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- EMDB-2785: Architecture of the RNA polymerase II-Mediator core transcription... -

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Basic information

Entry
Database: EMDB / ID: EMD-2785
TitleArchitecture of the RNA polymerase II-Mediator core transcription initiation complex
Map datacITC
Sample
  • Sample: cITC
  • Protein or peptide: x 16 types
  • DNA: x 2 types
  • RNA: x 1 types
Keywordstranscription / transcription initiation / RNA polymerase II / General Transcription Factors
Function / homology
Function and homology information


RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / promoter clearance from RNA polymerase II promoter / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / RPB4-RPB7 complex / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding / transcription open complex formation at RNA polymerase II promoter ...RNA polymerase II complex recruiting activity / TFIIA-class transcription factor complex binding / promoter clearance from RNA polymerase II promoter / transcription factor TFIIIB complex / RNA polymerase III preinitiation complex assembly / RNA polymerase III transcription regulatory region sequence-specific DNA binding / RPB4-RPB7 complex / regulation of transcription by RNA polymerase III / RNA polymerase I general transcription initiation factor binding / transcription open complex formation at RNA polymerase II promoter / transcription factor TFIIF complex / transcriptional start site selection at RNA polymerase II promoter / transposon integration / RNA polymerase III general transcription initiation factor activity / transcription factor TFIIA complex / general transcription initiation factor activity / RNA polymerase I preinitiation complex assembly / nuclear-transcribed mRNA catabolic process, exonucleolytic / recruitment of 3'-end processing factors to RNA polymerase II holoenzyme complex / mRNA export from nucleus in response to heat stress / positive regulation of transcription regulatory region DNA binding / DNA binding, bending / RNA Polymerase I Transcription Initiation / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / RNA polymerase II preinitiation complex assembly / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / termination of RNA polymerase II transcription / RNA polymerase II general transcription initiation factor activity / RNA Pol II CTD phosphorylation and interaction with CE / mRNA Capping / Formation of the Early Elongation Complex / transcription factor TFIID complex / RNA polymerase II transcribes snRNA genes / RNA polymerase II complex binding / termination of RNA polymerase III transcription / RNA polymerase II activity / transcription initiation from RNA polymerase III promoter / positive regulation of translational initiation / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Transcription Initiation / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA polymerase I activity / termination of RNA polymerase I transcription / RNA Polymerase II Transcription Elongation / Estrogen-dependent gene expression / tRNA transcription by RNA polymerase III / RNA Polymerase I Promoter Escape / transcription elongation from RNA polymerase I promoter / RNA Polymerase II Pre-transcription Events / transcription initiation from RNA polymerase I promoter / transcription by RNA polymerase I / transcription by RNA polymerase III / transcription-coupled nucleotide-excision repair / nucleolar large rRNA transcription by RNA polymerase I / mRNA cleavage / RNA polymerase I complex / RNA polymerase III complex / transcription preinitiation complex / RNA polymerase II, core complex / RNA polymerase II core promoter sequence-specific DNA binding / translesion synthesis / Formation of TC-NER Pre-Incision Complex / Gap-filling DNA repair synthesis and ligation in TC-NER / translation initiation factor binding / Dual incision in TC-NER / TBP-class protein binding / transcription elongation from RNA polymerase II promoter / transcription initiation from RNA polymerase II promoter / positive regulation of transcription elongation from RNA polymerase II promoter / P-body / ribonucleoside binding / transcription by RNA polymerase II / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / DNA-templated transcription, initiation / cytoplasmic stress granule / transcription, RNA-templated / single-stranded DNA binding / ribosome biogenesis / disordered domain specific binding / single-stranded RNA binding / DNA-binding transcription factor binding / nucleic acid binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / protein dimerization activity / mRNA binding / nucleotide binding / negative regulation of transcription, DNA-templated / chromatin binding / nucleolus / regulation of transcription, DNA-templated / positive regulation of transcription by RNA polymerase II / protein-containing complex / mitochondrion
Similarity search - Function
TFIIF, beta subunit, N-terminal / TFIIF, beta subunit N-terminus / Transcription initiation factor IIF, beta subunit / TFIIF, beta subunit HTH domain / TFIIF beta subunit, HTH domain / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription initiation factor IIF, alpha subunit / Transcription Factor IIF, Rap30/Rap74, interaction / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB repeat ...TFIIF, beta subunit, N-terminal / TFIIF, beta subunit N-terminus / Transcription initiation factor IIF, beta subunit / TFIIF, beta subunit HTH domain / TFIIF beta subunit, HTH domain / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription initiation factor IIF, alpha subunit / Transcription Factor IIF, Rap30/Rap74, interaction / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Transcription factor TFIIB, conserved site / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / TFIIB zinc-binding / Zinc finger, TFIIB-type / TATA-box binding protein, eukaryotic / Transcription factor TFIID repeat signature. / TATA-box binding protein, conserved site / TATA-box binding protein / Transcription factor TFIID (or TATA-binding protein, TBP) / DNA-directed RNA polymerase II subunit Rpb4-like / TBP domain superfamily / RNA polymerase Rpb4/RPC9, core / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb1 C-terminal repeat / Eukaryotic RNA polymerase II heptapeptide repeat. / RNA polymerase Rpb1, domain 7 / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 6 / RNA polymerase Rpb1, domain 7 superfamily / RNA polymerase Rpb1, domain 7 / Rpb4/RPC9 superfamily / RNA polymerase RBP11 / Pol II subunit B9, C-terminal zinc ribbon / RNA polymerase subunit Rpb4/RPC9 / RNA polymerase Rpb4 / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / RNA polymerase Rpb7-like , N-terminal / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / HRDC-like superfamily / RNA polymerase Rpb2, domain 4 / RNA polymerase Rpb2, domain 4 / RNA polymerase subunit Rpb7-like / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb2, domain 5 / RNA polymerase Rpb2, domain 5 / Zinc finger TFIIS-type signature. / RNA polymerases, subunit N, zinc binding site / RNA polymerase subunit RPB10 / DNA-directed RNA polymerase subunit RPABC5/Rpb10 / RNA polymerases N / 8 Kd subunits signature. / RNA polymerases N / 8 kDa subunit / RNA polymerase subunit 9 / RNA polymerases M/15 Kd subunit / DNA-directed RNA polymerase, M/15kDa subunit / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerases M / 15 Kd subunits signature. / RNA polymerase Rpb5, N-terminal domain / DNA-directed RNA polymerase subunit Rpo5/Rpb5 / DNA-directed RNA polymerase subunit/transcription factor S / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb8 / RNA polymerase subunit 8 / RNA polymerase, Rpb8 / DNA-directed RNA polymerase, subunit RPB6 / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase subunit CX / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / RNA polymerases D / 30 to 40 Kd subunits signature. / : / RPB5-like RNA polymerase subunit superfamily / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase Rpb5, C-terminal domain / RNA polymerases H / 23 Kd subunits signature. / RNA polymerases L / 13 to 16 Kd subunits signature. / : / RNA polymerase Rpb3/Rpb11 dimerisation domain / DNA-directed RNA polymerase, RBP11-like dimerisation domain / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / Archaeal Rpo6/eukaryotic RPB6 RNA polymerase subunit / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RNA polymerases K / 14 to 18 Kd subunits signature. / Zinc finger, TFIIS-type / C2C2 Zinc finger / Transcription factor S-II (TFIIS) / Zinc finger TFIIS-type profile. / S1 RNA binding domain / Ribosomal protein S1-like RNA-binding domain / RNA-binding domain, S1 / S1 domain / RNA polymerase Rpb1, domain 3 superfamily
Similarity search - Domain/homology
DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerase II subunit RPB7 / Transcription initiation factor IIB / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 ...DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase II subunit RPB11 / DNA-directed RNA polymerase II subunit RPB7 / Transcription initiation factor IIB / DNA-directed RNA polymerase II subunit RPB9 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase II subunit RPB4 / TATA-box-binding protein / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB1 / Transcription initiation factor IIF subunit alpha / Transcription initiation factor IIF subunit beta
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast) / Saccharomyces mikatae (yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.8 Å
AuthorsPlaschka C / Lariviere L / Wenzeck L / Hemann M / Tegunov D / Petrotchenko EV / Borchers CH / Baumeister W / Herzog F / Villa E / Cramer P
CitationJournal: Nature / Year: 2015
Title: Architecture of the RNA polymerase II-Mediator core initiation complex.
Authors: C Plaschka / L Larivière / L Wenzeck / M Seizl / M Hemann / D Tegunov / E V Petrotchenko / C H Borchers / W Baumeister / F Herzog / E Villa / P Cramer /
Abstract: The conserved co-activator complex Mediator enables regulated transcription initiation by RNA polymerase (Pol) II. Here we reconstitute an active 15-subunit core Mediator (cMed) comprising all ...The conserved co-activator complex Mediator enables regulated transcription initiation by RNA polymerase (Pol) II. Here we reconstitute an active 15-subunit core Mediator (cMed) comprising all essential Mediator subunits from Saccharomyces cerevisiae. The cryo-electron microscopic structure of cMed bound to a core initiation complex was determined at 9.7 Å resolution. cMed binds Pol II around the Rpb4-Rpb7 stalk near the carboxy-terminal domain (CTD). The Mediator head module binds the Pol II dock and the TFIIB ribbon and stabilizes the initiation complex. The Mediator middle module extends to the Pol II foot with a 'plank' that may influence polymerase conformation. The Mediator subunit Med14 forms a 'beam' between the head and middle modules and connects to the tail module that is predicted to bind transcription activators located on upstream DNA. The Mediator 'arm' and 'hook' domains contribute to a 'cradle' that may position the CTD and TFIIH kinase to stimulate Pol II phosphorylation.
History
DepositionSep 21, 2014-
Header (metadata) releaseOct 29, 2014-
Map releaseFeb 4, 2015-
UpdateMar 4, 2015-
Current statusMar 4, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0224
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  • Surface view colored by radius
  • Surface level: 0.0224
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4v1n
  • Surface level: 0.0224
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_2785.map.gz / Format: CCP4 / Size: 81.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationcITC
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 280 pix.
= 378. Å
1.35 Å/pix.
x 280 pix.
= 378. Å
1.35 Å/pix.
x 280 pix.
= 378. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.0224 / Movie #1: 0.0224
Minimum - Maximum-0.04059347 - 0.09173883
Average (Standard dev.)0.00022215 (±0.00373423)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 378.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z378.000378.000378.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-40-32-96
NX/NY/NZ8165193
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0410.0920.000

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Supplemental data

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Sample components

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Entire : cITC

EntireName: cITC
Components
  • Sample: cITC
  • Protein or peptide: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1Polymerase
  • Protein or peptide: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2Polymerase
  • Protein or peptide: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3Polymerase
  • Protein or peptide: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4Polymerase
  • Protein or peptide: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1RNA polymerase
  • Protein or peptide: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2RNA polymerase
  • Protein or peptide: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7Polymerase
  • Protein or peptide: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3RNA polymerase
  • Protein or peptide: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9Polymerase
  • Protein or peptide: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5RNA polymerase
  • Protein or peptide: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11Polymerase
  • Protein or peptide: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4RNA polymerase
  • Protein or peptide: TRANSCRIPTION INITIATION FACTOR IIB
  • Protein or peptide: TATA-box-binding protein
  • Protein or peptide: Transcription initiation factor IIF subunit alpha
  • Protein or peptide: Transcription initiation factor IIF subunit beta
  • DNA: template DNA
  • DNA: nontemplate DNA
  • RNA: RNA

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Supramolecule #1000: cITC

SupramoleculeName: cITC / type: sample / ID: 1000 / Number unique components: 19
Molecular weightTheoretical: 750 KDa

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Macromolecule #1: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1

MacromoleculeName: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB1 / type: protein_or_peptide / ID: 1 / Name.synonym: RPO21 RPB1 RPB220 SUA8 YDL140C D2150 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast) / Strain: BJ5464 Rpb3 His-Bio / synonym: Baker's yeast / Organelle: Nucleus
Molecular weightExperimental: 192 KDa / Theoretical: 192 KDa
SequenceUniProtKB: DNA-directed RNA polymerase II subunit RPB1

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Macromolecule #2: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2

MacromoleculeName: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB2 / type: protein_or_peptide / ID: 2 / Name.synonym: RPB2 RPB150 RPO22 YOR151C / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast) / Strain: BJ5464 Rpb3 His-Bio / synonym: Baker's yeast / Organelle: Nucleus
Molecular weightExperimental: 139 KDa / Theoretical: 139 KDa
SequenceUniProtKB: DNA-directed RNA polymerase II subunit RPB2

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Macromolecule #3: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3

MacromoleculeName: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB3 / type: protein_or_peptide / ID: 3 / Name.synonym: RPB3 YIL021W / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast) / Strain: BJ5464 Rpb3 His-Bio / synonym: Baker's yeast / Organelle: Nucleus
Molecular weightExperimental: 35 KDa / Theoretical: 35 KDa
SequenceUniProtKB: DNA-directed RNA polymerase II subunit RPB3

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Macromolecule #4: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4

MacromoleculeName: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB4 / type: protein_or_peptide / ID: 4 / Name.synonym: RPB4 YJL140W J0654 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast) / Strain: BJ5464 Rpb3 His-Bio / synonym: Baker's yeast / Organelle: Nucleus
Molecular weightExperimental: 25 KDa / Theoretical: 25 KDa
SequenceUniProtKB: DNA-directed RNA polymerase II subunit RPB4

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Macromolecule #5: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1

MacromoleculeName: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1
type: protein_or_peptide / ID: 5 / Name.synonym: RPB5 RPA7 RPC9 YBR154C YBR1204 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast) / Strain: BJ5464 Rpb3 His-Bio / synonym: Baker's yeast / Organelle: Nucleus
Molecular weightExperimental: 25 KDa / Theoretical: 25 KDa
SequenceUniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC1

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Macromolecule #6: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2

MacromoleculeName: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 2
type: protein_or_peptide / ID: 6 / Name.synonym: RPO26 RPB6 YPR187W P9677.8 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast) / Strain: BJ5464 Rpb3 His-Bio / synonym: Baker's yeast / Organelle: Nucleus
Molecular weightExperimental: 18 KDa / Theoretical: 18 KDa
SequenceUniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC2

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Macromolecule #7: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7

MacromoleculeName: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB7 / type: protein_or_peptide / ID: 7 / Name.synonym: RPB7 YDR404C D9509.22 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast) / Strain: BJ5464 Rpb3 His-Bio / synonym: Baker's yeast / Organelle: Nucleus
Molecular weightExperimental: 19 KDa / Theoretical: 19 KDa
SequenceUniProtKB: DNA-directed RNA polymerase II subunit RPB7

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Macromolecule #8: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3

MacromoleculeName: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 3
type: protein_or_peptide / ID: 8 / Name.synonym: RPB8 YOR224C YOR50-14 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast) / Strain: BJ5464 Rpb3 His-Bio / synonym: Baker's yeast / Organelle: Nucleus
Molecular weightExperimental: 17 KDa / Theoretical: 17 KDa
SequenceUniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC3

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Macromolecule #9: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9

MacromoleculeName: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB9 / type: protein_or_peptide / ID: 9 / Name.synonym: RPB9 YGL070C / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast) / Strain: BJ5464 Rpb3 His-Bio / synonym: Baker's yeast / Organelle: Nucleus
Molecular weightExperimental: 14 KDa / Theoretical: 14 KDa
SequenceUniProtKB: DNA-directed RNA polymerase II subunit RPB9

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Macromolecule #10: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5

MacromoleculeName: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 5
type: protein_or_peptide / ID: 10 / Name.synonym: RPB10 YOR210W / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast) / Strain: BJ5464 Rpb3 His-Bio / synonym: Baker's yeast / Organelle: Nucleus
Molecular weightExperimental: 8 KDa / Theoretical: 8 KDa
SequenceUniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC5

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Macromolecule #11: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11

MacromoleculeName: DNA-DIRECTED RNA POLYMERASE II SUBUNIT RPB11 / type: protein_or_peptide / ID: 11 / Name.synonym: RPB11 YOL005C / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast) / Strain: BJ5464 Rpb3 His-Bio / synonym: Baker's yeast / Organelle: Nucleus
Molecular weightExperimental: 13 KDa / Theoretical: 13 KDa
SequenceUniProtKB: DNA-directed RNA polymerase II subunit RPB11

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Macromolecule #12: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4

MacromoleculeName: DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 4
type: protein_or_peptide / ID: 12 / Name.synonym: RPC10 RPB12 YHR143W-A YHR143BW / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast) / Strain: BJ5464 Rpb3 His-Bio / synonym: Baker's yeast / Organelle: Nucleus
Molecular weightExperimental: 8 KDa / Theoretical: 8 KDa
SequenceUniProtKB: DNA-directed RNA polymerases I, II, and III subunit RPABC4

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Macromolecule #13: TRANSCRIPTION INITIATION FACTOR IIB

MacromoleculeName: TRANSCRIPTION INITIATION FACTOR IIB / type: protein_or_peptide / ID: 13 / Name.synonym: SUA7 YPR086W P9513.4 / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast) / synonym: Baker's yeast
Molecular weightExperimental: 38 KDa / Theoretical: 38 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Transcription initiation factor IIB

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Macromolecule #14: TATA-box-binding protein

MacromoleculeName: TATA-box-binding protein / type: protein_or_peptide / ID: 14 / Name.synonym: SPT15, BTF1, TBP1, YER148W / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast)
Molecular weightExperimental: 20 KDa / Theoretical: 20 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: TATA-box-binding protein

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Macromolecule #15: Transcription initiation factor IIF subunit alpha

MacromoleculeName: Transcription initiation factor IIF subunit alpha / type: protein_or_peptide / ID: 15 / Name.synonym: Tfg1 SSU71 RAP74 YGR186W / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces mikatae (yeast)
Molecular weightExperimental: 82 KDa / Theoretical: 82 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Transcription initiation factor IIB

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Macromolecule #16: Transcription initiation factor IIF subunit beta

MacromoleculeName: Transcription initiation factor IIF subunit beta / type: protein_or_peptide / ID: 16 / Name.synonym: TFG2, YGR005C / Number of copies: 1 / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast)
Molecular weightExperimental: 47 KDa / Theoretical: 47 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Transcription initiation factor IIF subunit beta

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Macromolecule #17: template DNA

MacromoleculeName: template DNA / type: dna / ID: 17 / Classification: DNA / Structure: SINGLE STRANDED / Synthetic?: Yes
Source (natural)Organism: synthetic construct (others)
SequenceString:
CGAGAACAGT AGCACGCTGT GTATATAATA GTGTGTTGTA CATAGCGGAG GTCGGTGGGG CACAACTGCG CT

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Macromolecule #18: nontemplate DNA

MacromoleculeName: nontemplate DNA / type: dna / ID: 18 / Classification: DNA / Structure: SINGLE STRANDED / Synthetic?: Yes
Source (natural)Organism: synthetic construct (others)
SequenceString:
AGCGCAGTTG TGCTATGATA TTTTTATGTA TGTACAACAC ACTATTATAT ACACAGCGTG CTACTGTTCT CG

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Macromolecule #19: RNA

MacromoleculeName: RNA / type: rna / ID: 19 / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: Yes
Source (natural)Organism: synthetic construct (others)
SequenceString:
AUAUCA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.15 mg/mL
BufferpH: 7.5
Details: 25 mM HEPES-KOH pH 7.5, 180 mM Potassium acetate, 5 % Glycerol, 5 mM DTT
VitrificationCryogen name: ETHANE / Instrument: OTHER
Method: Grids were glow-discharged for 20 s before deposition of 4 microliters sample and incubated for 30 s. Grids were washed twice with 4 microliters distilled water, blotted, and then vitrified.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 37169 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 37000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Number real images: 2972 / Average electron dose: 25 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.8 Å / Resolution method: OTHER / Software - Name: RELION, 1.2
Details: The density was filtered according to local resolution and further a temperature factor of minus 340 A2 was applied.
Number images used: 4439
DetailsParticles were picked using EMAN2 and were processed using RELION 1.2.

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