5FLM

Structure of transcribing mammalian RNA polymerase II

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history. 

Literature

Structure of Transcribing Mammalian RNA Polymerase II

Bernecky, C., Herzog, F., Baumeister, W., Plitzko, J.M., Cramer, P.

(2016) Nature 529: 551

  • DOI: 10.1038/nature16482

  • PubMed Abstract: 

    • RNA polymerase (Pol) II produces messenger RNA during transcription of protein-coding genes in all eukaryotic cells. The Pol II structure is known at high resolution from X-ray crystallography for two yeast species. Structural studies of mammalian Po ...

    RNA polymerase (Pol) II produces messenger RNA during transcription of protein-coding genes in all eukaryotic cells. The Pol II structure is known at high resolution from X-ray crystallography for two yeast species. Structural studies of mammalian Pol II, however, remain limited to low-resolution electron microscopy analysis of human Pol II and its complexes with various proteins. Here we report the 3.4 Å resolution cryo-electron microscopy structure of mammalian Pol II in the form of a transcribing complex comprising DNA template and RNA transcript. We use bovine Pol II, which is identical to the human enzyme except for seven amino-acid residues. The obtained atomic model closely resembles its yeast counterpart, but also reveals unknown features. Binding of nucleic acids to the polymerase involves 'induced fit' of the mobile Pol II clamp and active centre region. DNA downstream of the transcription bubble contacts a conserved 'TPSA motif' in the jaw domain of the Pol II subunit RPB5, an interaction that is apparently already established during transcription initiation. Upstream DNA emanates from the active centre cleft at an angle of approximately 105° with respect to downstream DNA. This position of upstream DNA allows for binding of the general transcription elongation factor DSIF (SPT4-SPT5) that we localize over the active centre cleft in a conserved position on the clamp domain of Pol II. Our results define the structure of mammalian Pol II in its functional state, indicate that previous crystallographic analysis of yeast Pol II is relevant for understanding gene transcription in all eukaryotes, and provide a starting point for a mechanistic analysis of human transcription.

    Organizational Affiliation: 

    Max Planck Institute for Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany.,Gene Center Munich, Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377 Munich, Germany.,Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Faßberg 11, 37077 Göttingen, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE
A
1970Bos taurusMutation(s): 0 
Gene Names: POLR2A
EC: 2.7.7.6
Find proteins for G3MZY8 (Bos taurus)
Go to Gene View: POLR2A
Go to UniProtKB:  G3MZY8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2
B
1174Bos taurusMutation(s): 0 
Gene Names: POLR2B
EC: 2.7.7.6
Find proteins for A5PJW8 (Bos taurus)
Go to Gene View: POLR2B
Go to UniProtKB:  A5PJW8
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3
C
275Bos taurusMutation(s): 0 
Gene Names: POLR2C
Find proteins for Q3T0Q3 (Bos taurus)
Go to Gene View: POLR2C
Go to UniProtKB:  Q3T0Q3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4
D
142Bos taurusMutation(s): 0 
Gene Names: POLR2D
Find proteins for Q1JQ91 (Bos taurus)
Go to Gene View: POLR2D
Go to UniProtKB:  Q1JQ91
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1
E
210Bos taurusMutation(s): 0 
Gene Names: POLR2E
Find proteins for Q2T9T3 (Bos taurus)
Go to Gene View: POLR2E
Go to UniProtKB:  Q2T9T3
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2
F
127Bos taurusMutation(s): 0 
Gene Names: POLR2F
Find proteins for Q32PE0 (Bos taurus)
Go to Gene View: POLR2F
Go to UniProtKB:  Q32PE0
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7
G
172Bos taurusMutation(s): 0 
Gene Names: POLR2G
Find proteins for Q5E9B8 (Bos taurus)
Go to Gene View: POLR2G
Go to UniProtKB:  Q5E9B8
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3
H
150Bos taurusMutation(s): 0 
Gene Names: POLR2H
Find proteins for F2Z4H3 (Bos taurus)
Go to Gene View: POLR2H
Go to UniProtKB:  F2Z4H3
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9
I
125Bos taurusMutation(s): 0 
Gene Names: POLR2I
Find proteins for Q32P73 (Bos taurus)
Go to Gene View: POLR2I
Go to UniProtKB:  Q32P73
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5
J
67Bos taurusMutation(s): 0 
Gene Names: POLR2L
Find proteins for Q32P78 (Bos taurus)
Go to Gene View: POLR2L
Go to UniProtKB:  Q32P78
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11
K
117Bos taurusMutation(s): 0 
Gene Names: POLR2J
Find proteins for Q32P79 (Bos taurus)
Go to Gene View: POLR2J
Go to UniProtKB:  Q32P79
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4
L
58Bos taurusMutation(s): 0 
Gene Names: POLR2K
Find proteins for Q3ZBC0 (Bos taurus)
Go to Gene View: POLR2K
Go to UniProtKB:  Q3ZBC0
Entity ID: 13
MoleculeChainsLengthOrganism
DNA, DNA-RNA ELONGATION SCAFFOLDN39synthetic construct
Entity ID: 14
MoleculeChainsLengthOrganism
RNA, DNA-RNA ELONGATION SCAFFOLDP20synthetic construct
Entity ID: 15
MoleculeChainsLengthOrganism
DNA, DNA-RNA ELONGATION SCAFFOLDT39synthetic 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
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-01-20
    Type: Initial release
  • Version 1.1: 2016-02-03
    Type: Database references
  • Version 1.2: 2016-02-10
    Type: Database references
  • Version 2.0: 2018-10-03
    Type: Atomic model, Data collection, Derived calculations