EMDB-8777: Pol I Initial Transcribing Complex with a truncated scaffold at 6...

Basic information

• Entry: Database: EMDB / ID: 8777
• Title: Pol I Initial Transcribing Complex with a truncated scaffold at 6.9 angstrom
• Map data: RNA polymerase I Initial Transcribing Complex with a truncated scaffold

Sample

RNA Polymerase I Initial Transcribing Complex with a truncated scaffold

• (DNA-directed RNA polymerase I subunit ...Polymerase) x 7
• (DNA-directed RNA polymerases I and III subunit ...) x 2
• (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 5
• (RNA polymerase I-specific transcription initiation factor ...) x 3
• (nucleic-acidNucleic acid) x 4

• Function / homology: Transcription initiation factor Rrn7, Zinc-finger / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RNA polymerase Rpb2, domain 6 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain superfamily / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RPB6/omega subunit-like superfamily / RPB5-like RNA polymerase subunit / Pol I subunit A12, C-terminal zinc ribbon / DNA-directed RNA polymerases I and III subunit AC40 / DNA-directed RNA polymerases I and III subunit AC19 / RNA polymerase I transcription initiation factor TAF1B/Rrn7 / DNA-directed RNA polymerase, subunit RPB6 / RNA polymerase Rpb3/RpoA insert domain / Transcription initiation factor Rrn11, budding yeast / DNA-directed RNA polymerase I, subunit RPA34.5 / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / RNA polymerase Rpb2, OB-fold / DNA-directed RNA pol I, largest subunit / DNA-directed RNA polymerase, subunit 2 / RNA polymerase I-specific transcription initiation factor Rrn6 / RNA polymerase I-specific transcription initiation factor RRN6-like / RNA polymerase subunit RPB10 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerase, subunit H/Rpb5, conserved site / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases, subunit N, zinc binding site / RNA Polymerase II Pre-transcription Events / RNA polymerase Rpb1, domain 2 / Transcription factor S-II (TFIIS) / Nucleic acid-binding, OB-fold / RNA polymerases D / 30 to 40 Kd subunits signature. / RNA polymerase I, Rpa2 specific domain / Yeast RNA polymerase I subunit RPA14 / DNA-directed RNA polymerase I subunit RPA34.5 / RNA polymerase I-specific transcription-initiation factor / Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7 / RNA polymerase Rpb3/Rpb11 dimerisation domain / Zinc finger TFIIS-type signature. / RNA polymerase Rpb1, domain 4 / RNA polymerases M / 15 Kd subunits signature. / RNA polymerases H / 23 Kd subunits signature. / RNA polymerases K / 14 to 18 Kd subunits signature. / RNA polymerases N / 8 Kd subunits signature. / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerases beta chain signature. / A49-like RNA polymerase I associated factor / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb5, C-terminal domain / RNA polymerase Rpb5, N-terminal domain / RNA polymerase Rpb6 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases N / 8 kDa subunit / RNA polymerases M/15 Kd subunit / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase Rpb8 / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb1, domain 1 / RNA polymerase I specific initiation factor / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 2 / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase I, subunit Rpa14, fungi / RNA polymerase subunit, RPB6/omega / Formation of the Early Elongation Complex / TP53 Regulates Transcription of DNA Repair Genes / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / Zinc finger, TFIIS-type / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase, alpha subunit / DNA-directed RNA polymerase, subunit N/Rpb10 / DNA-directed RNA polymerase subunit/transcription factor S / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / RNA polymerase II transcribes snRNA genes / RNA polymerase, Rpb8 / mRNA Capping / mRNA Splicing - Minor Pathway / RNA Polymerase I Transcription Initiation / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / DNA-directed RNA polymerase, M/15kDa subunit / Zinc finger TFIIS-type profile. / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb2, domain 3 / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb7, N-terminal / DNA-directed RNA polymerase, RBP11-like dimerisation domain
• Source: Saccharomyces cerevisiae S288c (yeast)
• Method: single particle reconstruction / cryo EM / 6.9 Å resolution
• Authors: Han Y / He Y
• 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
• Date: Deposition: Jun 16, 2017 / Header (metadata) release: Jul 5, 2017 / Map release: Jul 5, 2017 / Last update: Jul 18, 2018

Map

• File: emd_8777.map.gz (map file in CCP4 format, 8389 KB)
• Voxel size: X=Y=Z: 2.36 Å

Density

Contour Level:	0.07 (by author), 0.07 (movie #1):
Minimum - Maximum	-0.10179037 - 0.23072258
Average (Standard dev.)	0.0028788708 (0.015079218)

Details

EMDB XML:

Space Group Number	1
Map Geometry	Axis order X Y Z Dimensions 128 128 128 Origin 0. 0. 0. Limit 127. 127. 127. Spacing 128 128 128
Cell	A=B=C: 302.08 Å α=β=γ: 90.0 deg.

CCP4 map header:

mode	Image stored as Reals
Å/pix. X/Y/Z	2.36	2.36	2.36
M x/y/z	128	128	128
origin x/y/z	0.000	0.000	0.000
length x/y/z	302.080	302.080	302.080
α/β/γ	90.000	90.000	90.000
start NX/NY/NZ	-15	2	-37
NX/NY/NZ	99	82	71
MAP C/R/S	1	2	3
start NC/NR/NS	0	0	0
NC/NR/NS	128	128	128
D min/max/mean	-0.102	0.231	0.003

Supplemental data

Sample components

Entire RNA Polymerase I Initial Transcribing Complex with a truncated sc...

• Entire: Name: RNA Polymerase I Initial Transcribing Complex with a truncated scaffold; Number of components: 22

Component #1: protein, RNA Polymerase I Initial Transcribing Complex with a tru...

• Protein: Name: RNA Polymerase I Initial Transcribing Complex with a truncated scaffold; Recombinant expression: No
• Mass: Theoretical: 900 kDa
• Source: Species: Saccharomyces cerevisiae S288c (yeast)

Component #2: protein, DNA-directed RNA polymerase I subunit RPA190

• Protein: Name: DNA-directed RNA polymerase I subunit RPA190Polymerase; Recombinant expression: No
• Source: Species: Saccharomyces cerevisiae S288c (yeast)

Component #3: protein, DNA-directed RNA polymerase I subunit RPA135

• Protein: Name: DNA-directed RNA polymerase I subunit RPA135Polymerase; Recombinant expression: No
• Source: Species: Saccharomyces cerevisiae S288c (yeast)

Component #4: protein, DNA-directed RNA polymerases I and III subunit RPAC1

• Protein: Name: DNA-directed RNA polymerases I and III subunit RPAC1 / Recombinant expression: No
• Source: Species: Saccharomyces cerevisiae S288c (yeast)

Component #5: protein, DNA-directed RNA polymerase I subunit RPA14

• Protein: Name: DNA-directed RNA polymerase I subunit RPA14Polymerase / Recombinant expression: No
• Source: Species: Saccharomyces cerevisiae S288c (yeast)

Component #6: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC1

• Protein: Name: DNA-directed RNA polymerases I, II, and III subunit RPABC1RNA polymerase; Recombinant expression: No
• Source: Species: Saccharomyces cerevisiae S288c (yeast)

Component #7: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC2

• Protein: Name: DNA-directed RNA polymerases I, II, and III subunit RPABC2RNA polymerase; Recombinant expression: No
• Source: Species: Saccharomyces cerevisiae S288c (yeast)

Component #8: protein, DNA-directed RNA polymerase I subunit RPA43

• Protein: Name: DNA-directed RNA polymerase I subunit RPA43Polymerase / Recombinant expression: No
• Source: Species: Saccharomyces cerevisiae S288c (yeast)

Component #9: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC3

• Protein: Name: DNA-directed RNA polymerases I, II, and III subunit RPABC3RNA polymerase; Recombinant expression: No
• Source: Species: Saccharomyces cerevisiae S288c (yeast)

Component #10: protein, DNA-directed RNA polymerase I subunit RPA12

• Protein: Name: DNA-directed RNA polymerase I subunit RPA12Polymerase / Recombinant expression: No
• Source: Species: Saccharomyces cerevisiae S288c (yeast)

Component #11: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC5

• Protein: Name: DNA-directed RNA polymerases I, II, and III subunit RPABC5RNA polymerase; Recombinant expression: No
• Source: Species: Saccharomyces cerevisiae S288c (yeast)

Component #12: protein, DNA-directed RNA polymerases I and III subunit RPAC2

• Protein: Name: DNA-directed RNA polymerases I and III subunit RPAC2 / Recombinant expression: No
• Source: Species: Saccharomyces cerevisiae S288c (yeast)

Component #13: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC4

• Protein: Name: DNA-directed RNA polymerases I, II, and III subunit RPABC4RNA polymerase; Recombinant expression: No
• Source: Species: Saccharomyces cerevisiae S288c (yeast)

Component #14: protein, DNA-directed RNA polymerase I subunit RPA49

• Protein: Name: DNA-directed RNA polymerase I subunit RPA49Polymerase / Recombinant expression: No
• Source: Species: Saccharomyces cerevisiae S288c (yeast)

Component #15: protein, DNA-directed RNA polymerase I subunit RPA34

• Protein: Name: DNA-directed RNA polymerase I subunit RPA34Polymerase / Recombinant expression: No
• Source: Species: Saccharomyces cerevisiae S288c (yeast)

Component #16: protein, RNA polymerase I-specific transcription initiation facto...

• Protein: Name: RNA polymerase I-specific transcription initiation factor RRN6; Recombinant expression: No
• Source: Species: Saccharomyces cerevisiae S288c (yeast)
• Source (engineered): Expression System: Escherichia coli (E. coli)

Component #17: protein, RNA polymerase I-specific transcription initiation facto...

• Protein: Name: RNA polymerase I-specific transcription initiation factor RRN7; Recombinant expression: No
• Source: Species: Saccharomyces cerevisiae S288c (yeast)
• Source (engineered): Expression System: Escherichia coli (E. coli)

Component #18: protein, RNA polymerase I-specific transcription initiation facto...

• Protein: Name: RNA polymerase I-specific transcription initiation factor RRN11; Recombinant expression: No
• Source: Species: Saccharomyces cerevisiae S288c (yeast)
• Source (engineered): Expression System: Escherichia coli (E. coli)

Component #19: nucleic-acid, RNA

Nucleic-acid

Name: RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:

AUGCGA

• Source: Species: Saccharomyces cerevisiae S288c (yeast)

Component #20: nucleic-acid, template strand DNA

Nucleic-acid

Name: template strand DNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:

TGTCTTCAAC TGCTTTCGCA TGAAGTACCT CCCAACTACT TTTCCTCACA CTTG

• Source: Species: Saccharomyces cerevisiae S288c (yeast)

Component #21: nucleic-acid, upstream non-template strand DNA

Nucleic-acid

Name: upstream non-template strand DNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:

TGAGGAAAAG TAGTTGGG

• Source: Species: Saccharomyces cerevisiae S288c (yeast)

Component #22: nucleic-acid, downstream non-template strand DNA

Nucleic-acid

Name: downstream non-template strand DNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:

GCAGTTGAAG ACA

• Source: Species: Saccharomyces cerevisiae S288c (yeast)

Experimental details

Sample preparation

• Specimen: Specimen state: particle / Method: cryo EM
• Sample solution: pH: 7.6
• Vitrification: Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

Electron microscopy imaging

• Imaging: Microscope: JEOL 3200FS
• Electron gun: Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 17.2 e/Ų / Illumination mode: FLOOD BEAM
• Lens: Magnification: 15000. X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD
• Specimen Holder: Model: GATAN LIQUID NITROGEN
• Camera: Detector: GATAN K2 SUMMIT (4k x 4k)

Image processing

• Processing: Method: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 43843
• 3D reconstruction: CTF correction: CTF amplitude correction was performed following 3D auto refinement in relion.; Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF

Atomic model buiding

• Modeling #1: Refinement space: REAL