2VUM

Alpha-amanitin inhibited complete RNA polymerase II elongation complex

Structural Biology Knowledgebase: 2VUM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.288
  • R-Value Work: 0.255

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2VUM

Classification: TRANSFERASE / TOXIN

Total Structure Weight: 531506.25


Macromolecule Entities
Molecule Chains Length Organism Details
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 A 1733 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPO21 RPB1 RPB220 SUA8 YDL140C D2150
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 B 1224 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB2 RPB150 RPO22 YOR151C
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 C 318 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB3 YIL021W
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 D 221 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB4 YJL140W J0654
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1 E 215 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB5 RPA7 RPC9 YBR154C YBR1204
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2 F 155 Saccharomyces cerevisiae EC#: 4.2.1.99 IUBMB
Gene Name(s): RPO26 RPB6 YPR187W P9677.8
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 G 171 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB7 YDR404C D9509.22
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3 H 146 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB8 YOR224C YOR50-14
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 I 122 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB9 YGL070C
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5 J 70 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB10 YOR210W
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 K 120 Saccharomyces cerevisiae EC#: 2.7.7.6 IUBMB
Gene Name(s): RPB11 YOL005C
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4 L 70 Saccharomyces cerevisiae Gene Name(s): RPC10 RPB12 YHR143W-A YHR143BW
ALPHA-AMANITIN M 8 Amanita phalloides Gene Name(s):
Macromolecule Entities
Molecule Chains Length Organism Details
5'-D(*AP*AP*AP*CP*TP*AP*CP*TP*TP*GP*AP*GP*CP*T)-3' N 14 synthetic
5'-R(*AP*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3' P 11 synthetic
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' T 26 synthetic

Small Molecules
Ligands 2 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ZN
Query on ZN

A, B, C, I, J, L ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Biologically Interesting Molecules 1 Unique
ID Chains Name Type/Class 2D Diagram 3D Interactions
PRD_000201 (HYP,ASN,ILX,CSX,TRX,ILE,GLY) M Alpha-Amanitin Cyclic peptide /
Toxin
Ligand Explorer Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol) Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
BRU
Query on BRU
T DNA LINKING C9 H12 Br N2 O8 P DU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.4 Å
  • R-Value Free: 0.288
  • R-Value Work: 0.255
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 220.62 α = 90.00
b = 394.23 β = 90.00
c = 283.97 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-05-27
  • Released Date: 2008-06-17
  • Deposition author(s): Brueckner, F., Cramer, P.

Revision History

  • 2012-12-12
    Type: Other | Details: Add PRD info
  • 2011-07-13
    Type: Version format compliance | Details: Compliance with PDBx exchange dictionary V4
  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry