMPLEXED WITH ATP  1TWC  RNA POLYMERASE II COMPLEXED WITH GTP  1TWF  RNA POLYMERASE II COMPLEXED WITH UTP AT 2.3 A RESOLUTION  1TWG  RNA POLYMERASE II COMPLEXED WITH CTP  1TWH  RNA POLYMERASE II COMPLEXED WITH 2'DATP  1WCM  COMPLETE 12-SUBUNIT RNA POLYMERASE II AT 3.8 A  1Y14  CRYSTAL STRUCTURE OF YEAST SUBCOMPLEX OF RPB4 AND RPB7  1Y1V  REFINED RNA POLYMERASE II-TFIIS COMPLEX  1Y1W  COMPLETE RNA POLYMERASE II ELONGATION COMPLEX  1Y1Y  RNA POLYMERASE II-TFIIS-DNA/RNA COMPLEX  1Y77  COMPLETE RNA POLYMERASE II ELONGATION COMPLEX WITHSUBSTRATE ANALOGUE GMPCPP  2B63  COMPLETE RNA POLYMERASE II-RNA INHIBITOR COMPLEX  2B8K  12-SUBUNIT RNA POLYMERASE II  2JA5  CPD LESION CONTAINING RNA POLYMERASE II ELONGATION COMPLEX A  2JA6  CPD LESION CONTAINING RNA POLYMERASE II ELONGATION COMPLEX B  2JA7  CPD LESION CONTAINING RNA POLYMERASE II ELONGATION COMPLEX C  2JA8  CPD LESION CONTAINING RNA POLYMERASE II ELONGATION COMPLEX D  3CQZ  CRYSTAL STRUCTURE OF 10 SUBUNIT RNA POLYMERASE II COMPLEXED WITH THE INHIBITOR ALPHA-AMANITIN      Biologically Interesting Molecules (BIRD) Hide Identifier Image Name Type Class Chain ID   PRD_000201 Search  Alpha-Amanitin Cyclic peptide Toxin M   Ligand Explorer     Ligand Chemical Component Hide Identifier Formula Name Interactions MG Search  Download  Mg MAGNESIUM ION   Ligand Explorer ZN Search  Download  Zn ZINC ION   Ligand Explorer     Modified Residues Hide Identifier Formula Parent Type ILX Search  C6 H13 N O4 ILE lPeptideLinking TRX Search  C11 H12 N2 O3 TRP lPeptideLinking CSX Search  C3 H7 N O3 S CYS lPeptideLinking HYP Search  C5 H9 N O3 PRO lPeptideLinking BRU Search  C9 H12 Br N2 O8 P DU dnaLinking     External Domain Annotations Hide SCOP Classification v1.75: 9 Domains - data from SCOP   CATH Classification v3.4.0: 13 Domains - data from CATH   Pfam Classification: 30 Domains - data from Pfam   GO Terms: 191 Terms - data from GO      Structural Biology Knowledgebase Data Hide   Nucleic Acid Database Hide View the NDB ID associated with this structure: 2VUM     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Biological Assembly            View in 3D More Images... Biological assembly 1 assigned by authors and generated by PISA (software) Downloadable viewers: Simple Viewer Protein Workshop Ligand Explorer Kiosk Viewer Other Viewers  KiNG WebMol QuickPDB FirstGlance         MyPDB Personal Annotations Hide     Deposition Summary Hide Authors:   Brueckner, F.,  Cramer, P. Deposition:   2008-05-27 Release:   2008-06-17 Last Modified (REVDAT):   2011-07-13     Revision History    Hide Mouse over text for details 2012-12-12 Other 2011-07-13 Atom nomenclature 2011-07-13 Binding sites and description 2011-07-13 Polymer description 2011-07-13 Version format compliance 2011-07-13 Linkage 2011-07-13 Sequence database correspondence 2011-07-13 Function and keywords     Experimental Details Hide Method:   X-RAY DIFFRACTION Exp. Data:   Structure Factors EDS   Resolution[Å]:   3.40 R-Value: 0.255 (obs.) R-Free: 0.288 Space Group: C 2 2 21 Unit Cell:   Length [Å] Angles [°] a = 220.62 α = 90.00  b = 394.23 β = 90.00  c = 283.97 γ = 90.00      Molecule of the Month Hide RNA Polymerase