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- PDB-5m3m: Free monomeric RNA polymerase I at 4.0A resolution -

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Entry
Database: PDB / ID: 5m3m
TitleFree monomeric RNA polymerase I at 4.0A resolution
Components
  • (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
KeywordsTRANSCRIPTION / RNA polymerase I / transcription
Function / homologyRPA43 OB domain in RNA Pol I / RNA polymerase Rpb2, domain 6 / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 7 / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb5, N-terminal domain / RNA polymerase Rpb8 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerases N / 8 kDa subunit ...RPA43 OB domain in RNA Pol I / RNA polymerase Rpb2, domain 6 / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 7 / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb5, N-terminal domain / RNA polymerase Rpb8 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerases M/15 Kd subunit / RNA polymerases N / 8 kDa subunit / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase Rpb6 / RNA polymerase Rpb5, C-terminal domain / Transcription factor S-II (TFIIS) / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb1, domain 2 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase Rpb2, domain 3 / RPB6/omega subunit-like superfamily / RNA polymerase subunit RPB10 / DNA-directed RNA polymerase, subunit RPB6 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerases I and III subunit AC19 / Pol I subunit A12, C-terminal zinc ribbon / RPB5-like RNA polymerase subunit superfamily / RNA polymerase, RBP11-like subunit / DNA-directed RNA polymerase subunit Rpb5-like / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase beta subunit / RNA polymerase Rpb1, domain 3 / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / mRNA Splicing - Minor Pathway / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / TP53 Regulates Transcription of DNA Repair Genes / RNA polymerase II transcribes snRNA genes / mRNA Capping / RNA Polymerase I Transcription Initiation / Formation of the Early Elongation Complex / 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 / RNA Polymerase II Pre-transcription Events / Zinc finger TFIIS-type profile. / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / A49-like RNA polymerase I associated factor / RNA polymerase I, Rpa2 specific domain / Yeast RNA polymerase I subunit RPA14 / DNA-directed RNA polymerase I subunit RPA34.5 / RNA polymerases D / 30 to 40 Kd subunits signature. / RNA polymerases beta chain signature. / Zinc finger TFIIS-type signature. / 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, subunit N, zinc binding site / DNA-directed RNA polymerases I and III subunit AC40 / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / RNA polymerase, subunit omega/K/RPB6 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 3 / RNA polymerase, N-terminal / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / Archaeal RpoK/eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb7, N-terminal / RNA polymerase, beta subunit, conserved site / RNA polymerase, Rpb5, N-terminal / RNA polymerase, Rpb8 / DNA-directed RNA polymerase, M/15kDa subunit / 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 2, hybrid-binding domain / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 2 / Nucleic acid-binding, OB-fold / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA pol I, largest subunit / RNA polymerase Rpb2, OB-fold / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / DNA-directed RNA polymerase I, subunit RPA34.5
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4 Å resolution
AuthorsNeyer, S. / Kunz, M. / Geiss, C. / Hantsche, M. / Hodirnau, V.-V. / Seybert, A. / Engel, C. / Scheffer, M.P. / Cramer, P. / Frangakis, A.S.
CitationJournal: Nature / Year: 2016
Title: Structure of RNA polymerase I transcribing ribosomal DNA genes.
Authors: Simon Neyer / Michael Kunz / Christian Geiss / Merle Hantsche / Victor-Valentin Hodirnau / Anja Seybert / Christoph Engel / Margot P Scheffer / Patrick Cramer / Achilleas S Frangakis
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 15, 2016 / Release: Nov 23, 2016
RevisionDateData content typeGroupCategoryItemProviderType
1.0Nov 23, 2016Structure modelrepositoryInitial release
1.1Dec 28, 2016Structure modelDatabase references
1.2Aug 30, 2017Structure modelData collectionem_image_scans / em_software_em_software.name
1.3Feb 20, 2019Structure modelAdvisory / Data collection / Derived calculationsem_admin / pdbx_data_processing_status / pdbx_database_proc / pdbx_validate_close_contact / struct_conn / struct_conn_type_em_admin.last_update

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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
E: DNA-directed RNA polymerases I, II, and III subunit RPABC1
F: DNA-directed RNA polymerases I, II, and III subunit RPABC2
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
D: DNA-directed RNA polymerase I subunit RPA14
G: DNA-directed RNA polymerase I subunit RPA43
hetero molecules


Theoretical massNumber of molelcules
Total (without water)590,83222
Polyers590,27914
Non-polymers5548
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)69150
ΔGint (kcal/M)-378
Surface area (Å2)178180
MethodPISA

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Components

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

#1: Protein/peptide DNA-directed RNA polymerase I subunit RPA190 / Polymerase / 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) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P10964, DNA-directed RNA polymerase
#2: Protein/peptide DNA-directed RNA polymerase I subunit RPA135 / Polymerase / 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) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P22138, DNA-directed RNA polymerase
#7: Protein/peptide DNA-directed RNA polymerase I subunit RPA12 / Polymerase / 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) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P32529
#11: Protein/peptide DNA-directed RNA polymerase I subunit RPA49 / Polymerase / 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) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q01080
#12: Protein/peptide DNA-directed RNA polymerase I subunit RPA34 / Polymerase / 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) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P47006
#13: Protein/peptide DNA-directed RNA polymerase I subunit RPA14 / Polymerase / 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) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P50106
#14: Protein/peptide DNA-directed RNA polymerase I subunit RPA43 / Polymerase / 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) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P46669

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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) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P07703
#9: 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) (yeast)
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

#4: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase / 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) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P20434
#5: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerase / 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) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P20435
#6: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerase / 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) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P20436
#8: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerase / 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) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P22139
#10: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase / 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) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40422

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Non-polymers , 2 types, 8 molecules

#15: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Formula: Zn / Zinc
#16: Chemical ChemComp-SO4 / SULFATE ION


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

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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: Yeast RNA polymerase I elongation complex / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14 / Source: NATURAL
Molecular weightValue: 0.59 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast)
Buffer solutionpH: 7.8
Buffer component
IDConc.NameBuffer ID
15 mMHepes1
2150 mMPotassium acetate1
31 mMMagnesium chloride1
40.01 mMZinc chloride1
50.01 mMbeta-mercaptoethanol1
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 / Grid type: Quantifoil, UltrAuFoil, R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins / Details: blot force 13, blotting time 8.5s

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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
Image recordingElectron dose: 56 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM softwareName: RELION / Version: 1.4 / Category: 3D 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: 94000 / Symmetry type: POINT

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