6CND

Yeast RNA polymerase III natural open complex (nOC)

  • Classification: transcription/dna
  • Organism(s): Saccharomyces cerevisiae S288C
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2018-03-08 Released: 2018-08-22 
  • Deposition Author(s): Han, Y., He, Y.
  • Funding Organization(s): Northwestern University, Chicago Biomedical Consortium with support from the Searle Funds at The Chicago Community Trust, American Cancer Society, National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation XSEDE program, National Energy Research Scientific Computing Center

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 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

Structural visualization of RNA polymerase III transcription machineries.

Han, Y.Yan, C.Fishbain, S.Ivanov, I.He, Y.

(2018) Cell Discov 4: 40-40

  • DOI: https://doi.org/10.1038/s41421-018-0044-z
  • Primary Citation of Related Structures:  
    6CNB, 6CNC, 6CND, 6CNF

  • PubMed Abstract: 

    RNA polymerase III (Pol III) transcription initiation requires the action of the transcription factor IIIB (TFIIIB) and is highly regulated. Here, we determine the structures of Pol III pre-initiation complexes (PICs) using single particle cryo-electron microscopy (cryo-EM). We observe stable Pol III-TFIIIB complexes using nucleic acid scaffolds mimicking various functional states, in which TFIIIB tightly encircles the upstream promoter DNA. There is an intricate interaction between TFIIIB and Pol III, which stabilizes the winged-helix domains of the C34 subunit of Pol III over the active site cleft. The architecture of Pol III PIC more resembles that of the Pol II PIC than the Pol I PIC. In addition, we also obtain a 3D reconstruction of Pol III in complex with TFIIIB using the elongation complex (EC) scaffold, shedding light on the mechanism of facilitated recycling of Pol III prior to transcription re-initiation.


  • Organizational Affiliation

    1Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208 USA.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC11,460Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P04051 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC21,149Saccharomyces cerevisiae S288CMutation(s): 0 
EC: 2.7.7.6
UniProt
Find proteins for P22276 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I and III subunit RPAC1335Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P07703 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC9161Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P47076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC1215Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC2155Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC8212Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P35718 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC3146Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC10110Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC570Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I and III subunit RPAC2142Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P28000 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III subunit RPABC470Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC5282Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC4422Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
Find proteins for P25441 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC3654Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC6317Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-directed RNA polymerase III subunit RPC7,DNA-directed RNA polymerase III subunit RPC7,DNA-directed RNA polymerase III subunit RPC7,DNA-directed RNA polymerase III subunit RPC7,DNA-directed RNA polymerase III subunit RPC7251Saccharomyces cerevisiae S288CMutation(s): 0 
UniProt
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor IIIB 70 kDa subunit,TATA-box-binding protein,Transcription factor IIIB 70 kDa subunit736Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BRF1PCF4TDS4YGR246CSPT15BTF1TBP1YER148W
UniProt
Find proteins for P29056 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Find proteins for P13393 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription factor TFIIIB component B'',Transcription factor TFIIIB component B'',Transcription factor TFIIIB component B'',Transcription factor TFIIIB component B'',Transcription factor TFIIIB component B''594Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BDP1TFC5YNL039WN2682
UniProt
Find proteins for P46678 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 20
MoleculeChains LengthOrganismImage
DNA (71-MER)T [auth X]71Saccharomyces cerevisiae S288C
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Entity ID: 21
MoleculeChains LengthOrganismImage
DNA (71-MER)U [auth Y]71Saccharomyces cerevisiae S288C
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION2.1

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Released Date: 2018-08-22 
  • Deposition Author(s): Han, Y., He, Y.

Funding OrganizationLocationGrant Number
Northwestern UniversityUnited StatesCornew Innovation Award
Chicago Biomedical Consortium with support from the Searle Funds at The Chicago Community TrustUnited StatesCatalyst Award
American Cancer SocietyUnited StatesIRG-15-173-21
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM110387
National Science Foundation XSEDE programUnited StatesCHE110042
National Energy Research Scientific Computing CenterUnited StatesDE-AC02-05CH11231

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-22
    Type: Initial release
  • Version 1.1: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence