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- PDB-5oik: Structure of an RNA polymerase II-DSIF transcription elongation c... -

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Basic information

Entry
Database: PDB / ID: 5oik
TitleStructure of an RNA polymerase II-DSIF transcription elongation complex
Components
  • (DNA (43-MER)) x 2
  • (DNA-directed RNA polymerase II subunit ...Polymerase) x 5
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 4
  • (Transcription elongation factor ...) x 2
  • DNA-directed RNA polymerase subunit betaPolymerase
  • Polymerase (RNA) II (DNA directed) polypeptide D
  • RNA (5'-R(P*UP*AP*UP*AP*UP*AP*CP*AP*UP*AP*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3')
  • Uncharacterized protein
KeywordsTRANSCRIPTION / RNA polymerase II / transcription elongation
Function / homologyDNA-directed RNA polymerase, subunit RPB6 / RNA polymerase Rpb1, funnel domain superfamily / RPB6/omega subunit-like superfamily / RNA polymerase, RBP11-like subunit / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb5, N-terminal domain superfamily / NusG, 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 ...DNA-directed RNA polymerase, subunit RPB6 / RNA polymerase Rpb1, funnel domain superfamily / RPB6/omega subunit-like superfamily / RNA polymerase, RBP11-like subunit / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb5, N-terminal domain superfamily / NusG, 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 RBP11 / Rpb4/RPC9 superfamily / Pol II subunit B9, C-terminal zinc ribbon / Spt4 superfamily / RNA polymerase Rpb1, domain 7 superfamily / KOW motif / RNA polymerase Rpb2, domain 6 / S1 RNA binding domain / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb3/RpoA insert domain / Transcription factor S-II (TFIIS) / RNA polymerase Rpb5, C-terminal domain / RPB5-like RNA polymerase subunit / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RNA polymerase Rpb3/Rpb11 dimerisation domain / DNA-directed RNA polymerase, subunit 2 / HRDC-like superfamily / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase subunit, RPB6/omega / Nucleic acid-binding, OB-fold / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / Ribosomal protein L2, domain 2 / RNA polymerase Rpb2, OB-fold / Transcription elongation factor Spt5 / RNA Polymerase I Transcription Initiation / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerase, subunit H/Rpb5, conserved site / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases, subunit N, zinc binding site / Spt5 transcription elongation factor, N-terminal / Spt4/RpoE2 zinc finger / RNA-binding domain, S1 / RNA polymerase subunit RPB10 / Spt5 C-terminal domain / RNA polymerase Rpb6 / RNA polymerases N / 8 kDa subunit / DNA-directed RNA polymerase, RBP11-like dimerisation domain / B-WICH complex positively regulates rRNA expression / 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 beta chain signature. / Zinc finger TFIIS-type profile. / Formation of RNA Pol II elongation complex / Formation of the Early Elongation Complex / Transcriptional regulation by small RNAs / RNA polymerases D / 30 to 40 Kd subunits signature. / RNA Polymerase II Pre-transcription Events / 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 / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Major Pathway / Zinc finger TFIIS-type signature. / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerases M/15 Kd subunit / RNA polymerase Rpb2, domain 3 / Early transcription elongation factor of RNA pol II, NGN section / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase Rpb8 / RNA polymerase Rpb5, N-terminal domain / RNA polymerase Rpb4 / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 2 / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 7 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1 C-terminal repeat / Spt4/RpoE2 zinc finger / Spt5 transcription elongation factor, acidic N-terminal / Transcription initiation Spt4 / Translation protein SH3-like domain superfamily / Processing of Capped Intron-Containing Pre-mRNA / Formation of the Early Elongation Complex
Function and homology information
Specimen sourceHomo sapiens (human)
Bos taurus (cattle)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.7 Å resolution
AuthorsBernecky, C. / Plitzko, J.M. / Cramer, P.
CitationJournal: Nat. Struct. Mol. Biol. / Year: 2017
Title: Structure of a transcribing RNA polymerase II-DSIF complex reveals a multidentate DNA-RNA clamp.
Authors: Carrie Bernecky / Jürgen M Plitzko / Patrick Cramer
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 18, 2017 / Release: Sep 13, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 13, 2017Structure modelrepositoryInitial release
1.1Oct 18, 2017Structure modelDatabase referencescitation_citation.journal_volume / _citation.page_first / _citation.page_last
1.2Jan 24, 2018Structure modelSource and taxonomyentity_src_gen_entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant

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Structure visualization

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Assembly

Deposited unit
A: DNA-directed RNA polymerase II subunit RPB1
B: DNA-directed RNA polymerase subunit beta
C: DNA-directed RNA polymerase II subunit RPB3
D: Polymerase (RNA) II (DNA directed) polypeptide D
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 II subunit RPB7
H: Uncharacterized protein
I: DNA-directed RNA polymerase II subunit RPB9
J: DNA-directed RNA polymerases I, II, and III subunit RPABC5
K: DNA-directed RNA polymerase II subunit RPB11
L: DNA-directed RNA polymerases I, II, and III subunit RPABC4
N: DNA (43-MER)
P: RNA (5'-R(P*UP*AP*UP*AP*UP*AP*CP*AP*UP*AP*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3')
T: DNA (43-MER)
Y: Transcription elongation factor SPT4
Z: Transcription elongation factor SPT5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)694,73026
Polyers694,18317
Non-polymers5489
Water0
1


  • idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, native gel electrophoresis, microscopy
  • Download structure data
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

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DNA-directed RNA polymerase II subunit ... , 5 types, 5 molecules ACGIK

#1: Protein/peptide DNA-directed RNA polymerase II subunit RPB1 / Polymerase


Mass: 217436.062 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle)
References: UniProt: G3MZY8*PLUS, DNA-directed RNA polymerase
#3: Protein/peptide DNA-directed RNA polymerase II subunit RPB3 / Polymerase / RNA polymerase II subunit B3 / DNA-directed RNA polymerase II subunit C


Mass: 31466.098 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3T0Q3
#7: Protein/peptide DNA-directed RNA polymerase II subunit RPB7 / Polymerase / RNA polymerase II subunit B7 / DNA-directed RNA polymerase II subunit G


Mass: 19314.283 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q5E9B8
#9: Protein/peptide DNA-directed RNA polymerase II subunit RPB9 / Polymerase / RNA polymerase II subunit B9 / DNA-directed RNA polymerase II subunit I


Mass: 14507.205 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q32P73
#11: Protein/peptide DNA-directed RNA polymerase II subunit RPB11 / Polymerase / RNA polymerase II subunit B11 / DNA-directed RNA polymerase II subunit J


Mass: 13310.284 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q32P79

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Protein/peptide , 3 types, 3 molecules BDH

#2: Protein/peptide DNA-directed RNA polymerase subunit beta / Polymerase


Mass: 134041.422 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: A5PJW8, DNA-directed RNA polymerase
#4: Protein/peptide Polymerase (RNA) II (DNA directed) polypeptide D


Mass: 16347.255 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q1JQ91
#8: Protein/peptide Uncharacterized protein


Mass: 17162.273 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: F2Z4H3

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DNA-directed RNA polymerases I, II, and III subunit ... , 4 types, 4 molecules EFJL

#5: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerase / RNA polymerases I / II / and III subunit ABC1 / DNA-directed RNA polymerase II subunit E / RPB5 homolog


Mass: 24514.219 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q2T9T3
#6: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerase


Mass: 14491.026 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: F2Z4C9, UniProt: Q32PE0*PLUS
#10: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerase / RNA polymerases I / II / and III subunit ABC5 / DNA-directed RNA polymerase III subunit L


Mass: 7655.123 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q32P78
#12: Protein/peptide DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerase / RNA polymerases I / II / and III subunit ABC4 / DNA-directed RNA polymerase II subunit K


Mass: 7018.244 Da / Num. of mol.: 1 / Source: (natural) Bos taurus (cattle) / References: UniProt: Q3ZBC0

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DNA chain , 2 types, 2 molecules NT

#13: DNA chain DNA (43-MER)


Mass: 13303.563 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)
#15: DNA chain DNA (43-MER)


Mass: 13178.483 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)

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RNA chain , 1 types, 1 molecules P

#14: RNA chain RNA (5'-R(P*UP*AP*UP*AP*UP*AP*CP*AP*UP*AP*AP*AP*GP*AP*CP*CP*AP*GP*GP*C)-3')


Mass: 16081.696 Da / Num. of mol.: 1 / Source: (synth.) synthetic construct (others)

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Transcription elongation factor ... , 2 types, 2 molecules YZ

#16: Protein/peptide Transcription elongation factor SPT4 / hSPT4 / DRB sensitivity-inducing factor 14 kDa subunit / DSIF p14 / DRB sensitivity-inducing factor small subunit / DSIF small subunit


Mass: 13210.201 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: SUPT4H1, SPT4H, SUPT4H / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: P63272
#17: Protein/peptide Transcription elongation factor SPT5 / hSPT5 / DRB sensitivity-inducing factor 160 kDa subunit / DSIF p160 / DRB sensitivity-inducing factor large subunit / DSIF large subunit / Tat-cotransactivator 1 protein / Tat-CT1 protein


Mass: 121145.477 Da / Num. of mol.: 1 / Source: (gene. exp.) Homo sapiens (human) / Gene: SUPT5H, SPT5, SPT5H / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL / References: UniProt: O00267

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Non-polymers , 2 types, 9 molecules

#18: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Formula: Zn / Zinc
#19: Chemical ChemComp-MG / MAGNESIUM ION


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

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Details

Compound detailsIn order to illustrate the path of the nontemplate DNA, phosphate atoms (chain N residues 15-23) ...In order to illustrate the path of the nontemplate DNA, phosphate atoms (chain N residues 15-23) were placed in the center of the observed DNA density.
Sequence detailsChain A , corresponds to NCBI entry NP_001193242.1

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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 II-DSIF elongation complexCOMPLEX1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 170MULTIPLE SOURCES
2RNA polymerase IICOMPLEX1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 121NATURAL
3DSIFCOMPLEX16, 171RECOMBINANT
4DNA-RNA synthetic constructCOMPLEX13, 14, 151RECOMBINANT
Molecular weight
IDValueEntity assembly IDExperimental value
10.52 MDa2NO
20.13 MDa3NO
30.04 MDa4NO
40.69 MDa1NO
Source (natural)
IDEntity assembly IDNcbi tax IDOrganism
229913Bos taurus (cattle)
339606Homo sapiens (human)
4432630synthetic construct (others)
Source (recombinant)
IDEntity assembly IDNcbi tax IDOrganismStrain
23469008Escherichia coli (E. coli)BL21(DE3)
3432630synthetic construct (others)
Buffer solutionDetails: pH was adjusted at 25 degrees Celsius / pH: 7.25
Buffer component
IDConc.NameFormulaBuffer ID
15 mMHEPES1
2150 mMsodium chlorideNaCl1
30.01 mMzinc chlorideZnCl21
41 mMdithiothreitol1
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 kelvins
Details: Sample (four microliters) was applied to glow-discharged Quantifoil R 2/1 holey carbon grids, which were then blotted for 8.5s and plunge-frozen in liquid 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 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 37000 / Calibrated magnification: 37037 / Nominal defocus max: 3600 nm / Nominal defocus min: 600 nm / Calibrated defocus min: 600 nm / Calibrated defocus max: 3600 nm / Cs: 2.7 mm / C2 aperture diameter: 70 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 9.9 sec. / Electron dose: 33 e/Å2
Details: Movies were aligned and binned to the physical pixel size of 1.35 angstroms.
Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 1 / Number of real images: 2549
EM imaging opticsEnergyfilter name: GIF Quantum / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV
Image scansMovie frames/image: 33 / Used frames/image: 1-33

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Processing

SoftwareName: PHENIX / Version: 1.10_2155: / Classification: refinement
EM software
IDNameVersionCategory
1RELION1.4particle selection
2TOM Toolboximage acquisition
4CTFFIND4.0.16CTF correction
7Rosetta3.6model fitting
9RELION1.4initial Euler assignment
10RELION1.4final Euler assignment
12RELION1.43D reconstruction
13PHENIX1.10model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 687928
SymmetryPoint symmetry: C1
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 101140 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingRef space: REAL
Refine LS restraints
Refine IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.01138891
ELECTRON MICROSCOPYf_angle_d1.05952944
ELECTRON MICROSCOPYf_dihedral_angle_d10.91623475
ELECTRON MICROSCOPYf_chiral_restr0.0615931
ELECTRON MICROSCOPYf_plane_restr0.0066516

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