3H3V

Yeast RNAP II containing poly(A)-signal sequence in the active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Torpedo Nuclease Rat1 Is Insufficient to Terminate RNA Polymerase II in Vitro

Dengl, S.Cramer, P.

(2009) J Biol Chem 284: 21270-21279

  • DOI: 10.1074/jbc.M109.013847
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Termination of RNA polymerase (pol) II transcription in vivo requires the 5'-RNA exonuclease Rat1. It was proposed that Rat1 degrades RNA from the 5'-end that is created by transcript cleavage, catches up with elongating pol II, and acts like a Torpe ...

    Termination of RNA polymerase (pol) II transcription in vivo requires the 5'-RNA exonuclease Rat1. It was proposed that Rat1 degrades RNA from the 5'-end that is created by transcript cleavage, catches up with elongating pol II, and acts like a Torpedo that removes pol II from DNA. Here we test the Torpedo model in an in vitro system based on bead-coupled pol II elongation complexes (ECs). Recombinant Rat1 complexes with Rai1, and with Rai1 and Rtt103, degrade RNA extending from the EC until they reach the polymerase surface but fail to terminate pol II. Instead, the EC retains an approximately 18-nucleotide RNA that remains with its 3'-end at the active site and can be elongated. Thus, pol II termination apparently requires a factor or several factors in addition to Rat1, Rai1, and Rtt103, post-translational modifications of these factors, or unusual reaction conditions.


    Organizational Affiliation

    Gene Center and Center for Integrated Protein Science Munich, Department of Chemistry and Biochemistry, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.



Macromolecules

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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC2G155Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB9J122Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P27999 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB1B1733Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC5K70Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB11L120Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC4M70Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB2C1224Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB3D318Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB4E221Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC1F215Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit RPB7H171Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P34087 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC3I146Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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  • Reference Sequence
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Entity ID: 13
MoleculeChainsLengthOrganism
5'-D(*AP*GP*CP*TP*CP*AP*AP*GP*TP*AP*GP*CP*TP*GP*CP*TP*TP*TP*AP*TP*TP*GP*CP*AP*TP*T)-3'N14N/A
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Entity ID: 14
MoleculeChainsLengthOrganism
5'-D(*CP*AP*GP*CP*TP*AP*CP*TP*TP*GP*AP*GP*CP*T)-3'P16N/A

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Entity ID: 15
MoleculeChainsLengthOrganism
5'-R(*UP*GP*CP*AP*UP*UP*UP*CP*GP*CP*AP*AP*UP*AP*AP*A)-3'T26N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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B, C, D, J, K, M
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.205 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 222.47α = 90
b = 391.62β = 90
c = 284.12γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
CNSrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2009-04-17 
  • Released Date: 2009-06-16 
  • Deposition Author(s): Dengl, S., Cramer, P.

Revision History 

  • Version 1.0: 2009-06-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-11-06
    Changes: Data collection
  • Version 1.3: 2017-11-01
    Changes: Advisory, Refinement description