6F44

RNA Polymerase III closed complex CC2.

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 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

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
  • Structures With Same Primary Citation

  • 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 1 ...

    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

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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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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: 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: 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: 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: 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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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase III subunit RPC7Q251Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC31, ACP2, RPC8, YNL151C, N1769
Find proteins for P17890 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
TATA-box-binding proteinU240Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SPT15, BTF1, TBP1, YER148W
Find proteins for P13393 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
Transcription factor IIIB 70 kDa subunitV596Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BRF1, PCF4, TDS4, YGR246C
Find proteins for P29056 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Transcription factor TFIIIB component B''W594Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BDP1, TFC5, YNL039W, N2682
Find proteins for P46678 (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: 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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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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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: 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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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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  • Reference Sequence

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Entity ID: 22
MoleculeChainsLengthOrganism
Template DNAY81Saccharomyces cerevisiae S288C

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Entity ID: 21
MoleculeChainsLengthOrganism
Non-template DNAX81Saccharomyces 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, V
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 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

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

Revision History 

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-01-24
    Changes: Structure summary
  • Version 1.2: 2018-01-31
    Changes: Database references, Refinement description
  • Version 1.3: 2019-12-11
    Changes: Other