6F41

RNA Polymerase III initially transcribing complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Molecular mechanism of promoter opening by RNA polymerase III.

Vorlander, M.K.Khatter, H.Wetzel, R.Hagen, W.J.H.Muller, C.W.

(2018) Nature 553: 295-300

  • DOI: 10.1038/nature25440
  • Primary Citation of Related Structures:  
    6F40, 6F41, 6F42, 6F44

  • PubMed Abstract: 
  • RNA polymerase III (Pol III) and transcription factor IIIB (TFIIIB) assemble together on different promoter types to initiate the transcription of small, structured RNAs. Here we present structures of Pol III preinitiation complexes, comprising the 17-subunit Pol III and the heterotrimeric transcription factor TFIIIB, bound to a natural promoter in different functional states ...

    RNA polymerase III (Pol III) and transcription factor IIIB (TFIIIB) assemble together on different promoter types to initiate the transcription of small, structured RNAs. Here we present structures of Pol III preinitiation complexes, comprising the 17-subunit Pol III and the heterotrimeric transcription factor TFIIIB, bound to a natural promoter in different functional states. Electron cryo-microscopy reconstructions, varying from 3.7 Å to 5.5 Å resolution, include two early intermediates in which the DNA duplex is closed, an open DNA complex, and an initially transcribing complex with RNA in the active site. Our structures reveal an extremely tight, multivalent interaction between TFIIIB and promoter DNA, and explain how TFIIIB recruits Pol III. Together, TFIIIB and Pol III subunit C37 activate the intrinsic transcription factor-like activity of the Pol III-specific heterotrimer to initiate the melting of double-stranded DNA, in a mechanism similar to that of the Pol II system.


    Organizational Affiliation

    European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Meyerhofstrasse 1, 69117 Heidelberg, Germany.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC1A1460Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO31RPC1RPC160YOR116CO3254YOR3254C
EC: 2.7.7.6
UniProt
Find proteins for P04051 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P04051 
Go to UniProtKB:  P04051
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04051
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC2B1149Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RET1RPC128RPC2YOR207C
EC: 2.7.7.6
UniProt
Find proteins for P22276 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P22276 
Go to UniProtKB:  P22276
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22276
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I and III subunit RPAC1C335Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC40RPC5YPR110CP8283.18
UniProt
Find proteins for P07703 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P07703 
Go to UniProtKB:  P07703
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07703
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC9D161Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC17YJL011CJ1349
UniProt
Find proteins for P47076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P47076 
Go to UniProtKB:  P47076
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP47076
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1E215Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB5RPA7RPC9YBR154CYBR1204
UniProt
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20434 
Go to UniProtKB:  P20434
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20434
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2F155Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO26RPB6YPR187WP9677.8
UniProt
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20435 
Go to UniProtKB:  P20435
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20435
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC8G212Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC25YKL144CUNF1YKL1
UniProt
Find proteins for P35718 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P35718 
Go to UniProtKB:  P35718
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35718
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3H146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB8YOR224CYOR50-14
UniProt
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P20436 
Go to UniProtKB:  P20436
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20436
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC10I110Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC11YDR045CYD9609.01C
UniProt
Find proteins for Q04307 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q04307 
Go to UniProtKB:  Q04307
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04307
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC5J70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPB10YOR210W
UniProt
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P22139 
Go to UniProtKB:  P22139
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22139
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I and III subunit RPAC2K142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC19YNL113WN1937
UniProt
Find proteins for P28000 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P28000 
Go to UniProtKB:  P28000
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP28000
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC4L70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC10RPB12YHR143W-AYHR143BW
UniProt
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P40422 
Go to UniProtKB:  P40422
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP40422
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC5M282Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC37YKR025W
UniProt
Find proteins for P36121 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P36121 
Go to UniProtKB:  P36121
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36121
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC4N422Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC53RPC4YDL150WD1557
UniProt
Find proteins for P25441 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25441 
Go to UniProtKB:  P25441
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25441
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC3O654Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC82RPC3YPR190CP9677.11
UniProt
Find proteins for P32349 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32349 
Go to UniProtKB:  P32349
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32349
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC6P317Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC34YNR003CN2031
UniProt
Find proteins for P32910 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P32910 
Go to UniProtKB:  P32910
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP32910
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC7Q251Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC31ACP2RPC8YNL151CN1769
UniProt
Find proteins for P17890 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P17890 
Go to UniProtKB:  P17890
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17890
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
TATA-box-binding proteinR [auth U]240Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SPT15BTF1TBP1YER148W
UniProt
Find proteins for P13393 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P13393 
Go to UniProtKB:  P13393
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13393
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription factor IIIB 70 kDa subunitS [auth V]596Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BRF1PCF4TDS4YGR246C
UniProt
Find proteins for P29056 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P29056 
Go to UniProtKB:  P29056
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29056
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription factor TFIIIB component B''T [auth W]594Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BDP1TFC5YNL039WN2682
UniProt
Find proteins for P46678 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P46678 
Go to UniProtKB:  P46678
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP46678
Protein Feature View
Expand
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 21
MoleculeChainsLengthOrganismImage
RNAU [auth R]6Saccharomyces cerevisiae S288C
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 22
MoleculeChainsLengthOrganismImage
Non-Template DNAV [auth X]81Saccharomyces cerevisiae S288C
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 23
MoleculeChainsLengthOrganismImage
Template-DNAW [auth Y]81Saccharomyces cerevisiae S288C
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research CouncilERC-2013-AdG340964-POL1PIC

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Database references, Refinement description
  • Version 1.2: 2019-12-11
    Changes: Other