DNA-directed RNA polymerase I subunit RPA49 / DNA-directed RNA polymerase I subunit RPA12 / DNA-directed RNA polymerase I subunit RPA14 / DNA-directed RNA polymerase I subunit RPA34 / DNA-directed RNA polymerase I subunit RPA43 / RNA polymerase I-specific transcription initiation factor RRN7 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase I-specific transcription initiation factor RRN6 / DNA-directed RNA polymerases I and III subunit RPAC2 / DNA-directed RNA polymerases I and III subunit RPAC1 ...DNA-directed RNA polymerase I subunit RPA49 / DNA-directed RNA polymerase I subunit RPA12 / DNA-directed RNA polymerase I subunit RPA14 / DNA-directed RNA polymerase I subunit RPA34 / DNA-directed RNA polymerase I subunit RPA43 / RNA polymerase I-specific transcription initiation factor RRN7 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase I-specific transcription initiation factor RRN6 / DNA-directed RNA polymerases I and III subunit RPAC2 / DNA-directed RNA polymerases I and III subunit RPAC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase I subunit RPA135 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase I subunit RPA190 / RNA polymerase I-specific transcription initiation factor RRN11
National Institutes of Health/National Cancer Institute (NIH/NCI)
NCI 5K22CA184235
United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
NIGMS GM110387
United States
National Science Foundation (NSF, United States)
MCB-1149521
United States
Citation
Journal: Elife / Year: 2017 Title: Structural mechanism of ATP-independent transcription initiation by RNA polymerase I. Authors: Yan Han / Chunli Yan / Thi Hoang Duong Nguyen / Ashleigh J Jackobel / Ivaylo Ivanov / Bruce A Knutson / Yuan He / Abstract: Transcription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a ...Transcription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a structure of Pol I-CF-DNA to 3.8 Å resolution using single-particle cryo-electron microscopy. The structure reveals a bipartite architecture of Core Factor and its recognition of the promoter from -27 to -16. Core Factor's intrinsic mobility correlates well with different conformational states of the Pol I cleft, in addition to the stabilization of either Rrn7 N-terminal domain near Pol I wall or the tandem winged helix domain of A49 at a partially overlapping location. Comparison of the three states in this study with the Pol II system suggests that a ratchet motion of the Core Factor-DNA sub-complex at upstream facilitates promoter melting in an ATP-independent manner, distinct from a DNA translocase actively threading the downstream DNA in the Pol II PIC.
A: DNA-directed RNA polymerase I subunit RPA190 B: DNA-directed RNA polymerase I subunit RPA135 C: DNA-directed RNA polymerases I and III subunit RPAC1 D: DNA-directed RNA polymerase I subunit RPA14 E: DNA-directed RNA polymerases I, II, and III subunit RPABC1 F: DNA-directed RNA polymerases I, II, and III subunit RPABC2 G: DNA-directed RNA polymerase I subunit RPA43 H: DNA-directed RNA polymerases I, II, and III subunit RPABC3 I: DNA-directed RNA polymerase I subunit RPA12 J: DNA-directed RNA polymerases I, II, and III subunit RPABC5 K: DNA-directed RNA polymerases I and III subunit RPAC2 L: DNA-directed RNA polymerases I, II, and III subunit RPABC4 M: DNA-directed RNA polymerase I subunit RPA49 N: DNA-directed RNA polymerase I subunit RPA34 O: RNA polymerase I-specific transcription initiation factor RRN6 P: RNA polymerase I-specific transcription initiation factor RRN7 Q: RNA polymerase I-specific transcription initiation factor RRN11 R: RNA S: non-template strand DNA T: template strand DNA hetero molecules
Mass: 26933.518 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P47006
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DNA-directed RNA polymerases I and III subunit ... , 2 types, 2 molecules CK
#3: Protein/peptide
DNA-directedRNApolymerasesIandIIIsubunitRPAC1 / RNA polymerases I and III subunit AC1 / C37 / DNA-directed RNA polymerases I and III 40 kDa polypeptide / C40
Mass: 37732.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P07703
#11: Protein/peptide
DNA-directedRNApolymerasesIandIIIsubunitRPAC2 / RNA polymerases I and III subunit AC2 / AC19 / DNA-directed RNA polymerases I and III 16 kDa polypeptide / RPA19
Mass: 16167.860 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P28000
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DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL
#5: Protein/peptide
DNA-directedRNApolymerasesI, II, andIIIsubunitRPABC1 / RNA polymerase / RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 kDa polypeptide
Mass: 25117.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P20434
#6: Protein/peptide
DNA-directedRNApolymerasesI, II, andIIIsubunitRPABC2 / RNA polymerase / RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 kDa polypeptide
Mass: 17931.834 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P20435
#8: Protein/peptide
DNA-directedRNApolymerasesI, II, andIIIsubunitRPABC3 / RNA polymerase / RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I / and III 14.5 kDa polypeptide
Mass: 16525.363 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P20436
#10: Protein/peptide
DNA-directedRNApolymerasesI, II, andIIIsubunitRPABC5 / RNA polymerase / RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I / and III 8.3 kDa polypeptide
Mass: 8290.732 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P22139
#12: Protein/peptide
DNA-directedRNApolymerasesI, II, andIIIsubunitRPABC4 / RNA polymerase / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha
Mass: 7729.969 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P40422
Average exposure time: 12 sec. / Electron dose: 56.8 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scans
Movie frames/image: 40
-
Processing
EM software
ID
Name
Version
Category
Details
2
Leginon
3.1
imageacquisition
4
Gctf
0.5
CTFcorrection
7
NAMD
2.8
modelfitting
MDFFflexiblefitting
8
UCSF Chimera
1.11.2
modelfitting
rigidbodyfitting
10
Coot
0.8.8
modelrefinement
11
PHENIX
1.10.1
modelrefinement
12
RELION
2
initialEulerassignment
13
RELION
2
finalEulerassignment
14
RELION
2
classification
15
RELION
2
3Dreconstruction
CTF correction
Details: CTF amplitude correction was performed following 3D auto refinement in relion. Type: PHASE FLIPPING ONLY
Symmetry
Point symmetry: C1 (asymmetric)
3D reconstruction
Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26913 / Symmetry type: POINT
Atomic model building
Protocol: FLEXIBLE FIT / Space: REAL
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