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
  • 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: 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
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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
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase III subunit RPC10I110Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC11YDR045CYD9609.01C
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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
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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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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC4L70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPC10RPB12YHR143W-AYHR143BW
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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
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
TATA-box-binding proteinU240Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SPT15BTF1TBP1YER148W
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: BRF1PCF4TDS4YGR246C
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
Transcription factor TFIIIB component B''W594Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BDP1TFC5YNL039WN2682
Find proteins for P46678 (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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  • Reference Sequence
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Entity ID: 21
MoleculeChainsLengthOrganism
RNAR6Saccharomyces cerevisiae S288C

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Entity ID: 22
MoleculeChainsLengthOrganism
Non-Template DNAX81Saccharomyces cerevisiae S288C

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Entity ID: 23
MoleculeChainsLengthOrganism
Template-DNAY81Saccharomyces 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: 4.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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: 2018-01-31
    Changes: Database references, Refinement description
  • Version 1.2: 2019-12-11
    Changes: Other