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- PDB-5w5y: RNA polymerase I Initial Transcribing Complex -

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Entry
Database: PDB / ID: 5w5y
TitleRNA polymerase I Initial Transcribing Complex
Components
  • (DNA-directed RNA polymerase I subunit ...) x 7
  • (DNA-directed RNA polymerases I and III subunit ...) x 2
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • (RNA polymerase I-specific transcription initiation factor ...) x 3
  • RNA
  • non-template strand DNA
  • template strand DNA
KeywordsTRANSCRIPTION / RNA Polymerase I Core Factor Transcription
Function / homologyRNA polymerase transcription factor SL1 complex / RNA polymerase I transcription initiation factor TAF1B/Rrn7 / RNA polymerase I core factor complex / Transcription initiation factor Rrn7, Zinc-finger / RNA polymerase I-specific transcription initiation factor RRN6-like / Transcription initiation factor Rrn11, budding yeast / RNA polymerase I-specific transcription initiation factor Rrn6 / Transcription initiation factor Rrn11 / RNA polymerase I regulatory region DNA binding / RNA polymerase I-specific transcription-initiation factor ...RNA polymerase transcription factor SL1 complex / RNA polymerase I transcription initiation factor TAF1B/Rrn7 / RNA polymerase I core factor complex / Transcription initiation factor Rrn7, Zinc-finger / RNA polymerase I-specific transcription initiation factor RRN6-like / Transcription initiation factor Rrn11, budding yeast / RNA polymerase I-specific transcription initiation factor Rrn6 / Transcription initiation factor Rrn11 / RNA polymerase I regulatory region DNA binding / RNA polymerase I-specific transcription-initiation factor / RNA polymerase I specific initiation factor / Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7 / Pol I subunit A12, C-terminal zinc ribbon / DNA-directed RNA pol I, largest subunit / DNA-directed RNA polymerase I subunit RPA2, domain 4 / RNA polymerase I, subunit Rpa14, fungi / DNA-directed RNA polymerase I, subunit RPA34.5 / RNA polymerase I associated factor, A49-like / RNA polymerase II sequence-specific DNA binding transcription factor binding / RNA polymerase I CORE element sequence-specific DNA binding / RNA polymerase I transcription factor binding / DNA-directed RNA polymerases I and III subunit AC19 / DNA-directed RNA polymerases I and III subunit AC40 / RNA polymerase I, Rpa2 specific domain / Yeast RNA polymerase I subunit RPA14 / DNA-directed RNA polymerase I subunit RPA34.5 / A49-like RNA polymerase I associated factor / transcription initiation from RNA polymerase I promoter / nucleolar large rRNA transcription by RNA polymerase I / transposon integration / regulation of transcription by RNA polymerase I / transcription elongation from RNA polymerase I promoter / termination of RNA polymerase I transcription / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb7, N-terminal / termination of RNA polymerase III transcription / RNA Polymerase I Transcription Initiation / tRNA transcription by RNA polymerase III / Zinc finger TFIIS-type signature. / RNA polymerase I activity / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / 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 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / TP53 Regulates Transcription of DNA Repair Genes / RNA polymerases M / 15 Kd subunits signature. / DNA-directed RNA polymerase, subunit RPB6 / DNA-directed RNA polymerase, M/15kDa subunit / RNA polymerase, Rpb5, N-terminal / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase, Rpb8 / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / RNA polymerases N / 8 Kd subunits signature. / RNA polymerases, subunit N, zinc binding site / RNA Polymerase II Pre-transcription Events / Archaeal RpoK/eukaryotic RPB6 RNA polymerase subunit / Zinc finger TFIIS-type profile. / RNA polymerase subunit RPB10 / DNA-directed RNA polymerase, subunit N/Rpb10 / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / Zinc finger, TFIIS-type / RNA polymerases K / 14 to 18 Kd subunits signature. / RNA polymerases D / 30 to 40 Kd subunits signature. / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / transcription by RNA polymerase I / RNA polymerases L / 13 to 16 Kd subunits signature. / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerases H / 23 Kd subunits signature. / RPB5-like RNA polymerase subunit / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase, RBP11-like dimerisation domain / DNA-directed RNA polymerase III complex / DNA-directed RNA polymerase I complex / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / transcription by RNA polymerase III / promoter-specific chromatin binding / DNA-directed RNA polymerase II, core complex / mRNA cleavage / transcription, RNA-templated / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / mRNA Splicing - Minor Pathway / Formation of TC-NER Pre-Incision Complex / RNA polymerase subunit, RPB6/omega / RNA polymerase Rpb1, funnel domain superfamily / RPB6/omega subunit-like superfamily / RNA polymerase, subunit omega/K/RPB6 / RNA polymerases M/15 Kd subunit / RNA polymerase Rpb5, N-terminal domain / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, domain 2
Function and homology information
Specimen sourceSaccharomyces cerevisiae / Yeast / yeast /
Saccharomyces cerevisiae s288c / Yeast / yeast / image: Saccharomyces cerevisiae
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsHan, Y. / He, Y.
CitationJournal: 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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 16, 2017 / Release: Jul 26, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 26, 2017Structure modelrepositoryInitial release
1.1Sep 20, 2017Structure modelAuthor supporting evidence / Data collectionem_software / pdbx_audit_support_em_software.name / _pdbx_audit_support.funding_organization
1.2Nov 8, 2017Structure modelDerived calculationspdbx_struct_assembly_pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details

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Structure visualization

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Assembly

Deposited unit
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


Theoretical massNumber of molelcules
Total (without water)846,24126
Polyers845,84920
Non-polymers3926
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)109350
ΔGint (kcal/M)-613
Surface area (Å2)238290

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Components

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DNA-directed RNA polymerase I subunit ... , 7 types, 7 molecules ABDGIMN

#1: Protein/peptide DNA-directed RNA polymerase I subunit RPA190 / DNA-directed RNA polymerase I 190 kDa polypeptide / A190 / DNA-directed RNA polymerase I largest subunit


Mass: 186676.969 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Strain: ATCC 204508 / S288c
References: UniProt:P10964, EC:2.7.7.6 (DNA-directed RNA polymerase)
#2: Protein/peptide DNA-directed RNA polymerase I subunit RPA135 / DNA-directed RNA polymerase I 135 kDa polypeptide / A135 / DNA-directed RNA polymerase I polypeptide 2 / RNA polymerase I subunit 2


Mass: 135910.328 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Strain: ATCC 204508 / S288c
References: UniProt:P22138, EC:2.7.7.6 (DNA-directed RNA polymerase)
#4: Protein/peptide DNA-directed RNA polymerase I subunit RPA14 / A14 / DNA-directed RNA polymerase I 14 kDa polypeptide


Mass: 14599.128 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Strain: ATCC 204508 / S288c / References: UniProt:P50106
#7: Protein/peptide DNA-directed RNA polymerase I subunit RPA43 / A43 / DNA-directed DNA-dependent RNA polymerase 36 kDa polypeptide


Mass: 36264.852 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Strain: ATCC 204508 / S288c / References: UniProt:P46669
#9: Protein/peptide DNA-directed RNA polymerase I subunit RPA12 / A12 / A12.2 / DNA-directed RNA polymerase I 13.7 kDa polypeptide


Mass: 13676.566 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Strain: ATCC 204508 / S288c / References: UniProt:P32529
#13: Protein/peptide DNA-directed RNA polymerase I subunit RPA49 / A49 / DNA-directed RNA polymerase I 49 kDa polypeptide


Mass: 46721.707 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Strain: ATCC 204508 / S288c / References: UniProt:Q01080
#14: Protein/peptide DNA-directed RNA polymerase I subunit RPA34 / A34 / DNA-directed DNA-dependent RNA polymerase 34.5 kDa polypeptide / A34.5


Mass: 26933.518 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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-directed RNA polymerases I and III subunit RPAC1 / 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: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Strain: ATCC 204508 / S288c / References: UniProt:P07703
#11: Protein/peptide DNA-directed RNA polymerases I and III subunit RPAC2 / 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: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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-directed RNA polymerases I, II, and III subunit RPABC1 / 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: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Strain: ATCC 204508 / S288c / References: UniProt:P20434
#6: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC2 / 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: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Strain: ATCC 204508 / S288c / References: UniProt:P20435
#8: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC3 / 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: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Strain: ATCC 204508 / S288c / References: UniProt:P20436
#10: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC5 / 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: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Strain: ATCC 204508 / S288c / References: UniProt:P22139
#12: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha


Mass: 7729.969 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Strain: ATCC 204508 / S288c / References: UniProt:P40422

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RNA polymerase I-specific transcription initiation factor ... , 3 types, 3 molecules OPQ

#15: Protein/peptide RNA polymerase I-specific transcription initiation factor RRN6


Mass: 100721.156 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Strain: ATCC 204508 / S288c / Gene: RRN6, YBL014C, YBL0311, YBL0312 / Production host: Escherichia coli / References: UniProt:P32786
#16: Protein/peptide RNA polymerase I-specific transcription initiation factor RRN7


Mass: 60435.195 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Strain: ATCC 204508 / S288c / Gene: RRN7, YJL025W, J1273 / Production host: Escherichia coli / References: UniProt:P40992
#17: Protein/peptide RNA polymerase I-specific transcription initiation factor RRN11


Mass: 59334.262 Da / Num. of mol.: 1
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Strain: ATCC 204508 / S288c / Gene: RRN11, YML043C, YM9827.09C / Production host: Escherichia coli / References: UniProt:Q04712

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DNA chain , 2 types, 2 molecules ST

#19: DNA chain non-template strand DNA


Mass: 16803.787 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae S288c
#20: DNA chain template strand DNA


Mass: 16360.488 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae S288c

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RNA chain / Non-polymers , 2 types, 7 molecules R

#18: RNA chain RNA


Mass: 1915.213 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae S288c
#21: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Formula: Zn / Zinc

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Details

Sequence detailsDUE TO LOW RESOLUTION THE SEQUENCE CORRESPONDING TO UNK SEGMENT COULD NOT BE MODELED

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: RNA Polymerase I Initial Transcribing Complex / Type: COMPLEX
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20
Source: MULTIPLE SOURCES
Molecular weightValue: 0.9 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae S288c
Source (recombinant)Organism: Escherichia coli
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil S7/2
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 / Calibrated defocus min: 1500 nm / Calibrated defocus max: 4500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage 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 scansMovie frames/image: 40

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Processing

EM software
IDNameVersionCategoryDetails
2Leginon3.1image acquisition
4Gctf0.5CTF correction
7NAMD2.8model fittingMDFF flexible fitting
8Chimera1.11.2model fittingrigid body fitting
10Coot0.8.8model refinement
11PHENIX1.10.1model refinement
12RELION2.0initial Euler assignment
13RELION2.0final Euler assignment
14RELION2.0classification
15RELION2.03D reconstruction
CTF correctionDetails: CTF amplitude correction was performed following 3D auto refinement in relion.
Type: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 124112 / Symmetry type: POINT
Atomic model buildingRef protocol: FLEXIBLE FIT / Ref space: REAL

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