6EU3

Apo RNA Polymerase III - closed conformation (cPOL3)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis of RNA polymerase III transcription initiation.

Abascal-Palacios, G.Ramsay, E.P.Beuron, F.Morris, E.Vannini, A.

(2018) Nature 553: 301-306

  • DOI: 10.1038/nature25441
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • RNA polymerase (Pol) III transcribes essential non-coding RNAs, including the entire pool of transfer RNAs, the 5S ribosomal RNA and the U6 spliceosomal RNA, and is often deregulated in cancer cells. The initiation of gene transcription by Pol III re ...

    RNA polymerase (Pol) III transcribes essential non-coding RNAs, including the entire pool of transfer RNAs, the 5S ribosomal RNA and the U6 spliceosomal RNA, and is often deregulated in cancer cells. The initiation of gene transcription by Pol III requires the activity of the transcription factor TFIIIB to form a transcriptionally active Pol III preinitiation complex (PIC). Here we present electron microscopy reconstructions of Pol III PICs at 3.4-4.0 Å and a reconstruction of unbound apo-Pol III at 3.1 Å. TFIIIB fully encircles the DNA and restructures Pol III. In particular, binding of the TFIIIB subunit Bdp1 rearranges the Pol III-specific subunits C37 and C34, thereby promoting DNA opening. The unwound DNA directly contacts both sides of the Pol III cleft. Topologically, the Pol III PIC resembles the Pol II PIC, whereas the Pol I PIC is more divergent. The structures presented unravel the molecular mechanisms underlying the first steps of Pol III transcription and also the general conserved mechanisms of gene transcription initiation.


    Organizational Affiliation

    The Institute of Cancer Research, London SW7 3RP, UK.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase III subunit RPC1A1460Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO31RPC1RPC160YOR116CO3254YOR3254C
EC: 2.7.7.6
Find proteins for P04051 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase III subunit RPC2B1149Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RET1RPC128RPC2YOR207C
EC: 2.7.7.6
Find proteins for P22276 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I and III subunit RPAC1C335Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC40RPC5YPR110CP8283.18
Find proteins for P07703 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase III subunit RPC9D161Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC17YJL011CJ1349
Find proteins for P47076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC1E215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB5RPA7RPC9YBR154CYBR1204
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC2F155Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO26RPB6YPR187WP9677.8
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase III subunit RPC8G212Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC25YKL144CUNF1YKL1
Find proteins for P35718 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC3H146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB8YOR224CYOR50-14
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase III subunit RPC10I110Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC11YDR045CYD9609.01C
Find proteins for Q04307 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC5J70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB10YOR210W
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC4L70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC10RPB12YHR143W-AYHR143BW
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase III subunit RPC5M282Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC37YKR025W
Find proteins for P36121 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase III subunit RPC4N422Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC53RPC4YDL150WD1557
Find proteins for P25441 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase III subunit RPC3O654Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC82RPC3YPR190CP9677.11
Find proteins for P32349 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase III subunit RPC6P317Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC34YNR003CN2031
Find proteins for P32910 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase III subunit RPC7Q251Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC31ACP2RPC8YNL151CN1769
Find proteins for P17890 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I and III subunit RPAC2K142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC19YNL113WN1937
Find proteins for P28000 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A, B, I, J, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/K014390/1
Cancer Research UK Programme FoundationUnited KingdomCR-UK C47547/A21536
Wellcome TrustUnited Kingdom200818/Z/16/Z
Marie Sklodowska-Curie Intra-European FellowshipUnited Kingdom655238

Revision History 

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Author supporting evidence, Database references
  • Version 1.2: 2019-02-20
    Changes: Advisory, Data collection, Derived calculations
  • Version 1.3: 2019-12-11
    Changes: Other