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- PDB-6h67: Yeast RNA polymerase I elongation complex stalled by cyclobutane ... -

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Entry
Database: PDB / ID: 6h67
TitleYeast RNA polymerase I elongation complex stalled by cyclobutane pyrimidine dimer (CPD)
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 / UV-damage / stalling / Cyclobutane Pyrimidine Dimers (CPD)
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 / DNA-directed RNA polymerases I and III subunit AC40 / 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 / Pol I subunit A12, C-terminal zinc ribbon / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / RNA polymerase Rpb7, N-terminal / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 1 / RNA polymerase, N-terminal / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / Archaeal RpoK/eukaryotic RPB6 RNA polymerase subunit / RNA polymerase, subunit omega/K/RPB6 / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb2, domain 7 / 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 / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerase, beta subunit, conserved site / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 2 / RNA polymerase subunit, RPB6/omega / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA pol I, largest subunit / RNA polymerase, beta subunit, protrusion / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus
Function and homology information
Specimen sourceSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.6 Å resolution
AuthorsSanz-Murillo, M. / Xu, J. / Gil-Carton, D. / Wang, D. / Fernandez-Tornero, C.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural basis of RNA polymerase I stalling at UV light-induced DNA damage.
Authors: Marta Sanz-Murillo / Jun Xu / Georgiy A Belogurov / Olga Calvo / David Gil-Carton / María Moreno-Morcillo / Dong Wang / Carlos Fernández-Tornero
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 26, 2018 / Release: Aug 29, 2018
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 29, 2018Structure modelrepositoryInitial release
1.1Sep 12, 2018Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last

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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
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
T: Template DNA
U: Non-template DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)625,81524
Polyers625,39817
Non-polymers4177
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area (Å2)82660
ΔGint (kcal/M)-423
Surface area (Å2)174810
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 (strain ATCC 204508 / S288c) (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 (strain ATCC 204508 / S288c) (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 (strain ATCC 204508 / S288c) (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 (strain ATCC 204508 / S288c) (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 (strain ATCC 204508 / S288c) (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 (strain ATCC 204508 / S288c) (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 (strain ATCC 204508 / S288c) (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 (strain ATCC 204508 / S288c) (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 (strain ATCC 204508 / S288c) (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 (strain ATCC 204508 / S288c) (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 (strain ATCC 204508 / S288c) (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 (strain ATCC 204508 / S288c) (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 (strain ATCC 204508 / S288c) (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 (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P40422

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RNA chain , 1 types, 1 molecules R

#15: RNA chain RNA /


Mass: 3264.036 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae (baker's yeast)

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DNA chain , 2 types, 2 molecules TU

#16: DNA chain Template DNA


Mass: 15816.096 Da / Num. of mol.: 1
Details: Cyclobutane Pyrimidine Dimer at position 18 of the DNA sequence.
Source: (synth.) Saccharomyces cerevisiae (baker's yeast)
#17: DNA chain Non-template DNA


Mass: 16039.287 Da / Num. of mol.: 1 / Source: (synth.) Saccharomyces cerevisiae (baker's yeast)

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Non-polymers , 2 types, 7 molecules

#18: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Formula: Zn / Zinc
#19: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium

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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 stalling at DNA damageCOMPLEX1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 170MULTIPLE SOURCES
2RNA Polymerase I stalling at DNA damageCOMPLEX1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 141NATURAL
3RNA Polymerase I stalling at DNA damageCOMPLEX15, 16, 171NATURAL
Molecular weightValue: 0.631 MDa / Experimental value: NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
12559292Saccharomyces cerevisiae S288C (yeast)
234932Saccharomyces cerevisiae (baker's yeast)
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer ID
110 mM4-(2-hydroxyethyl)-1-piperazineethanesulfonic acidC8H18N2O4S1
2150 mMSodium ChlorideNaCl1
35 mM(2S,3S)-1,4-Bis(sulfanyl)butane-2,3-diolC4H10O2S21
SpecimenConc.: 0.22 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 277.15 kelvins

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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 / Nominal defocus max: 4000 nm / Nominal defocus min: 1500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 5.25 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 2056
Image scansMovie frames/image: 32

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4Gctf0.5.0CTF correction
7UCSF Chimera1.10.2model fitting
9RELION2.0.5initial Euler assignment
10RELION2.0.5final Euler assignment
11RELION2.0.5classification
12RELION2.0.53D reconstruction
13Coot0.8.2model refinement
14PHENIX1.11.1-2575model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 1500
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 254079 / Symmetry type: POINT
Atomic model buildingOverall b value: 93.9 / Ref protocol: AB INITIO MODEL / Ref space: REAL
Atomic model building
IDPDB-ID 3D fitting ID
14C3I1
25M3F1
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00634557
ELECTRON MICROSCOPYf_angle_d0.88746888
ELECTRON MICROSCOPYf_dihedral_angle_d7.23120912
ELECTRON MICROSCOPYf_chiral_restr0.0555245
ELECTRON MICROSCOPYf_plane_restr0.0075905

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