6EXV

Structure of mammalian RNA polymerase II elongation complex inhibited by Alpha-amanitin

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history. 

Literature

Cryo-EM structure of a mammalian RNA polymerase II elongation complex inhibited by alpha-amanitin.

Liu, X., Farnung, L., Wigge, C., Cramer, P.

(2018) J. Biol. Chem. 293: 7189-7194

  • DOI: 10.1074/jbc.RA118.002545

  • PubMed Abstract: 

    • RNA polymerase II (Pol II) is the central enzyme that transcribes eukaryotic protein-coding genes to produce mRNA. The mushroom toxin α-amanitin binds Pol II and inhibits transcription at the step of RNA chain elongation. Pol II from yeast binds α-am ...

    RNA polymerase II (Pol II) is the central enzyme that transcribes eukaryotic protein-coding genes to produce mRNA. The mushroom toxin α-amanitin binds Pol II and inhibits transcription at the step of RNA chain elongation. Pol II from yeast binds α-amanitin with micromolar affinity, whereas metazoan Pol II enzymes exhibit nanomolar affinities. Here, we present the high-resolution cryo-EM structure of α-amanitin bound to and inhibited by its natural target, the mammalian Pol II elongation complex. The structure revealed that the toxin is located in a pocket previously identified in yeast Pol II but forms additional contacts with metazoan-specific residues, which explains why its affinity to mammalian Pol II is ∼3000 times higher than for yeast Pol II. Our work provides the structural basis for the inhibition of mammalian Pol II by the natural toxin α-amanitin and highlights that cryo-EM is well suited to studying interactions of a small molecule with its macromolecular target.

    Organizational Affiliation: 

    From the Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.,From the Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany pcramer@mpibpc.mpg.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
A
1970Sus scrofaMutation(s): 0 
Gene Names: POLR2A
EC: 2.7.7.6
Find proteins for I3LJR4 (Sus scrofa)
Go to Gene View: POLR2A
Go to UniProtKB:  I3LJR4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2
B
1167Sus scrofaMutation(s): 0 
Gene Names: POLR2B
EC: 2.7.7.6
Find proteins for I3LGP4 (Sus scrofa)
Go to Gene View: POLR2B
Go to UniProtKB:  I3LGP4
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3
C
275Sus scrofaMutation(s): 0 
Gene Names: POLR2C
Find proteins for I3LCH3 (Sus scrofa)
Go to Gene View: POLR2C
Go to UniProtKB:  I3LCH3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3
D
142Sus scrofaMutation(s): 0 
Gene Names: POLR2D
Find proteins for A0A287ADR4 (Sus scrofa)
Go to Gene View: POLR2D
Go to UniProtKB:  A0A287ADR4
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1
E
210Sus scrofaMutation(s): 0 
Gene Names: POLR2E
Find proteins for I3LSI7 (Sus scrofa)
Go to Gene View: POLR2E
Go to UniProtKB:  I3LSI7
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1
F
127Sus scrofaMutation(s): 0 
Gene Names: POLR2F
Find proteins for F1SKN8 (Sus scrofa)
Go to Gene View: POLR2F
Go to UniProtKB:  F1SKN8
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7
G
172Sus scrofaMutation(s): 0 
Gene Names: POLR2G
Find proteins for I3LJZ9 (Sus scrofa)
Go to Gene View: POLR2G
Go to UniProtKB:  I3LJZ9
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3
H
150Sus scrofaMutation(s): 0 
Gene Names: POLR2H
Find proteins for I3LCB2 (Sus scrofa)
Go to Gene View: POLR2H
Go to UniProtKB:  I3LCB2
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB9
I
125Sus scrofaMutation(s): 0 
Gene Names: POLR2I
Find proteins for P60899 (Sus scrofa)
Go to Gene View: POLR2I
Go to UniProtKB:  P60899
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC5
J
67Sus scrofaMutation(s): 0 
Gene Names: POLR2L
Find proteins for A0A287B432 (Sus scrofa)
Go to Gene View: POLR2L
Go to UniProtKB:  A0A287B432
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4
K
117Sus scrofaMutation(s): 0 
Gene Names: POLR2J
Find proteins for F1RKE4 (Sus scrofa)
Go to Gene View: POLR2J
Go to UniProtKB:  F1RKE4
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4
L
58Sus scrofaMutation(s): 0 
Gene Names: POLR2K
Find proteins for I3LN51 (Sus scrofa)
Go to Gene View: POLR2K
Go to UniProtKB:  I3LN51
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
DNA (25-MER)N43synthetic construct
Entity ID: 15
MoleculeChainsLengthOrganism
RNA (5'-R(P*CP*AP*UP*AP*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3')P20synthetic construct
Entity ID: 16
MoleculeChainsLengthOrganism
DNA (36-MER)T43synthetic 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
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000201
Query on PRD_000201		MAlpha-AmanitinCyclic peptide / Toxin

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.6 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Research CouncilGermany693023
German Research FoundationGermanySFB860
German Research FoundationGermanySPP1935

Revision History 

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-03-28
    Type: Data collection, Database references
  • Version 1.2: 2018-05-23
    Type: Data collection, Database references
  • Version 1.3: 2018-06-13
    Type: Data collection, Database references, Structure summary
  • Version 1.4: 2019-04-10
    Type: Data collection, Database references