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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 A resolution / 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

DateDeposition: Feb 14, 2017 / Release: Apr 5, 2017 / Last modification: Apr 12, 2017

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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 (A2)100210
ΔGint (kcal/M)-595
Surface area (A2)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 experimentReconstruction method: SINGLE PARTICLE

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Sample preparation

Component
IDNameTypeAssembly id
1RNA polymerase I initially transcribing complexCOMPLEX1
2RNA polymerase I1
3Initiation factor Rrn31
4Core Factor1
5Initial transcription DNA/RNA scaffold1
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 / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
ComputingStructure refinement: PHENIX (1.10.1_2155: phenix.real_space_refine)
3D reconstructionResolution: 3.4 / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 345000
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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