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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
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
  • Non-template DNA
  • RNA
  • Template DNA
KeywordsTRANSCRIPTION / RNA Polymerase I / elongation / transcription
Function / homologyDNA-directed RNA polymerases I and III subunit AC19 / RPB6/omega subunit-like superfamily / RNA polymerase Rpb5, C-terminal domain / Transcription factor S-II (TFIIS) / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb2, domain 6 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily ...DNA-directed RNA polymerases I and III subunit AC19 / RPB6/omega subunit-like superfamily / RNA polymerase Rpb5, C-terminal domain / Transcription factor S-II (TFIIS) / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb2, domain 6 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain superfamily / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RPB5-like RNA polymerase subunit / RNA polymerase Rpb3/Rpb11 dimerisation domain / Pol I subunit A12, C-terminal zinc ribbon / DNA-directed RNA polymerases I and III subunit AC40 / Gap-filling DNA repair synthesis and ligation in TC-NER / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, subunit RPB6 / RNA polymerase subunit RPB10 / RNA polymerases, subunit N, zinc binding site / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / RNA polymerase, subunit H/Rpb5, conserved site / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA pol I, largest subunit / RNA polymerase Rpb6 / RNA polymerases N / 8 kDa subunit / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / Yeast RNA polymerase I subunit RPA14 / RNA Polymerase II Pre-transcription Events / Formation of the Early Elongation Complex / Zinc finger TFIIS-type profile. / RNA polymerases beta chain signature. / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerases N / 8 Kd subunits signature. / RNA polymerases K / 14 to 18 Kd subunits signature. / RNA polymerases H / 23 Kd subunits signature. / RNA polymerases M / 15 Kd subunits signature. / Zinc finger TFIIS-type signature. / RNA polymerases D / 30 to 40 Kd subunits signature. / RNA polymerase Rpb3/Rpb11 dimerisation domain / DNA-directed RNA polymerase I subunit RPA34.5 / RNA polymerase I, Rpa2 specific domain / RNA polymerases M/15 Kd subunit / A49-like RNA polymerase I associated factor / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 3 / RNA polymerase beta subunit / 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 polymerase Rpb2, OB-fold / DNA-directed RNA polymerase I, subunit RPA34.5 / Dual incision in TC-NER / TP53 Regulates Transcription of DNA Repair Genes / 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 I, subunit Rpa14, fungi / RNA polymerase, alpha subunit / DNA-directed RNA polymerase, subunit N/Rpb10 / RNA polymerase II transcribes snRNA genes / RNA polymerase, subunit omega/K/RPB6 / mRNA Capping / mRNA Splicing - Minor Pathway / RNA Polymerase I Transcription Initiation / 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 Rpb7, N-terminal / RNA polymerase, subunit H/Rpb5 C-terminal / Archaeal RpoK/eukaryotic RPB6 RNA polymerase subunit / RNA polymerase, beta subunit, protrusion / Nucleic acid-binding, OB-fold / RNA polymerase subunit, RPB6/omega / DNA-directed RNA polymerase subunit/transcription factor S / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase I subunit RPA2, domain 4 / RNA polymerase I associated factor, A49-like / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / RNA polymerase Rpb2, domain 3 / DNA-directed RNA polymerase, RBP11-like dimerisation domain / Formation of TC-NER Pre-Incision Complex
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4 Å resolution
AuthorsTafur, L. / Sadian, Y. / Hoffmann, N.A. / Jakobi, A.J. / Wetzel, R. / Hagen, W.J.H. / Sachse, C. / Muller, C.W.
CitationJournal: Mol. Cell / Year: 2016
Title: Molecular Structures of Transcribing RNA Polymerase I.
Authors: Lucas Tafur / Yashar Sadian / Niklas A Hoffmann / Arjen J Jakobi / Rene Wetzel / Wim J H Hagen / Carsten Sachse / Christoph W Müller
Abstract: RNA polymerase I (Pol I) is a 14-subunit enzyme that solely synthesizes pre-ribosomal RNA. Recently, the crystal structure of apo Pol I gave unprecedented insight into its molecular architecture. ...RNA polymerase I (Pol I) is a 14-subunit enzyme that solely synthesizes pre-ribosomal RNA. Recently, the crystal structure of apo Pol I gave unprecedented insight into its molecular architecture. Here, we present three cryo-EM structures of elongating Pol I, two at 4.0 Å and one at 4.6 Å resolution, and a Pol I open complex at 3.8 Å resolution. Two modules in Pol I mediate the narrowing of the DNA-binding cleft by closing the clamp domain. The DNA is bound by the clamp head and by the protrusion domain, allowing visualization of the upstream and downstream DNA duplexes in one of the elongation complexes. During formation of the Pol I elongation complex, the bridge helix progressively folds, while the A12.2 C-terminal domain is displaced from the active site. Our results reveal the conformational changes associated with elongation complex formation and provide additional insight into the Pol I transcription cycle.
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: 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 (baker's yeast) / 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 (baker's yeast) / References: UniProt: P22138, DNA-directed RNA polymerase
#4: 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 (baker's yeast) / References: UniProt: P50106
#7: 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 (baker's yeast) / References: UniProt: P46669
#9: 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 (baker's yeast) / References: UniProt: P32529
#13: 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 (baker's yeast) / References: UniProt: Q01080
#14: 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 (baker's yeast) / 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 (baker's yeast) / 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 (baker's yeast) / 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 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 (baker's yeast) / References: UniProt: P20434
#6: 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 (baker's yeast) / References: UniProt: P20435
#8: 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 (baker's yeast) / References: UniProt: P20436
#10: 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 (baker's yeast) / References: UniProt: P22139
#12: 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 (baker's yeast) / References: UniProt: P40422

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DNA chain , 2 types, 2 molecules ST

#16: DNA chain Non-template DNA


Mass: 11756.600 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae (baker's yeast)
#17: DNA chain Template DNA


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

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

#15: RNA chain RNA /


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


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

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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

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 (baker's yeast)
324932Saccharomyces cerevisiae (baker's yeast)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameBuffer ID
1150 mMAmmonium sulfate1
215 mMHEPES-NaOH1
310 mMDTT1
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 FIELDBright-field microscopy
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: 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: 83787 / Symmetry type: POINT
Atomic model buildingRef space: REAL

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