2VUM image
Deposition Date 2008-05-27
Release Date 2008-06-17
Last Version Date 2023-12-13
Entry Detail
PDB ID:
2VUM
Keywords:
Title:
Alpha-amanitin inhibited complete RNA polymerase II elongation complex
Biological Source:
Source Organism:
Method Details:
Experimental Method:
Resolution:
3.40 Å
R-Value Free:
0.28
R-Value Work:
0.25
R-Value Observed:
0.25
Space Group:
C 2 2 21
Macromolecular Entities
Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1
Gene (Uniprot):RPO21
Chain IDs:A
Chain Length:1733
Number of Molecules:1
Biological Source:SACCHAROMYCES CEREVISIAE
Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2
Gene (Uniprot):RPB2
Chain IDs:B
Chain Length:1224
Number of Molecules:1
Biological Source:SACCHAROMYCES CEREVISIAE
Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3
Gene (Uniprot):RPB3
Chain IDs:C
Chain Length:318
Number of Molecules:1
Biological Source:SACCHAROMYCES CEREVISIAE
Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4
Gene (Uniprot):RPB4
Chain IDs:D
Chain Length:221
Number of Molecules:1
Biological Source:SACCHAROMYCES CEREVISIAE
Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1
Gene (Uniprot):RPB5
Chain IDs:E
Chain Length:215
Number of Molecules:1
Biological Source:SACCHAROMYCES CEREVISIAE
Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2
Gene (Uniprot):RPO26
Chain IDs:F
Chain Length:155
Number of Molecules:1
Biological Source:SACCHAROMYCES CEREVISIAE
Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7
Gene (Uniprot):RPB7
Chain IDs:G
Chain Length:171
Number of Molecules:1
Biological Source:SACCHAROMYCES CEREVISIAE
Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3
Gene (Uniprot):RPB8
Chain IDs:H
Chain Length:146
Number of Molecules:1
Biological Source:SACCHAROMYCES CEREVISIAE
Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9
Gene (Uniprot):RPB9
Chain IDs:I
Chain Length:122
Number of Molecules:1
Biological Source:SACCHAROMYCES CEREVISIAE
Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5
Gene (Uniprot):RPB10
Chain IDs:J
Chain Length:70
Number of Molecules:1
Biological Source:SACCHAROMYCES CEREVISIAE
Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11
Gene (Uniprot):RPB11
Chain IDs:K
Chain Length:120
Number of Molecules:1
Biological Source:SACCHAROMYCES CEREVISIAE
Polymer Type:polypeptide(L)
Molecule:DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4
Gene (Uniprot):RPC10
Chain IDs:L
Chain Length:70
Number of Molecules:1
Biological Source:SACCHAROMYCES CEREVISIAE
Polymer Type:polypeptide(L)
Molecule:AMATOXIN
Chain IDs:M
Chain Length:8
Number of Molecules:1
Biological Source:AMANITA PHALLOIDES
Polymer Type:polydeoxyribonucleotide
Molecule:5'-D(*AP*AP*AP*CP*TP*AP*CP*TP*TP*GP *AP*GP*CP*T)-3'
Chain IDs:N
Chain Length:14
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polyribonucleotide
Molecule:5'-R(*AP*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3'
Chain IDs:O (auth: P)
Chain Length:11
Number of Molecules:1
Biological Source:synthetic construct
Polymer Type:polydeoxyribonucleotide
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'
Chain IDs:P (auth: T)
Chain Length:26
Number of Molecules:1
Biological Source:synthetic construct
Modified Residue
Compound ID Chain ID Parent Comp ID Details 2D Image
BRU P DU ?
CSX M CYS S-OXY CYSTEINE
HYP M PRO 4-HYDROXYPROLINE
ILX M ILE 4,5-DIHYDROXYISOLEUCINE
TRX M TRP 6-HYDROXYTRYPTOPHAN
Primary Citation
Structural Basis of Transcription Inhibition by Alpha-Amanitin and Implications for RNA Polymerase II Translocation.
Nat.Struct.Mol.Biol. 15 811 ? (2008)
PMID: 18552824 DOI: 10.1038/NSMB.1458

Abstact

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.

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