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: 10.1038/s41421-018-0044-z
  • Structures With Same Primary Citation

  • 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-elect ...

    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
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase III subunit RPC1A1460Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPO31, RPC1, RPC160, YOR116C, O3254, YOR3254C
EC: 2.7.7.6
Find proteins for P04051 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P04051
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase III subunit RPC2B1149Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RET1, RPC128, RPC2, YOR207C
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: RPC40, RPC5, YPR110C, P8283.18
Find proteins for P07703 (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: RPB5, RPA7, RPC9, YBR154C, YBR1204
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P20434
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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: RPO26, RPB6, YPR187W, P9677.8
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: RPC25, YKL144C, UNF1, YKL1
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: RPB8, YOR224C, YOR50-14
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: RPC11, YDR045C, YD9609.01C
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: RPB10, YOR210W
Find proteins for P22139 (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: RPC19, YNL113W, N1937
Find proteins for P28000 (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: RPC10, RPB12, YHR143W-A, YHR143BW
Find proteins for P40422 (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: RPC53, RPC4, YDL150W, D1557
Find proteins for P25441 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P25441
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase III subunit RPC3O654Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC82, RPC3, YPR190C, P9677.11
Find proteins for P32349 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P32349
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Transcription factor IIIB 70 kDa subunit,TATA-box-binding protein,Transcription factor IIIB 70 kDa subunitR736Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BRF1, PCF4, TDS4, YGR246C
Find proteins for P29056 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P29056
Find proteins for P13393 (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: RPC37, YKR025W
Find proteins for P36121 (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: RPC34, YNR003C, N2031
Find proteins for P32910 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P32910
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
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 RPC7Q251Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC31
Find proteins for P17890 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
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''S594Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BDP1, TFC5, YNL039W, N2682
Find proteins for P46678 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P46678
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase III subunit RPC9D161Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC17, YJL011C, J1349
Find proteins for P47076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P47076
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  • Reference Sequence

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Entity ID: 20
MoleculeChainsLengthOrganism
DNA (71-MER)X71Saccharomyces cerevisiae S288C

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Entity ID: 21
MoleculeChainsLengthOrganism
DNA (71-MER)Y71Saccharomyces cerevisiae S288C
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download CCD File 
A, B, I, J, L, R
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-03-08 
  • 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 

  • 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