Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 12-mer - A1B1C1D1E1F1G1H1I1J1K1L1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 548.25 kDa 
• Atom Count: 32,712 
• Modelled Residue Count: 3,976 
• Deposited Residue Count: 4,685 
• Unique protein chains: 12
• Unique nucleic acid chains: 3

 5FLM

Structure of transcribing mammalian RNA polymerase II

• PDB DOI: 10.2210/pdb5FLM/pdb
• EM Map EMD-3218: EMDB EMDataResource

• Classification: TRANSCRIPTION
• Organism(s): Bos taurus, synthetic construct
• Mutation(s): No 


• Deposited: 2015-10-26 Released: 2016-01-20 
• Deposition Author(s): Bernecky, C., Herzog, F., Baumeister, W., Plitzko, J.M., Cramer, P.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of Transcribing Mammalian RNA Polymerase II

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

(2016) Nature 529: 551

• PubMed: 26789250 
• DOI: 10.1038/nature16482
• Primary Citation of Related Structures:  
  5FLM


• 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 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.

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Organizational Affiliation: 

Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Am Faßberg 11, 37077 Göttingen, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE	A	1,970	Bos taurus	Mutation(s): 0  Gene Names: POLR2A EC: 2.7.7.6
UniProt
Find proteins for G3MZY8 (Bos taurus) Explore G3MZY8  Go to UniProtKB:  G3MZY8

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2	B	1,174	Bos taurus	Mutation(s): 0  Gene Names: POLR2B EC: 2.7.7.6
UniProt
Find proteins for A5PJW8 (Bos taurus) Explore A5PJW8  Go to UniProtKB:  A5PJW8

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3	C	275	Bos taurus	Mutation(s): 0  Gene Names: POLR2C
UniProt
Find proteins for Q3T0Q3 (Bos taurus) Explore Q3T0Q3  Go to UniProtKB:  Q3T0Q3

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4	D	142	Bos taurus	Mutation(s): 0  Gene Names: POLR2D
UniProt
Find proteins for Q1JQ91 (Bos taurus) Explore Q1JQ91  Go to UniProtKB:  Q1JQ91

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC1	E	210	Bos taurus	Mutation(s): 0  Gene Names: POLR2E
UniProt
Find proteins for Q2T9T3 (Bos taurus) Explore Q2T9T3  Go to UniProtKB:  Q2T9T3

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC2	F	127	Bos taurus	Mutation(s): 0  Gene Names: POLR2F
UniProt
Find proteins for Q32PE0 (Bos taurus) Explore Q32PE0  Go to UniProtKB:  Q32PE0

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7	G	172	Bos taurus	Mutation(s): 0  Gene Names: POLR2G
UniProt
Find proteins for Q5E9B8 (Bos taurus) Explore Q5E9B8  Go to UniProtKB:  Q5E9B8

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC3	H	150	Bos taurus	Mutation(s): 0  Gene Names: POLR2H
UniProt
Find proteins for F2Z4H3 (Bos taurus) Explore F2Z4H3  Go to UniProtKB:  F2Z4H3

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9	I	125	Bos taurus	Mutation(s): 0  Gene Names: POLR2I
UniProt
Find proteins for Q32P73 (Bos taurus) Explore Q32P73  Go to UniProtKB:  Q32P73

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC5	J	67	Bos taurus	Mutation(s): 0  Gene Names: POLR2L
UniProt
Find proteins for Q32P78 (Bos taurus) Explore Q32P78  Go to UniProtKB:  Q32P78

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11	K	117	Bos taurus	Mutation(s): 0  Gene Names: POLR2J
UniProt
Find proteins for Q32P79 (Bos taurus) Explore Q32P79  Go to UniProtKB:  Q32P79

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC4	L	58	Bos taurus	Mutation(s): 0  Gene Names: POLR2K
UniProt
Find proteins for Q3ZBC0 (Bos taurus) Explore Q3ZBC0  Go to UniProtKB:  Q3ZBC0

Entity ID: 13
Molecule	Chains	Length	Organism	Image
DNA, DNA-RNA ELONGATION SCAFFOLD	M [auth N]	39	synthetic construct

Entity ID: 14
Molecule	Chains	Length	Organism	Image
RNA, DNA-RNA ELONGATION SCAFFOLD	N [auth P]	20	synthetic construct

Entity ID: 15
Molecule	Chains	Length	Organism	Image
DNA, DNA-RNA ELONGATION SCAFFOLD	O [auth T]	39	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	P [auth A], Q [auth A], S [auth B], T [auth C], U [auth I], V [auth I], W [auth J], X [auth L]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	R [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-01-20 
Deposition Author(s): Bernecky, C., Herzog, F., Baumeister, W., Plitzko, J.M., Cramer, P.

Revision History  

• Version 1.0: 2016-01-20
  Type: Initial release
  
• Version 1.1: 2016-02-03
  Changes: Database references
• Version 1.2: 2016-02-10
  Changes: Database references
• Version 2.0: 2018-10-03
  Changes: Atomic model, Data collection, Derived calculations
• Version 2.1: 2019-12-18
  Changes: Other