[English] 日本語
Yorodumi
- PDB-7uio: Mediator-PIC Early (Composite Model) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7uio
TitleMediator-PIC Early (Composite Model)
Components
  • (DNA-directed RNA polymerase II subunit ...) x 8
  • (DNA-directed RNA polymerases I, II, and III subunit ...) x 5
  • (Mediator of RNA polymerase II transcription subunit ...) x 21
  • (Transcription ...) x 4
  • DNA (37-MER)
  • DNA (38-MER)
  • Regulatory protein GAL4
KeywordsTRANSCRIPTION / Divergent transcription / Mediator / RNA Polymerase II / PIC / Pre-Initiation / Activation / Transcription Factor / Gal4 / Gal4VP16
Function / homology
Function and homology information


TFIIE-class transcription factor complex binding / regulation of establishment of protein localization to chromosome / regulation of transcription from RNA polymerase II promoter by galactose / meiotic gene conversion / positive regulation of invasive growth in response to glucose limitation / RNA polymerase II complex recruiting activity / transcription open complex formation at RNA polymerase II promoter / regulation of mRNA 3'-end processing / TFIIH-class transcription factor complex binding / galactose metabolic process ...TFIIE-class transcription factor complex binding / regulation of establishment of protein localization to chromosome / regulation of transcription from RNA polymerase II promoter by galactose / meiotic gene conversion / positive regulation of invasive growth in response to glucose limitation / RNA polymerase II complex recruiting activity / transcription open complex formation at RNA polymerase II promoter / regulation of mRNA 3'-end processing / TFIIH-class transcription factor complex binding / galactose metabolic process / core mediator complex / negative regulation of ribosomal protein gene transcription by RNA polymerase II / TFIIF-class transcription factor complex binding / transcriptional start site selection at RNA polymerase II promoter / transcription factor TFIIF complex / RPB4-RPB7 complex / mediator complex / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / transcription preinitiation complex / RNA Polymerase I Transcription Initiation / Processing of Capped Intron-Containing Pre-mRNA / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the Early Elongation Complex / mRNA Capping / RNA polymerase II transcribes snRNA genes / termination of RNA polymerase II transcription / RNA polymerase II general transcription initiation factor activity / TP53 Regulates Transcription of DNA Repair Genes / 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 / termination of RNA polymerase III transcription / RNA Polymerase II Pre-transcription Events / RNA-templated transcription / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / Formation of TC-NER Pre-Incision Complex / transcription initiation at RNA polymerase III promoter / RNA Polymerase I Promoter Escape / termination of RNA polymerase I transcription / transcription initiation at RNA polymerase I promoter / nucleolar large rRNA transcription by RNA polymerase I / Gap-filling DNA repair synthesis and ligation in TC-NER / RNA polymerase II complex binding / TFIID-class transcription factor complex binding / TFIIB-class transcription factor binding / Estrogen-dependent gene expression / maintenance of transcriptional fidelity during transcription elongation by RNA polymerase II / nuclear-transcribed mRNA catabolic process / transcription by RNA polymerase III / positive regulation of translational initiation / protein phosphatase activator activity / replicative senescence / Dual incision in TC-NER / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription initiation by RNA polymerase II / translesion synthesis / RNA polymerase I complex / transcription elongation by RNA polymerase I / RNA polymerase III complex / cellular response to nutrient levels / RNA polymerase II core promoter sequence-specific DNA binding / RNA polymerase II preinitiation complex assembly / RNA polymerase II, core complex / tRNA transcription by RNA polymerase III / transcription by RNA polymerase I / translation initiation factor binding / transcription-coupled nucleotide-excision repair / transcription repressor complex / TBP-class protein binding / response to endoplasmic reticulum stress / transcription coregulator activity / RNA polymerase II transcription regulatory region sequence-specific DNA binding / transcription antitermination / transcription initiation at RNA polymerase II promoter / transcription elongation by RNA polymerase II / P-body / DNA-templated transcription initiation / positive regulation of transcription elongation by RNA polymerase II / ribonucleoside binding / mRNA processing / DNA-directed RNA polymerase / cytoplasmic stress granule / DNA-directed RNA polymerase activity / transcription corepressor activity / peroxisome / single-stranded DNA binding / ribosome biogenesis / cellular response to heat / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA recombination / protein-macromolecule adaptor activity / DNA-binding transcription factor binding / nucleic acid binding / RNA polymerase II-specific DNA-binding transcription factor binding / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / single-stranded RNA binding
Similarity search - Function
Mediator of RNA polymerase II transcription subunit 3 / Mediator complex, subunit Med2, fungi / Mediator complex subunit 2 / Mediator complex subunit 3 fungal / Mediator complex, subunit Med5, fungi / Mediator complex subunit Med5 / Gal4 dimerisation domain / Gal4-like dimerisation domain / Mediator complex, subunit Med15, fungi / Gal11, coactivator domain ...Mediator of RNA polymerase II transcription subunit 3 / Mediator complex, subunit Med2, fungi / Mediator complex subunit 2 / Mediator complex subunit 3 fungal / Mediator complex, subunit Med5, fungi / Mediator complex subunit Med5 / Gal4 dimerisation domain / Gal4-like dimerisation domain / Mediator complex, subunit Med15, fungi / Gal11, coactivator domain / Mediator complex subunit 15, KIX domain / Mediator complex subunit 15 / KIX domain / Gal11 activator-binding domain (ABD1) / : / Mediator complex, subunit Med19, fungi / Fungal specific transcription factor domain / Rox3 mediator complex subunit / Transcription factor domain, fungi / Fungal specific transcription factor domain / Mediator of RNA polymerase II transcription subunit 22, Saccharomycetes / Mediator of RNA polymerase II transcription subunit 20 / Mediator complex, subunit Med6, fungi / : / Mediator complex subunit 16, C-terminal / Mediator complex, subunit Med16 / : / Mediator complex subunit 16, N-terminal / Mediator complex, subunit Med10 / Transcription factor subunit Med10 of Mediator complex / Mediator of RNA polymerase II transcription subunit 9 / RNA polymerase II transcription mediator complex subunit 9 / Mediator complex, subunit Med4 / Vitamin-D-receptor interacting Mediator subunit 4 / Mediator complex, subunit Med31 / Mediator complex, subunit Med21 / Mediator of RNA polymerase II, subunit Med31 superfamily / SOH1 / Subunit 21 of Mediator complex / Mediator complex, subunit Med7 / Mediator complex, subunit Med7/Med21-like / Mediator complex, subunit Med7 superfmaily / : / MED7 protein / Mediator complex, subunit Med20 / Mediator complex, subunit Med14 / TATA-binding related factor (TRF) of subunit 20 of Mediator complex / Mediator complex subunit MED14 / Mediator complex, subunit Med6 / Mediator complex, subunit Med17 / Mediator complex, subunit Med6 superfamily / MED6 mediator sub complex component / Subunit 17 of Mediator complex / Zn(2)-C6 fungal-type DNA-binding domain signature. / Mediator of RNA polymerase II transcription subunit 22 / Mediator complex, subunit Med8, fungi/metazoa / Mediator complex, subunit Med11 / Surfeit locus protein 5 subunit 22 of Mediator complex / Mediator of RNA polymerase II transcription complex subunit 8 / Mediator complex protein / Mediator complex, subunit Med18 / Med18 protein / Transcription elongation factor, TFIIS / Transcription elongation factor, IIS-type / Fungal Zn(2)-Cys(6) binuclear cluster domain / Zn(2)-C6 fungal-type DNA-binding domain superfamily / Zn(2)-C6 fungal-type DNA-binding domain profile. / GAL4-like Zn(II)2Cys6 (or C6 zinc) binuclear cluster DNA-binding domain / Zn(2)-C6 fungal-type DNA-binding domain / Transcription factor S-II (TFIIS), central domain / Domain in the central regions of transcription elongation factor S-II (and elsewhere) / Transcription elongation factor S-II, central domain / Transcription elongation factor S-II, central domain superfamily / TFIIS central domain profile. / Transcription elongation factor, TFIIS/CRSP70, N-terminal, sub-type / Domain in the N-terminus of transcription elongation factor S-II (and elsewhere) / Mediator complex, subunit Med1 / Mediator of RNA polymerase II transcription subunit 1 / TFIIS N-terminal domain profile. / Transcription factor IIS, N-terminal / TFIIS helical bundle-like domain / Transcription initiation factor IIF, beta subunit / TFIIF beta subunit, HTH domain / TFIIF, beta subunit, N-terminal / TFIIF, beta subunit HTH domain / TFIIF, beta subunit N-terminus / Transcription initiation factor IIF, alpha subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription Factor IIF, Rap30/Rap74, interaction / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / Zinc finger, TFIIB-type / TFIIB zinc-binding / Coactivator CBP, KIX domain superfamily / TFIIS/LEDGF domain superfamily / Basic-leucine zipper domain superfamily
Similarity search - Domain/homology
ALANINE / ASPARTIC ACID / THREONINE / DNA / DNA (> 10) / DNA-directed RNA polymerase II subunit RPB1 / Regulatory protein GAL4 / Transcription elongation factor S-II / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 ...ALANINE / ASPARTIC ACID / THREONINE / DNA / DNA (> 10) / DNA-directed RNA polymerase II subunit RPB1 / Regulatory protein GAL4 / Transcription elongation factor S-II / DNA-directed RNA polymerase II subunit RPB2 / DNA-directed RNA polymerase II subunit RPB3 / Mediator of RNA polymerase II transcription subunit 14 / Mediator of RNA polymerase II transcription subunit 15 / DNA-directed RNA polymerase II subunit RPB4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / Mediator of RNA polymerase II transcription subunit 19 / DNA-directed RNA polymerase II subunit RPB9 / Transcription initiation factor IIB / Mediator of RNA polymerase II transcription subunit 16 / Mediator of RNA polymerase II transcription subunit 17 / Mediator of RNA polymerase II transcription subunit 22 / Mediator of RNA polymerase II transcription subunit 18 / Mediator of RNA polymerase II transcription subunit 9 / DNA-directed RNA polymerase II subunit RPB7 / Mediator of RNA polymerase II transcription subunit 20 / Mediator of RNA polymerase II transcription subunit 8 / Mediator of RNA polymerase II transcription subunit 31 / Mediator of RNA polymerase II transcription subunit 6 / DNA-directed RNA polymerase II subunit RPB11 / Mediator of RNA polymerase II transcription subunit 3 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / Transcription initiation factor IIF subunit alpha / Transcription initiation factor IIF subunit beta / Mediator of RNA polymerase II transcription subunit 21 / Mediator of RNA polymerase II transcription subunit 5 / Mediator of RNA polymerase II transcription subunit 10 / Mediator of RNA polymerase II transcription subunit 7 / Mediator of RNA polymerase II transcription subunit 2 / Mediator of RNA polymerase II transcription subunit 1 / Mediator of RNA polymerase II transcription subunit 4 / Mediator of RNA polymerase II transcription subunit 11
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsGorbea Colon, J.J. / Chen, S.-F. / Tsai, K.L. / Murakami, K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM123233-01 United States
CitationJournal: Mol Cell / Year: 2023
Title: Structural basis of a transcription pre-initiation complex on a divergent promoter.
Authors: Jose J Gorbea Colón / Leon Palao / Shin-Fu Chen / Hee Jong Kim / Laura Snyder / Yi-Wei Chang / Kuang-Lei Tsai / Kenji Murakami /
Abstract: Most eukaryotic promoter regions are divergently transcribed. As the RNA polymerase II pre-initiation complex (PIC) is intrinsically asymmetric and responsible for transcription in a single ...Most eukaryotic promoter regions are divergently transcribed. As the RNA polymerase II pre-initiation complex (PIC) is intrinsically asymmetric and responsible for transcription in a single direction, it is unknown how divergent transcription arises. Here, the Saccharomyces cerevisiae Mediator complexed with a PIC (Med-PIC) was assembled on a divergent promoter and analyzed by cryoelectron microscopy. The structure reveals two distinct Med-PICs forming a dimer through the Mediator tail module, induced by a homodimeric activator protein localized near the dimerization interface. The tail dimer is associated with ∼80-bp upstream DNA, such that two flanking core promoter regions are positioned and oriented in a suitable form for PIC assembly in opposite directions. Also, cryoelectron tomography visualized the progress of the PIC assembly on the two core promoter regions, providing direct evidence for the role of the Med-PIC dimer in divergent transcription.
History
DepositionMar 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.2Jun 12, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / em_3d_fitting_list
Item: _em_3d_fitting_list.initial_refinement_model_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA (38-MER)
B: DNA (37-MER)
Ao: Mediator of RNA polymerase II transcription subunit 15
Ab: Mediator of RNA polymerase II transcription subunit 2
Ac: Mediator of RNA polymerase II transcription subunit 3
An: Mediator of RNA polymerase II transcription subunit 14
Ae: Mediator of RNA polymerase II transcription subunit 5
Ap: Mediator of RNA polymerase II transcription subunit 16
GA: Regulatory protein GAL4
GB: Regulatory protein GAL4
At: Mediator of RNA polymerase II transcription subunit 20
Ag: Mediator of RNA polymerase II transcription subunit 7
Ah: Mediator of RNA polymerase II transcription subunit 8
Ai: Mediator of RNA polymerase II transcription subunit 9
Aj: Mediator of RNA polymerase II transcription subunit 10
Ak: Mediator of RNA polymerase II transcription subunit 11
Aq: Mediator of RNA polymerase II transcription subunit 17
Ar: Mediator of RNA polymerase II transcription subunit 18
As: Mediator of RNA polymerase II transcription subunit 19
Au: Mediator of RNA polymerase II transcription subunit 21
Av: Mediator of RNA polymerase II transcription subunit 22
Aw: Mediator of RNA polymerase II transcription subunit 31
Az: DNA-directed RNA polymerase II subunit RPB1
AA: DNA-directed RNA polymerase II subunit RPB1
AB: DNA-directed RNA polymerase II subunit RPB2
AC: DNA-directed RNA polymerase II subunit RPB3
AD: DNA-directed RNA polymerase II subunit RPB4
AE: DNA-directed RNA polymerases I, II, and III subunit RPABC1
AF: DNA-directed RNA polymerases I, II, and III subunit RPABC2
AG: DNA-directed RNA polymerase II subunit RPB7
AH: DNA-directed RNA polymerases I, II, and III subunit RPABC3
AI: DNA-directed RNA polymerase II subunit RPB9
AJ: DNA-directed RNA polymerases I, II, and III subunit RPABC5
AK: DNA-directed RNA polymerase II subunit RPB11
AL: DNA-directed RNA polymerases I, II, and III subunit RPABC4
AM: Transcription initiation factor IIB
AP: Transcription initiation factor IIF subunit alpha
AQ: Transcription initiation factor IIF subunit beta
AS: Transcription elongation factor S-II
Aa: Mediator of RNA polymerase II transcription subunit 1
Ad: Mediator of RNA polymerase II transcription subunit 4
Af: Mediator of RNA polymerase II transcription subunit 6
Bo: Mediator of RNA polymerase II transcription subunit 15
Bb: Mediator of RNA polymerase II transcription subunit 2
Bc: Mediator of RNA polymerase II transcription subunit 3
Bn: Mediator of RNA polymerase II transcription subunit 14
Be: Mediator of RNA polymerase II transcription subunit 5
Bp: Mediator of RNA polymerase II transcription subunit 16
Bt: Mediator of RNA polymerase II transcription subunit 20
Bg: Mediator of RNA polymerase II transcription subunit 7
Bh: Mediator of RNA polymerase II transcription subunit 8
Bi: Mediator of RNA polymerase II transcription subunit 9
Bj: Mediator of RNA polymerase II transcription subunit 10
Bk: Mediator of RNA polymerase II transcription subunit 11
Bq: Mediator of RNA polymerase II transcription subunit 17
Br: Mediator of RNA polymerase II transcription subunit 18
Bs: Mediator of RNA polymerase II transcription subunit 19
Bu: Mediator of RNA polymerase II transcription subunit 21
Bv: Mediator of RNA polymerase II transcription subunit 22
Bw: Mediator of RNA polymerase II transcription subunit 31
Bz: DNA-directed RNA polymerase II subunit RPB1
BA: DNA-directed RNA polymerase II subunit RPB1
BB: DNA-directed RNA polymerase II subunit RPB2
BC: DNA-directed RNA polymerase II subunit RPB3
BD: DNA-directed RNA polymerase II subunit RPB4
BE: DNA-directed RNA polymerases I, II, and III subunit RPABC1
BF: DNA-directed RNA polymerases I, II, and III subunit RPABC2
BG: DNA-directed RNA polymerase II subunit RPB7
BH: DNA-directed RNA polymerases I, II, and III subunit RPABC3
BI: DNA-directed RNA polymerase II subunit RPB9
BJ: DNA-directed RNA polymerases I, II, and III subunit RPABC5
BK: DNA-directed RNA polymerase II subunit RPB11
BL: DNA-directed RNA polymerases I, II, and III subunit RPABC4
BM: Transcription initiation factor IIB
BP: Transcription initiation factor IIF subunit alpha
BQ: Transcription initiation factor IIF subunit beta
BS: Transcription elongation factor S-II
Ba: Mediator of RNA polymerase II transcription subunit 1
Bd: Mediator of RNA polymerase II transcription subunit 4
Bf: Mediator of RNA polymerase II transcription subunit 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,456,48687
Polymers3,455,88380
Non-polymers6037
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
DNA chain , 2 types, 2 molecules AB

#1: DNA chain DNA (38-MER)


Mass: 11666.479 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae S288C (yeast)
#2: DNA chain DNA (37-MER)


Mass: 11424.310 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Saccharomyces cerevisiae S288C (yeast)

+
Mediator of RNA polymerase II transcription subunit ... , 21 types, 42 molecules AoBoAbBbAcBcAnBnAeBeApBpAtBtAgBgAhBhAiBiAjBjAkBkAqBqArBrAsBs...

#3: Protein Mediator of RNA polymerase II transcription subunit 15 / Autonomous replication regulatory protein 3 / Basal expression activator protein 1 / Defective ...Autonomous replication regulatory protein 3 / Basal expression activator protein 1 / Defective silencing suppressor protein 4 / Mediator complex subunit 15 / Transcription regulatory protein GAL11 / Ty insertion suppressor protein 13


Mass: 120432.242 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P19659
#4: Protein Mediator of RNA polymerase II transcription subunit 2 / Mediator complex subunit 2


Mass: 47754.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q12124
#5: Protein Mediator of RNA polymerase II transcription subunit 3 / Hyper-recombination suppressor protein 1 / Mediator complex subunit 3 / Poly-glutamine domain protein 1


Mass: 43116.039 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P40356
#6: Protein Mediator of RNA polymerase II transcription subunit 14 / Glucose repression regulatory protein 1 / Mediator complex subunit 14


Mass: 123500.695 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P19263
#7: Protein Mediator of RNA polymerase II transcription subunit 5 / Mediator complex subunit 5 / Negative regulator of URS2 protein 1


Mass: 128918.750 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P53114
#8: Protein Mediator of RNA polymerase II transcription subunit 16 / Global transcriptional regulator SIN4 / Mediator complex subunit 16 / SNF1 suppressor protein 4 / ...Global transcriptional regulator SIN4 / Mediator complex subunit 16 / SNF1 suppressor protein 4 / SWI4 suppressor protein 5 / Transcriptional silencing factor 3 / YGP1 expression regulatory protein 1


Mass: 111423.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P32259
#10: Protein Mediator of RNA polymerase II transcription subunit 20 / Hyper-recombination suppressor protein 2 / Mediator complex subunit 20 / Suppressor of RNA polymerase B 2


Mass: 22918.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P34162
#11: Protein Mediator of RNA polymerase II transcription subunit 7 / Mediator complex subunit 7


Mass: 25616.062 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q08278
#12: Protein Mediator of RNA polymerase II transcription subunit 8 / Mediator complex subunit 8


Mass: 25297.234 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P38304
#13: Protein Mediator of RNA polymerase II transcription subunit 9 / Chromosome segregation protein 2 / Mediator complex subunit 9


Mass: 17400.377 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P33308
#14: Protein Mediator of RNA polymerase II transcription subunit 10 / Mediator complex subunit 10 / Negative regulator of URS2 protein 2


Mass: 17927.926 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q06213
#15: Protein Mediator of RNA polymerase II transcription subunit 11 / Mediator complex subunit 11


Mass: 13324.189 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q99278
#16: Protein Mediator of RNA polymerase II transcription subunit 17 / Mediator complex subunit 17 / Suppressor of RNA polymerase B 4


Mass: 78582.836 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P32569
#17: Protein Mediator of RNA polymerase II transcription subunit 18 / Mediator complex subunit 18 / Suppressor of RNA polymerase B 5


Mass: 34316.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P32585
#18: Protein Mediator of RNA polymerase II transcription subunit 19 / Hypoxic gene repressor protein 3 / Mediator complex subunit 19 / Negative regulator of URS2 protein ...Hypoxic gene repressor protein 3 / Mediator complex subunit 19 / Negative regulator of URS2 protein 3 / SNF1 suppressor protein 7


Mass: 24885.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P25046
#19: Protein Mediator of RNA polymerase II transcription subunit 21 / Mediator complex subunit 21 / RNAPII complex component SRB7 / Suppressor of RNA polymerase B 7


Mass: 16093.368 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P47822
#20: Protein Mediator of RNA polymerase II transcription subunit 22 / Mediator complex subunit 22 / Suppressor of RNA polymerase B 6


Mass: 13774.628 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P32570
#21: Protein Mediator of RNA polymerase II transcription subunit 31 / Hpr1 suppressor protein 1 / Mediator complex subunit 31


Mass: 14747.739 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P38633
#39: Protein Mediator of RNA polymerase II transcription subunit 1 / Mediator complex subunit 1


Mass: 64314.953 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q12321
#40: Protein Mediator of RNA polymerase II transcription subunit 4 / Mediator complex subunit 4


Mass: 32244.895 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: Q12343
#41: Protein Mediator of RNA polymerase II transcription subunit 6 / Mediator complex subunit 6


Mass: 32844.746 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P38782

-
Protein , 1 types, 2 molecules GAGB

#9: Protein Regulatory protein GAL4


Mass: 16895.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: GAL4, YPL248C / Production host: Escherichia coli (E. coli) / References: UniProt: P04386

-
DNA-directed RNA polymerase II subunit ... , 8 types, 16 molecules AzBzAABAABBBACBCADBDAGBGAIBIAKBK

#22: Protein/peptide DNA-directed RNA polymerase II subunit RPB1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II ...RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit B220


Mass: 2611.681 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P04050, DNA-directed RNA polymerase
#23: Protein DNA-directed RNA polymerase II subunit RPB1 / RNA polymerase II subunit 1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III ...RNA polymerase II subunit 1 / RNA polymerase II subunit B1 / DNA-directed RNA polymerase III largest subunit / RNA polymerase II subunit B220


Mass: 162951.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P04050, DNA-directed RNA polymerase
#24: Protein DNA-directed RNA polymerase II subunit RPB2 / RNA polymerase II subunit 2 / B150 / DNA-directed RNA polymerase II 140 kDa polypeptide


Mass: 138937.297 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P08518, DNA-directed RNA polymerase
#25: Protein DNA-directed RNA polymerase II subunit RPB3 / RNA polymerase II subunit B3 / B44.5 / DNA-directed RNA polymerase II 45 kDa polypeptide


Mass: 35330.457 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P16370
#26: Protein DNA-directed RNA polymerase II subunit RPB4 / RNA polymerase II subunit B4 / B32 / DNA-directed RNA polymerase II 32 kDa polypeptide


Mass: 25451.191 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P20433
#29: Protein DNA-directed RNA polymerase II subunit RPB7 / RNA polymerase II subunit B7 / B16


Mass: 19081.053 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P34087
#31: Protein DNA-directed RNA polymerase II subunit RPB9 / RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA- ...RNA polymerase II subunit B9 / B12.6 / DNA-directed RNA polymerase II 14.2 kDa polypeptide / DNA-directed RNA polymerase II subunit 9


Mass: 14308.161 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P27999
#33: Protein DNA-directed RNA polymerase II subunit RPB11 / RNA polymerase II subunit B11 / B13.6 / DNA-directed RNA polymerase II 13.6 kDa polypeptide


Mass: 13633.493 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P38902

-
DNA-directed RNA polymerases I, II, and III subunit ... , 5 types, 10 molecules AEBEAFBFAHBHAJBJALBL

#27: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC1 / RNA polymerases I / II / and III subunit ABC1 / ABC27 / DNA-directed RNA polymerases I / and III 27 ...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.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P20434
#28: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC2 / RNA polymerases I / II / and III subunit ABC2 / ABC23 / DNA-directed RNA polymerases I / and III 23 ...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.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P20435
#30: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA polymerases I / II / and III subunit ABC3 / ABC14.4 / ABC14.5 / DNA-directed RNA polymerases I ...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.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P20436
#32: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC5 / RNA polymerases I / II / and III subunit ABC5 / ABC10-beta / ABC8 / DNA-directed RNA polymerases I ...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.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P22139
#34: Protein DNA-directed RNA polymerases I, II, and III subunit RPABC4 / RNA polymerases I / II / and III subunit ABC4 / ABC10-alpha


Mass: 7729.969 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P40422

-
Transcription ... , 4 types, 8 molecules AMBMAPBPAQBQASBS

#35: Protein Transcription initiation factor IIB / General transcription factor TFIIB / Transcription factor E


Mass: 38257.340 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P29055
#36: Protein Transcription initiation factor IIF subunit alpha / TFIIF-alpha / TFIIF large subunit / Transcription factor G 105 kDa subunit / P105


Mass: 82320.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P41895
#37: Protein Transcription initiation factor IIF subunit beta / ATP-dependent helicase TFG2 / TFIIF medium subunit / TFIIF-beta / Transcription factor G 54 kDa subunit


Mass: 46684.492 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288C (yeast) / References: UniProt: P41896, DNA helicase
#38: Protein Transcription elongation factor S-II / DNA strand transfer protein alpha / STP-alpha / DNA strand transferase 1 / Pyrimidine pathway ...DNA strand transfer protein alpha / STP-alpha / DNA strand transferase 1 / Pyrimidine pathway regulatory protein 2


Mass: 34903.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: DST1, PPR2, YGL043W / Production host: Escherichia coli (E. coli) / References: UniProt: P07273

-
Non-polymers , 4 types, 7 molecules

#42: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#43: Chemical ChemComp-THR / THREONINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO3
#44: Chemical ChemComp-ALA / ALANINE


Type: L-peptide linking / Mass: 89.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2
#45: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H7NO4

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: Med-PICearly / Type: COMPLEX / Entity ID: #1-#41 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Buffer solutionpH: 7.6
SpecimenConc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: Quantifoil
VitrificationInstrument: LEICA EM CPC / Cryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 64000 X / Calibrated magnification: 64000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Calibrated defocus min: 500 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.4 sec. / Electron dose: 42 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM software
IDNameCategory
7UCSF Chimeramodel fitting
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1102984 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
17UI9

7ui9

17UI91PDBexperimental model
27UIL

7uil

17UIL2PDBexperimental model
37UIK

7uik

17UIK3PDBexperimental model

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more