2VUM

Alpha-amanitin inhibited complete RNA polymerase II elongation complex


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Basis of Transcription Inhibition by Alpha-Amanitin and Implications for RNA Polymerase II Translocation.

Brueckner, F.Cramer, P.

(2008) Nat.Struct.Mol.Biol. 15: 811

  • DOI: 10.1038/nsmb.1458

  • PubMed Abstract: 
  • To study how RNA polymerase II translocates after nucleotide incorporation, we prepared elongation complex crystals in which pre- and post-translocation states interconvert. Crystal soaking with the inhibitor alpha-amanitin locked the elongation comp ...

    To study how RNA polymerase II translocates after nucleotide incorporation, we prepared elongation complex crystals in which pre- and post-translocation states interconvert. Crystal soaking with the inhibitor alpha-amanitin locked the elongation complex in a new state, which was refined at 3.4-A resolution and identified as a possible translocation intermediate. The DNA base entering the active site occupies a 'pretemplating' position above the central bridge helix, which is shifted and occludes the templating position. A leucine residue in the trigger loop forms a wedge at the shifted bridge helix, but moves by 13 A to close the active site during nucleotide incorporation. Our results support a Brownian ratchet mechanism that involves swinging of the trigger loop between open, wedged and closed positions, and suggest that alpha-amanitin impairs nucleotide incorporation and translocation by trapping the trigger loop and bridge helix.


    Organizational Affiliation

    Gene Center and Center for Integrated Protein Science Munich (CIPSM), Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universit√§t M√ľnchen, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
A
1733Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPO21 (RPB1, RPB220, SUA8)
EC: 2.7.7.6
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04050
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2
B
1224Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB2 (RPB150, RPO22)
EC: 2.7.7.6
Find proteins for P08518 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P08518
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3
C
318Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB3
Find proteins for P16370 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P16370
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4
D
221Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB4
Find proteins for P20433 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20433
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1
E
215Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB5 (RPA7, RPC9)
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20434
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2
F
155Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPO26 (RPB6)
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20435
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7
G
171Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB7
Find proteins for P34087 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P34087
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3
H
146Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB8
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20436
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9
I
122Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB9
Find proteins for P27999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P27999
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5
J
70Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB10
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22139
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11
K
120Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB11
Find proteins for P38902 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38902
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4
L
70Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPC10 (RPB12)
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40422
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
AMATOXIN
M
8Amanita phalloidesMutation(s): 0 
Find proteins for P85421 (Amanita phalloides)
Go to UniProtKB:  P85421
Entity ID: 14
MoleculeChainsLengthOrganism
5'-D(*AP*AP*AP*CP*TP*AP*CP*TP*TP*GP *AP*GP*CP*T)-3'N14synthetic construct
Entity ID: 15
MoleculeChainsLengthOrganism
5'-R(*AP*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3'P11synthetic construct
Entity ID: 16
MoleculeChainsLengthOrganism
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'T26synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C, I, J, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
ILX
Query on ILX
M
L-PEPTIDE LINKINGC6 H13 N O4ILE
CSX
Query on CSX
M
L-PEPTIDE LINKINGC3 H7 N O3 SCYS
BRU
Query on BRU
T
DNA LINKINGC9 H12 Br N2 O8 PDU
HYP
Query on HYP
M
L-PEPTIDE LINKINGC5 H9 N O3PRO
TRX
Query on TRX
M
L-PEPTIDE LINKINGC11 H12 N2 O3TRP
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
Unit Cell:
Length (Å)Angle (°)
a = 220.619α = 90.00
b = 394.234β = 90.00
c = 283.966γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-06-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Structure summary, Version format compliance
  • Version 1.2: 2012-11-30
    Type: Other
  • Version 1.3: 2018-06-27
    Type: Data collection, Source and taxonomy, Structure summary