6CND

Yeast RNA polymerase III natural open complex (nOC)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.8 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
  • Primary Citation of Related Structures:  

  • 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: 

    2Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30302 USA.,1Department of Molecular Biosciences, Northwestern University, Evanston, IL 60208 USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase III subunit RPC1
A
1460Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPO31 (RPC1, RPC160)
EC: 2.7.7.6
Find proteins for P04051 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04051
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase III subunit RPC2
B
1149Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RET1 (RPC128, RPC2)
EC: 2.7.7.6
Find proteins for P22276 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22276
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I and III subunit RPAC1
C
335Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPC40 (RPC5)
Find proteins for P07703 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P07703
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase III subunit RPC9
D
161Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPC17
Find proteins for P47076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P47076
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC1
E
215Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB5 (RPA7, RPC9)
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20434
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC2
F
155Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPO26 (RPB6)
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20435
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase III subunit RPC8
G
212Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPC25
Find proteins for P35718 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P35718
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC3
H
146Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB8
Find proteins for P20436 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P20436
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase III subunit RPC10
I
110Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPC11
Find proteins for Q04307 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q04307
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC5
J
70Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPB10
Find proteins for P22139 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P22139
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I and III subunit RPAC2
K
142Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPC19
Find proteins for P28000 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P28000
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III subunit RPABC4
L
70Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPC10 (RPB12)
Find proteins for P40422 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P40422
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase III subunit RPC5
M
282Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPC37
Find proteins for P36121 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P36121
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase III subunit RPC4
N
422Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPC53 (RPC4)
Find proteins for P25441 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25441
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase III subunit RPC3
O
654Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPC82 (RPC3)
Find proteins for P32349 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32349
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase III subunit RPC6
P
317Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPC34
Find proteins for P32910 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P32910
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 RPC7
Q
251Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPC31 (ACP2, RPC8)
Find proteins for P17890 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P17890
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
Transcription factor IIIB 70 kDa subunit,TATA-box-binding protein,Transcription factor IIIB 70 kDa subunit
R
736Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SPT15 (BTF1, TBP1), BRF1 (PCF4, TDS4)
Find proteins for P13393 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P13393
Find proteins for P29056 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: BRF1
Go to UniProtKB:  P29056
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''
S
594Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: BDP1 (TFC5)
Find proteins for P46678 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: BDP1
Go to UniProtKB:  P46678
Entity ID: 20
MoleculeChainsLengthOrganism
DNA (71-MER)X71Saccharomyces cerevisiae S288C
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 SDF File 
Download CCD File 
A, B, I, J, L, R
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
Q, S
L-PEPTIDE LINKINGC4 H9 N O2

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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.8 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


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
    Type: Author supporting evidence, Data collection
  • Version 1.2: 2020-01-08
    Type: Author supporting evidence