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- PDB-5m5x: RNA Polymerase I elongation complex 1 -

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Entry
Database: PDB / ID: 5m5x
TitleRNA Polymerase I elongation complex 1
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
KeywordsTRANSCRIPTION / RNA Polymerase I / elongation / transcription
Specimen sourceSaccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /
MethodElectron microscopy (4 Å resolution / Particle / Single particle)
AuthorsTafur, L. / Sadian, Y. / Hoffmann, N.A. / Jakobi, A.J. / Wetzel, R. / Hagen, W.J.H. / Sachse, C. / Muller, C.W.
CitationMol. Cell, 2016, 64, 1135-1143

Mol. Cell, 2016, 64, 1135-1143 Yorodumi Papers
Molecular Structures of Transcribing RNA Polymerase I.
Lucas Tafur / Yashar Sadian / Niklas A Hoffmann / Arjen J Jakobi / Rene Wetzel / Wim J H Hagen / Carsten Sachse / Christoph W Müller

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 23, 2016 / Release: Dec 21, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Dec 21, 2016Structure modelrepositoryInitial release
1.1Dec 28, 2016Structure modelDatabase references
1.2Aug 30, 2017Structure modelAuthor supporting evidence / Derived calculations / Experimental preparationem_sample_support / pdbx_audit_support / struct_conn_em_sample_support.grid_type / _pdbx_audit_support.funding_organization

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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
R: RNA
S: Non-template DNA
T: Template DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)620,47223
Polyers620,08017
Non-polymers3926
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)85270
ΔGint (kcal/M)-413
Surface area (Å2)179580
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 / 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 / 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 / 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 / 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 / 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 / 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 / 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 / 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 / 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 / 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 / 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 / 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 / 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 / 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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DNA chain , 2 types, 2 molecules ST

#16: DNA chainNon-template DNA


Mass: 11756.600 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae
#17: DNA chainTemplate DNA


Mass: 11629.489 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae

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

#15: RNA chainRNA


Mass: 6414.902 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae
#18: Chemical
ChemComp-ZN / ZINC ION


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

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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 elongation complex 1COMPLEX1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 170NATURAL
2Transcription ScaffoldCOMPLEX15, 16, 171MULTIPLE SOURCES
Molecular weight
IDUnitsEntity assembly IDExperimental value
1MEGADALTONS1NO
12
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
214932Saccharomyces cerevisiae
324932Saccharomyces cerevisiae
Buffer solutionpH: 7.5
Buffer component
IDConc.UnitsNameBuffer ID
1150mMAmmonium sulfate1
215mMHEPES-NaOH1
310mMDTT1
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: MOLYBDENUM / Grid mesh size: 400 / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293.15 kelvins
Details: 2.5 ul of sample 15 seconds wait time Blot time for 8 seconds

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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: 40 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 20

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Processing

EM softwareName: RELION / Version: 1.4 / Category: RECONSTRUCTION
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 83787 / Symmetry type: POINT
Atomic model buildingRef space: REAL

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