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- PDB-5n61: RNA polymerase I initially transcribing complex -

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Entry
Database: PDB / ID: 5n61
TitleRNA polymerase I initially transcribing complex
Descriptor(DNA-directed RNA polymerase I subunit ...) x 7
(DNA-directed RNA polymerases I and III subunit ...) x 2
(DNA-directed RNA polymerases I/II/III subunit ...) x 5
(RNA polymerase I-specific transcription initiation factor ...) x 4
KeywordsTRANSFERASE / RNA polymerase I / initially transcribing complex / transferase
Specimen sourceSaccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /
Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast / Baker's yeast /
MethodElectron microscopy (3.4 Å resolution / Particle / Single particle)
AuthorsEngel, C. / Gubbey, T. / Neyer, S. / Sainsbury, S. / Oberthuer, C. / Baejen, C. / Bernecky, C. / Cramer, P.
CitationCell, 2017, 169, 120-131.e22

Cell, 2017, 169, 120-131.e22 StrPapers
Structural Basis of RNA Polymerase I Transcription Initiation.
Christoph Engel / Tobias Gubbey / Simon Neyer / Sarah Sainsbury / Christiane Oberthuer / Carlo Baejen / Carrie Bernecky / Patrick Cramer

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 14, 2017 / Release: Apr 5, 2017
RevisionDateData content typeGroupProviderType
1.0Apr 5, 2017Structure modelrepositoryInitial release
1.1Apr 12, 2017Structure modelStructure summary

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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 RRN3
P: RNA polymerase I-specific transcription initiation factor RRN6
Q: RNA polymerase I-specific transcription initiation factor RRN7
R: RNA polymerase I-specific transcription initiation factor RRN11
S: product RNA
T: template DNA
U: non-template DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)913,42930
Polyers912,85121
Non-polymers5789
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)100210
ΔGint (kcal/M)-595
Surface area (Å2)240000
MethodPISA

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Components

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

#1: Polypeptide(L)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)
References: UniProt: P10964, EC: 2.7.7.6

Cellular component

Molecular function

Biological process

  • ribosome biogenesis (GO: 0042254)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO: 0042790)
#2: Polypeptide(L)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)
References: UniProt: P22138, EC: 2.7.7.6

Cellular component

Molecular function

Biological process

  • ribosome biogenesis (GO: 0042254)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO: 0042790)
#4: Polypeptide(L)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)
References: UniProt: P50106

Cellular component

Molecular function

Biological process

  • ribosome biogenesis (GO: 0042254)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO: 0042790)
#7: Polypeptide(L)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)
References: UniProt: P46669

Cellular component

Molecular function

Biological process

  • ribosome biogenesis (GO: 0042254)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO: 0042790)
#9: Polypeptide(L)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)
References: UniProt: P32529

Cellular component

Molecular function

Biological process

  • mRNA cleavage (GO: 0006379)
  • negative regulation of transcription from RNA polymerase II promoter (GO: 0000122)
  • ribosome biogenesis (GO: 0042254)
  • termination of RNA polymerase I transcription (GO: 0006363)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO: 0042790)
#13: Polypeptide(L)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)
References: UniProt: Q01080

Cellular component

Molecular function

Biological process

  • ribosome biogenesis (GO: 0042254)
  • transcription elongation from RNA polymerase I promoter (GO: 0006362)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO: 0042790)
#14: Polypeptide(L)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)
References: UniProt: P47006

Cellular component

Molecular function

Biological process

  • ribosome biogenesis (GO: 0042254)
  • transcription elongation from RNA polymerase I promoter (GO: 0006362)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO: 0042790)

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DNA-directed RNA polymerases I and III subunit ... , 2 types, 2 molecules CK

#3: Polypeptide(L)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)
References: UniProt: P07703

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)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)
References: UniProt: P28000

Cellular component

Molecular function

Biological process

  • ribosome biogenesis (GO: 0042254)
  • termination of RNA polymerase III transcription (GO: 0006386)
  • transcription elongation from RNA polymerase III promoter (GO: 0006385)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription from RNA polymerase III promoter (GO: 0006383)
  • tRNA transcription from RNA polymerase III promoter (GO: 0042797)

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DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 5 molecules EFHJL

#5: Polypeptide(L)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)
References: UniProt: P20434

Cellular component

Molecular function

Biological process

  • ribosome biogenesis (GO: 0042254)
  • termination of RNA polymerase III transcription (GO: 0006386)
  • transcription elongation from RNA polymerase III promoter (GO: 0006385)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription from RNA polymerase II promoter (GO: 0006366)
  • transcription from RNA polymerase III promoter (GO: 0006383)
  • transcription, RNA-templated (GO: 0001172)
  • tRNA transcription from RNA polymerase III promoter (GO: 0042797)
#6: Polypeptide(L)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)
References: UniProt: P20435

Cellular component

Molecular function

Biological process

  • ribosome biogenesis (GO: 0042254)
  • termination of RNA polymerase III transcription (GO: 0006386)
  • transcription elongation from RNA polymerase III promoter (GO: 0006385)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription from RNA polymerase II promoter (GO: 0006366)
  • transcription from RNA polymerase III promoter (GO: 0006383)
  • transcription, RNA-templated (GO: 0001172)
  • tRNA transcription from RNA polymerase III promoter (GO: 0042797)
#8: Polypeptide(L)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)
References: UniProt: P20436

Cellular component

Molecular function

Biological process

  • ribosome biogenesis (GO: 0042254)
  • termination of RNA polymerase III transcription (GO: 0006386)
  • transcription elongation from RNA polymerase III promoter (GO: 0006385)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription from RNA polymerase II promoter (GO: 0006366)
  • transcription from RNA polymerase III promoter (GO: 0006383)
  • transcription, RNA-templated (GO: 0001172)
  • tRNA transcription from RNA polymerase III promoter (GO: 0042797)
#10: Polypeptide(L)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)
References: UniProt: P22139

Cellular component

Molecular function

Biological process

  • ribosome biogenesis (GO: 0042254)
  • termination of RNA polymerase III transcription (GO: 0006386)
  • transcription elongation from RNA polymerase III promoter (GO: 0006385)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription from RNA polymerase II promoter (GO: 0006366)
  • transcription from RNA polymerase III promoter (GO: 0006383)
  • transcription, RNA-templated (GO: 0001172)
  • tRNA transcription from RNA polymerase III promoter (GO: 0042797)
#12: Polypeptide(L)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)
References: UniProt: P40422

Cellular component

Molecular function

Biological process

  • ribosome biogenesis (GO: 0042254)
  • termination of RNA polymerase III transcription (GO: 0006386)
  • transcription elongation from RNA polymerase III promoter (GO: 0006385)
  • transcription from RNA polymerase I promoter (GO: 0006360)
  • transcription from RNA polymerase II promoter (GO: 0006366)
  • transcription from RNA polymerase III promoter (GO: 0006383)
  • transcription, RNA-templated (GO: 0001172)
  • tRNA transcription from RNA polymerase III promoter (GO: 0042797)

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RNA polymerase I-specific transcription initiation factor ... , 4 types, 4 molecules OPQR

#15: Polypeptide(L)RNA polymerase I-specific transcription initiation factor RRN3


Mass: 72458.258 Da / Num. of mol.: 1 / Source: (gene. exp.) Saccharomyces cerevisiae / References: UniProt: P36070

Cellular component

Molecular function

  • rDNA binding (GO: 0000182)
  • RNA polymerase I core binding (GO: 0001042)
  • RNA polymerase I transcription factor binding (GO: 0001179)
  • transcription factor activity, core RNA polymerase I binding (GO: 0001181)
  • transcription factor activity, RNA polymerase I transcription factor binding (GO: 0001082)

Biological process

  • transcription initiation from RNA polymerase I promoter for nuclear large rRNA transcript (GO: 0001180)
#16: Polypeptide(L)RNA polymerase I-specific transcription initiation factor RRN6


Mass: 102163.227 Da / Num. of mol.: 1 / Source: (gene. exp.) Saccharomyces cerevisiae / References: UniProt: P32786

Cellular component

Molecular function

  • RNA polymerase I regulatory region DNA binding (GO: 0001013)
  • RNA polymerase I transcription factor binding (GO: 0001179)
  • transcription factor activity, RNA polymerase I CORE element binding transcription factor recruiting (GO: 0001187)

Biological process

  • transcription initiation from RNA polymerase I promoter (GO: 0006361)
  • transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO: 0042790)
#17: Polypeptide(L)RNA polymerase I-specific transcription initiation factor RRN7


Mass: 60435.195 Da / Num. of mol.: 1 / Source: (gene. exp.) Saccharomyces cerevisiae / References: UniProt: P40992

Cellular component

Molecular function

  • metal ion binding (GO: 0046872)
  • RNA polymerase I CORE element sequence-specific DNA binding (GO: 0001164)
  • TBP-class protein binding (GO: 0017025)
  • transcription factor activity, RNA polymerase I CORE element binding transcription factor recruiting (GO: 0001187)

Biological process

  • transcription initiation from RNA polymerase I promoter (GO: 0006361)
  • transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO: 0042790)
#18: Polypeptide(L)RNA polymerase I-specific transcription initiation factor RRN11


Mass: 59334.262 Da / Num. of mol.: 1 / Source: (gene. exp.) Saccharomyces cerevisiae / References: UniProt: Q04712

Cellular component

Molecular function

  • RNA polymerase I CORE element sequence-specific DNA binding (GO: 0001164)
  • TBP-class protein binding (GO: 0017025)
  • transcription factor activity, RNA polymerase I CORE element binding transcription factor recruiting (GO: 0001187)

Biological process

  • transcription initiation from RNA polymerase I promoter (GO: 0006361)
  • transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO: 0042790)

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RNA chain , 1 types, 1 molecules S

#19: RNA chainproduct RNA


Mass: 1585.024 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae

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DNA chain , 2 types, 2 molecules TU

#20: DNA chaintemplate DNA


Mass: 13763.725 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae
#21: DNA chainnon-template DNA


Mass: 12833.022 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae

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Non-polymers , 3 types, 9 molecules

#22: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Formula: Zn / Source: (gene. exp.) Saccharomyces cerevisiae
#23: ChemicalChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg
#24: ChemicalChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Formula: SO4

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Details

Sequence detailsUpstream DNA contains no bases to emphasize the uncertainty in the exact register.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

Component
IDNameTypeEntity IDParent IDSource
1RNA polymerase I initially transcribing complexCOMPLEX1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 210MULTIPLE SOURCES
2RNA polymerase I1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 141NATURAL
3Initiation factor Rrn3151RECOMBINANT
4Core Factor16, 17, 181RECOMBINANT
5Initial transcription DNA/RNA scaffold19, 20, 211RECOMBINANT
Molecular weight
IDValueUnitsEntity assembly ID
10.95MEGADALTONS1
20.59MEGADALTONS2
30.07MEGADALTONS3
40.22MEGADALTONS4
50.06MEGADALTONS5
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
12559292Saccharomyces cerevisiae
23559292Saccharomyces cerevisiae
34559292Saccharomyces cerevisiae
45559292Saccharomyces cerevisiae
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganism
13469008Escherichia coli
24469008Escherichia coli
3532630Synthetic construct
Buffer solutionpH: 7.8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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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 FIELD
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 345000 / Symmetry type: POINT
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00938394
ELECTRON MICROSCOPYf_angle_d0.86251996
ELECTRON MICROSCOPYf_dihedral_angle_d7.59231976
ELECTRON MICROSCOPYf_chiral_restr0.0485808
ELECTRON MICROSCOPYf_plane_restr0.0056559

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