6EXV

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

PDB DOI: https://doi.org/10.2210/pdb6EXV/pdb
EM Map EMD-3981: EMDB EMDataResource
NAKB: 6EXV

Classification: TRANSCRIPTION
Organism(s): Sus scrofa, Amanita phalloides, synthetic construct
Mutation(s): No

Deposited: 2017-11-09 Released: 2018-03-21
Deposition Author(s): Liu, X., Farnung, L., Wigge, C., Cramer, P.
Funding Organization(s): European Research Council, German Research Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.5 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

PubMed: 29550768 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1074/jbc.RA118.002545
Primary Citation of Related Structures:
6EXV

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-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

Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.

Macromolecule Content

Total Structure Weight: 550.93 kDa
Atom Count: 32,717
Modelled Residue Count: 3,980
Deposited Residue Count: 4,694
Unique protein chains: 13
Unique nucleic acid chains: 3

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1	A	1,970	Sus scrofa	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for I3LJR4 (Sus scrofa) Explore I3LJR4 Go to UniProtKB: I3LJR4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I3LJR4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2	B	1,167	Sus scrofa	Mutation(s): 0 EC: 2.7.7.6
UniProt
Find proteins for I3LGP4 (Sus scrofa) Explore I3LGP4 Go to UniProtKB: I3LGP4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I3LGP4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3	C	275	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for I3LCH3 (Sus scrofa) Explore I3LCH3 Go to UniProtKB: I3LCH3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I3LCH3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3	D	142	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A287ADR4 (Sus scrofa) Explore A0A287ADR4 Go to UniProtKB: A0A287ADR4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A287ADR4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1	E	210	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for I3LSI7 (Sus scrofa) Explore I3LSI7 Go to UniProtKB: I3LSI7
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I3LSI7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1	F	127	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A4X1VEK9 (Sus scrofa) Explore A0A4X1VEK9 Go to UniProtKB: A0A4X1VEK9
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4X1VEK9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7	G	172	Sus scrofa	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3	H	150	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for I3LCB2 (Sus scrofa) Explore I3LCB2 Go to UniProtKB: I3LCB2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	I3LCB2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB9	I	125	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for P60899 (Sus scrofa) Explore P60899 Go to UniProtKB: P60899
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P60899
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerases I, II, and III subunit RPABC5	J	67	Sus scrofa	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4	K	117	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for F1RKE4 (Sus scrofa) Explore F1RKE4 Go to UniProtKB: F1RKE4
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F1RKE4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4	L	58	Sus scrofa	Mutation(s): 0
UniProt
Find proteins for A0A4X1TRS6 (Sus scrofa) Explore A0A4X1TRS6 Go to UniProtKB: A0A4X1TRS6
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A4X1TRS6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
AMATOXIN	M	8	Amanita phalloides	Mutation(s): 0
UniProt
Find proteins for P85421 (Amanita phalloides) Explore P85421 Go to UniProtKB: P85421
Entity Groups
UniProt Group	P85421
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 14
Molecule	Chains	Length	Organism	Image
DNA (25-MER)	N	43	synthetic construct
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 15
Molecule	Chains	Length	Organism	Image
RNA (5'-R(PCPAPUPAPAPAPGPAPCPCPAPGPGPC)-3')	O [auth P]	20	synthetic construct
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 16
Molecule	Chains	Length	Organism	Image
DNA (36-MER)	P [auth T]	43	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain T [auth B] SDF format, chain V [auth I] SDF format, chain W [auth I] SDF format, chain Y [auth L] SDF format, chain U [auth C] SDF format, chain X [auth J] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain T [auth B] MOL2 format, chain V [auth I] MOL2 format, chain W [auth I] MOL2 format, chain Y [auth L] MOL2 format, chain U [auth C] MOL2 format, chain X [auth J]	Q [auth A] R [auth A] T [auth B] U [auth C] V [auth I] Q [auth A], R [auth A], T [auth B], U [auth C], V [auth I], W [auth I], X [auth J], Y [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain Q [auth A] Focus chain R [auth A] Focus chain T [auth B] Focus chain U [auth C] Focus chain V [auth I] Focus chain W [auth I] Focus chain X [auth J] Focus chain Y [auth L] Interactions & Density Focus chain Q [auth A] Focus chain R [auth A] Focus chain T [auth B] Focus chain U [auth C] Focus chain V [auth I] Focus chain W [auth I] Focus chain X [auth J] Focus chain Y [auth L]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain S [auth A] MOL2 format, chain S [auth A]	S [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain S [auth A] Interactions & Density Focus chain S [auth A]

Modified Residues 4 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSX Query on CSX	M	L-PEPTIDE LINKING	C₃ H₇ N O₃ S		CYS
HYP Query on HYP	M	L-PEPTIDE LINKING	C₅ H₉ N O₃		PRO
ILX Query on ILX	M	L-PEPTIDE LINKING	C₆ H₁₃ N O₄		ILE
TRX Query on TRX	M	L-PEPTIDE LINKING	C₁₁ H₁₂ N₂ O₃		TRP

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 13
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000201 Query on PRD_000201	M	Alpha-Amanitin	Cyclic peptide / Toxin		Interactions Focus chain M Interactions & Density Focus chain M

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.60 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION
MODEL REFINEMENT	PHENIX

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2018-03-21

Deposition Author(s):

Funding Organization	Location	Grant Number
European Research Council	Germany	693023
German Research Foundation	Germany	SFB860
German Research Foundation	Germany	SPP1935

Revision History (Full details and data files)

Version 1.0: 2018-03-21
Type: Initial release
Version 1.1: 2018-03-28
Changes: Data collection, Database references
Version 1.2: 2018-05-23
Changes: Data collection, Database references
Version 1.3: 2018-06-13
Changes: Data collection, Database references, Structure summary
Version 1.4: 2019-04-10
Changes: Data collection, Database references
Version 1.5: 2019-12-11
Changes: Other

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

Prepare Data

Validate Data

Deposit Data

Help and Resources

6EXV

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

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

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Entity ID: 2

UniProt

Entity Groups

Sequence Annotations

Entity ID: 3

UniProt

Entity Groups

Sequence Annotations

Entity ID: 4

UniProt

Entity Groups

Sequence Annotations

Entity ID: 5

UniProt

Entity Groups

Sequence Annotations

Entity ID: 6

UniProt

Entity Groups

Sequence Annotations

Entity ID: 7

Entity Groups

Sequence Annotations

Entity ID: 8

UniProt

Entity Groups

Sequence Annotations

Entity ID: 9

UniProt

Entity Groups

Sequence Annotations

Entity ID: 10

Entity Groups

Sequence Annotations

Entity ID: 11

UniProt

Entity Groups

Sequence Annotations

Entity ID: 12

UniProt

Entity Groups

Sequence Annotations

Entity ID: 13

UniProt

Entity Groups

Sequence Annotations

Entity ID: 14

Sequence Annotations

Entity ID: 15

Sequence Annotations

Entity ID: 16

Sequence Annotations

Entity ID: 13

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)