[English] 日本語
Yorodumi
- EMDB-31110: TFIID-based intermediate PIC on PUMA promoter -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-31110
TitleTFIID-based intermediate PIC on PUMA promoter
Map data
SampleTFIID-based intermediate PIC on PUMA promoter
  • TFIIDTranscription factor II D
  • RNA POLYMERASE II
  • TFIIATranscription factor II A
  • TFIIBTranscription factor II B
  • TFIIFTranscription factor II F
  • DNA(PUMA promoters)
  • TFIIETranscription factor II E
  • (Transcription initiation factor ...) x 17
  • TATA-box-binding protein
  • (General transcription factor IIF subunit ...) x 2
  • General transcription factor IIE subunit 1
  • (DNA-directed RNA polymerase ...Polymerase) x 8
  • DNA-directed RNA polymerases I, II, and III subunit RPABC3RNA polymerase
  • RPB10
  • RNA_pol_L_2 domain-containing protein
  • RPB12
  • (nucleic-acidNucleic acid) x 2
  • (ligand) x 2
Function / homology
Function and homology information


spermine transport / negative regulation of MHC class I biosynthetic process / TFIIH-class transcription factor complex binding / Processing of Capped Intron-Containing Pre-mRNA / Formation of the Early Elongation Complex / Formation of RNA Pol II elongation complex / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Major Pathway ...spermine transport / negative regulation of MHC class I biosynthetic process / TFIIH-class transcription factor complex binding / Processing of Capped Intron-Containing Pre-mRNA / Formation of the Early Elongation Complex / Formation of RNA Pol II elongation complex / FGFR2 alternative splicing / RNA polymerase II transcribes snRNA genes / mRNA Capping / mRNA Splicing - Major Pathway / mRNA Splicing - Minor Pathway / TP53 Regulates Transcription of DNA Repair Genes / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Pre-transcription Events / Transcriptional regulation by small RNAs / pre-snoRNP complex / Estrogen-dependent gene expression / RNA Pol II CTD phosphorylation and interaction with CE / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Transcription Elongation / RNA Polymerase II Transcription Initiation / negative regulation of histone H4 acetylation / DNA-templated transcription open complex formation / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / STAGA complex / negative regulation of protein autoubiquitination / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / RNA polymerase II core complex assembly / transcription factor TFTC complex / negative regulation of MHC class II biosynthetic process / PCAF complex / regulation of cell cycle G1/S phase transition / phosphatase activator activity / transcription factor TFIIE complex / TFIIF-class transcription factor complex binding / SLIK (SAGA-like) complex / RNA polymerase I general transcription initiation factor activity / positive regulation of core promoter binding / regulation of DNA binding / transcription open complex formation at RNA polymerase II promoter / transcription regulator inhibitor activity / transcription factor TFIIF complex / transcriptional start site selection at RNA polymerase II promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 1 Promoter / SAGA complex / RNA Polymerase III Transcription Initiation From Type 3 Promoter / RNA polymerase II-specific DNA-binding transcription factor binding / positive regulation of response to cytokine stimulus / inner cell mass cell proliferation / RNA Polymerase III Abortive And Retractive Initiation / maintenance of protein location in nucleus / Abortive elongation of HIV-1 transcript in the absence of Tat / positive regulation of androgen receptor activity / transcription factor TFIIA complex / RNA polymerase III general transcription initiation factor activity / histone deubiquitination / hepatocyte differentiation / RNA Polymerase I Transcription Termination / box C/D snoRNP assembly / transcription factor catabolic process / general transcription initiation factor activity / RNA polymerase II general transcription initiation factor binding / negative regulation of histone acetylation / RNA Pol II CTD phosphorylation and interaction with CE during HIV infection / RNA Pol II CTD phosphorylation and interaction with CE / Formation of the HIV-1 Early Elongation Complex / Formation of the Early Elongation Complex / C2H2 zinc finger domain binding / positive regulation by host of viral transcription / mRNA Capping / FGFR2 alternative splicing / male pronucleus / female pronucleus / Viral Messenger RNA Synthesis / positive regulation of viral transcription / RNA polymerase binding / transcription initiation from RNA polymerase I promoter / RNA polymerase II preinitiation complex assembly / thyroid hormone receptor binding / Processing of Capped Intron-Containing Pre-mRNA / vitamin D receptor binding / midbrain development / Transcription of the HIV genome / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / RNA polymerase complex / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Promoter Escape / maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter / Tat-mediated HIV elongation arrest and recovery / Pausing and recovery of Tat-mediated HIV elongation / regulation of fat cell differentiation / termination of RNA polymerase I transcription / HIV elongation arrest and recovery
Similarity search - Function
TAFII28-like protein / hTAFII28-like protein conserved region / TAFII55 protein conserved region / TAFII55 protein conserved region / TAFII55 protein, conserved region / Transcription initiation factor TFIID subunit 7 / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 8 / Transcription factor TFIID complex subunit 8 C-term / Transcription factor TFIID, subunit 8, C-terminal ...TAFII28-like protein / hTAFII28-like protein conserved region / TAFII55 protein conserved region / TAFII55 protein conserved region / TAFII55 protein, conserved region / Transcription initiation factor TFIID subunit 7 / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 8 / Transcription factor TFIID complex subunit 8 C-term / Transcription factor TFIID, subunit 8, C-terminal / Transcription initiation factor TFIID component TAF4 family / Transcription initiation factor IID, subunit 13 / Transcription initiation factor IID, 18kD subunit / Transcription initiation factor TFIID component TAF4 / NHR1 homology to TAF / Bromodomain associated / TAFH/NHR1 domain profile. / Bromodomain transcription factors and PHD domain containing proteins / TAFH/NHR1 domain superfamily / TAF homology / Bromodomain associated domain / Transcription initiation factor IID, 31kD subunit / Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit A / TAFH/NHR1 / Transcription factor TFIIE alpha subunit, C-terminal / WD40 associated region in TFIID subunit, NTD2 domain / TFIID subunit TAF5, NTD2 domain superfamily / C-terminal general transcription factor TFIIE alpha / Transcription initiation factor TAFII31 / TATA box binding protein associated factor (TAF) / TAF6 C-terminal HEAT repeat domain / Transcription initiation factor TFIID subunit 6 / TFIID subunit TAF5, NTD2 domain / Transcription initiation factor TFIID subunit 12 domain / TATA box-binding protein binding / TAFII-230 TBP-binding / Transcription initiation factor TFIID subunit 1, animal / TAFII-230 TBP-binding domain superfamily / TAF6, C-terminal HEAT repeat domain / Zinc knuckle / Zinc knuckle / Transcription initiation factor TFIID 23-30kDa subunit / Transcription initiation factor TFIID subunit 1, domain of unknown function / Protein of unknown function (DUF3591) / Transcription initiation factor TFIID, 23-30kDa subunit / Transcription initiation factor TFIID subunit 1 / Transcription initiation factor TFIIE, beta subunit / TFIIE beta subunit core domain / TFIIE beta central core DNA-binding domain profile. / TFA2, Winged helix domain 2 / Transcription factor TFIIE beta subunit, DNA-binding domain / TFA2 Winged helix domain 2 / Transcription initiation factor IIE / Transcription factor TFE/TFIIEalpha HTH domain / TFE/IIEalpha-type HTH domain profile. / TFIIE alpha subunit / Transcription initiation factor IIE subunit alpha, N-terminal / Transcription factor E / TFIIEalpha/SarR/Rpc3 HTH domain / TFIIF, beta subunit N-terminus / TFIIF beta subunit, HTH domain / Transcription initiation factor IIF, beta subunit / TFIIF, beta subunit HTH domain / TFIIF, beta subunit, N-terminal / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription initiation factor IIF, alpha subunit / Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) / Transcription Factor IIF, Rap30/Rap74, interaction / Transcription factor IIA, alpha-helical domain / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription factor IIA, beta-barrel / Transcription initiation factor IIA, gamma subunit / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit / LIS1 homology (LisH) motif profile. / LIS1 homology motif / Transcription factor TFIIB repeat signature. / Transcription factor TFIIB repeat / Transcription factor TFIIB, conserved site / Transcription factor TFIIB, cyclin-like domain / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / TFIIB zinc-binding / Zinc finger, TFIIB-type / TATA-box binding protein, eukaryotic / TATA-box binding protein / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / TATA-box binding protein, conserved site / DNA-directed RNA-polymerase II subunit / RNA polymerase Rpb4/RPC9, core / TBP domain superfamily / RNA polymerase Rpb1, domain 6 / RNA polymerase II, heptapeptide repeat, eukaryotic / RNA polymerase Rpb1, domain 7
Similarity search - Domain/homology
General transcription factor IIF subunit 1 / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 3 / Transcription initiation factor TFIID subunit 9 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 7 / Transcription initiation factor TFIID subunit 11 / Transcription initiation factor TFIID subunit 13 / Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID subunit 10 ...General transcription factor IIF subunit 1 / Transcription initiation factor TFIID subunit 2 / Transcription initiation factor TFIID subunit 3 / Transcription initiation factor TFIID subunit 9 / Transcription initiation factor TFIID subunit 12 / Transcription initiation factor TFIID subunit 7 / Transcription initiation factor TFIID subunit 11 / Transcription initiation factor TFIID subunit 13 / Transcription initiation factor TFIID subunit 5 / Transcription initiation factor TFIID subunit 10 / Transcription initiation factor IIB / DNA-directed RNA polymerase II subunit RPB9 / Transcription initiation factor IIA subunit 2 / Transcription initiation factor IIA subunit 1 / Transcription initiation factor TFIID subunit 6 / Transcription initiation factor IIE subunit beta / DNA-directed RNA polymerase subunit / General transcription factor IIE subunit 1 / Transcription initiation factor TFIID subunit 1 / TATA-box-binding protein / General transcription factor IIF subunit 2 / Transcription initiation factor TFIID subunit 4 / DNA-directed RNA polymerase II subunit E / DNA-directed RNA polymerase II subunit RPB7 / DNA-directed RNA polymerase II subunit F / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / RNA_pol_L_2 domain-containing protein / DNA-directed RNA polymerase subunit beta / Uncharacterized protein / DNA-directed RNA polymerase II subunit RPB3 / DNA-directed RNA polymerase II subunit RPB4 / Transcription initiation factor TFIID subunit 8
Similarity search - Component
Biological speciesHomo sapiens (human) / Sus scrofa (pig) / Pig (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsChen X / Wu Z / Hou H / Qi Y / Wang X / Li J / Xu Y
CitationJournal: Science / Year: 2021
Title: Structural insights into preinitiation complex assembly on core promoters.
Authors: Xizi Chen / Yilun Qi / Zihan Wu / Xinxin Wang / Jiabei Li / Dan Zhao / Haifeng Hou / Yan Li / Zishuo Yu / Weida Liu / Mo Wang / Yulei Ren / Ze Li / Huirong Yang / Yanhui Xu /
Abstract: Transcription factor IID (TFIID) recognizes core promoters and supports preinitiation complex (PIC) assembly for RNA polymerase II (Pol II)-mediated eukaryotic transcription. We determined the ...Transcription factor IID (TFIID) recognizes core promoters and supports preinitiation complex (PIC) assembly for RNA polymerase II (Pol II)-mediated eukaryotic transcription. We determined the structures of human TFIID-based PIC in three stepwise assembly states and revealed two-track PIC assembly: stepwise promoter deposition to Pol II and extensive modular reorganization on track I (on TATA-TFIID-binding element promoters) versus direct promoter deposition on track II (on TATA-only and TATA-less promoters). The two tracks converge at an ~50-subunit holo PIC in identical conformation, whereby TFIID stabilizes PIC organization and supports loading of cyclin-dependent kinase (CDK)-activating kinase (CAK) onto Pol II and CAK-mediated phosphorylation of the Pol II carboxyl-terminal domain. Unexpectedly, TBP of TFIID similarly bends TATA box and TATA-less promoters in PIC. Our study provides structural visualization of stepwise PIC assembly on highly diversified promoters.
History
DepositionMar 24, 2021-
Header (metadata) releaseMay 5, 2021-
Map releaseMay 5, 2021-
UpdateMay 19, 2021-
Current statusMay 19, 2021Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0085
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0085
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7ega
  • Surface level: 0.0085
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7ega
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_31110.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 480 pix.
= 508.8 Å
1.06 Å/pix.
x 480 pix.
= 508.8 Å
1.06 Å/pix.
x 480 pix.
= 508.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.0085 / Movie #1: 0.0085
Minimum - Maximum-0.06887306 - 0.11375606
Average (Standard dev.)-8.694758e-05 (±0.002183764)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 508.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z508.800508.800508.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS480480480
D min/max/mean-0.0690.114-0.000

-
Supplemental data

-
Additional map: 3.8 Angstrom TBP module

Fileemd_31110_additional_1.map
Annotation3.8 Angstrom TBP module
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Additional map: 4.6 Angstrom TFIID module

Fileemd_31110_additional_2.map
Annotation4.6 Angstrom TFIID module
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Additional map: 3.2 Angstrom Pol II module

Fileemd_31110_additional_3.map
Annotation3.2 Angstrom Pol II module
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

+
Entire TFIID-based intermediate PIC on PUMA promoter

EntireName: TFIID-based intermediate PIC on PUMA promoter / Number of components: 45

+
Component #1: protein, TFIID-based intermediate PIC on PUMA promoter

ProteinName: TFIID-based intermediate PIC on PUMA promoter / Recombinant expression: No

+
Component #2: protein, TFIID

ProteinName: TFIIDTranscription factor II D / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK239T

+
Component #3: protein, RNA POLYMERASE II

ProteinName: RNA POLYMERASE II / Recombinant expression: No
SourceSpecies: Sus scrofa (pig)

+
Component #4: protein, TFIIA

ProteinName: TFIIATranscription factor II A / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293T

+
Component #5: protein, TFIIB

ProteinName: TFIIBTranscription factor II B / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293T

+
Component #6: protein, TFIIF

ProteinName: TFIIFTranscription factor II F / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293T

+
Component #7: protein, DNA(PUMA promoters)

ProteinName: DNA(PUMA promoters) / Recombinant expression: No

+
Component #8: protein, TFIIE

ProteinName: TFIIETranscription factor II E / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human) / Cell of expression system: HEK293T

+
Component #9: protein, Transcription initiation factor TFIID subunit 1

ProteinName: Transcription initiation factor TFIID subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 212.956172 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #10: protein, Transcription initiation factor TFIID subunit 2

ProteinName: Transcription initiation factor TFIID subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 137.159984 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #11: protein, Transcription initiation factor TFIID subunit 4

ProteinName: Transcription initiation factor TFIID subunit 4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 110.221883 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #12: protein, Transcription initiation factor TFIID subunit 5

ProteinName: Transcription initiation factor TFIID subunit 5 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 86.932109 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #13: protein, Transcription initiation factor TFIID subunit 6

ProteinName: Transcription initiation factor TFIID subunit 6 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 72.749297 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #14: protein, Transcription initiation factor TFIID subunit 7

ProteinName: Transcription initiation factor TFIID subunit 7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.325117 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #15: protein, Transcription initiation factor TFIID subunit 8

ProteinName: Transcription initiation factor TFIID subunit 8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.304359 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #16: protein, Transcription initiation factor TFIID subunit 9

ProteinName: Transcription initiation factor TFIID subunit 9 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 29.006838 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #17: protein, Transcription initiation factor TFIID subunit 10

ProteinName: Transcription initiation factor TFIID subunit 10 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 21.731248 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #18: protein, Transcription initiation factor TFIID subunit 12

ProteinName: Transcription initiation factor TFIID subunit 12 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 17.948467 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #19: protein, Transcription initiation factor IIA subunit 2

ProteinName: Transcription initiation factor IIA subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 12.469091 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #20: protein, TATA-box-binding protein

ProteinName: TATA-box-binding protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.729938 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #21: protein, Transcription initiation factor IIA subunit 1

ProteinName: Transcription initiation factor IIA subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 41.544551 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #22: protein, Transcription initiation factor IIB

ProteinName: Transcription initiation factor IIB / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.877949 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #23: protein, General transcription factor IIF subunit 1

ProteinName: General transcription factor IIF subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 58.343578 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #24: protein, General transcription factor IIF subunit 2

ProteinName: General transcription factor IIF subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.427309 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #25: protein, General transcription factor IIE subunit 1

ProteinName: General transcription factor IIE subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.516094 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #26: protein, Transcription initiation factor IIE subunit beta

ProteinName: Transcription initiation factor IIE subunit beta / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 33.106824 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #27: protein, Transcription initiation factor TFIID subunit 3

ProteinName: Transcription initiation factor TFIID subunit 3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 103.76932 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #28: protein, Transcription initiation factor TFIID subunit 11

ProteinName: Transcription initiation factor TFIID subunit 11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 23.340094 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #29: protein, Transcription initiation factor TFIID subunit 13

ProteinName: Transcription initiation factor TFIID subunit 13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.307068 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

+
Component #30: protein, DNA-directed RNA polymerase subunit

ProteinName: DNA-directed RNA polymerase subunitPolymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 167.953234 kDa
SourceSpecies: Pig (pig)

+
Component #31: protein, DNA-directed RNA polymerase subunit beta

ProteinName: DNA-directed RNA polymerase subunit betaPolymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 134.041422 kDa
SourceSpecies: Pig (pig)

+
Component #32: protein, DNA-directed RNA polymerase II subunit RPB3

ProteinName: DNA-directed RNA polymerase II subunit RPB3Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.211814 kDa
SourceSpecies: Pig (pig)

+
Component #33: protein, DNA-directed RNA polymerase II subunit RPB4

ProteinName: DNA-directed RNA polymerase II subunit RPB4Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 16.331255 kDa
SourceSpecies: Pig (pig)

+
Component #34: protein, DNA-directed RNA polymerase II subunit E

ProteinName: DNA-directed RNA polymerase II subunit EPolymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.644318 kDa
SourceSpecies: Pig (pig)

+
Component #35: protein, DNA-directed RNA polymerase II subunit F

ProteinName: DNA-directed RNA polymerase II subunit FPolymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.477001 kDa
SourceSpecies: Pig (pig)

+
Component #36: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC3

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC3RNA polymerase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.162273 kDa
SourceSpecies: Pig (pig)

+
Component #37: protein, DNA-directed RNA polymerase II subunit RPB9

ProteinName: DNA-directed RNA polymerase II subunit RPB9Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.541221 kDa
SourceSpecies: Pig (pig)

+
Component #38: protein, RPB10

ProteinName: RPB10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.283671 kDa
SourceSpecies: Pig (pig)

+
Component #39: protein, RNA_pol_L_2 domain-containing protein

ProteinName: RNA_pol_L_2 domain-containing protein / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 13.310284 kDa
SourceSpecies: Pig (pig)

+
Component #40: protein, RPB12

ProteinName: RPB12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 7.018244 kDa
SourceSpecies: Pig (pig)

+
Component #41: nucleic-acid, DNA (85-MER)

nucleic acidName: DNA (85-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DA)(DG)(DA)(DA)(DG)(DT)(DC)(DT)(DG)(DA) (DC)(DA)(DT)(DC)(DC)(DT)(DT)(DA)(DC)(DT) (DC)(DA)(DG)(DC)(DC)(DA)(DG)(DC)(DC)(DC) (DC)(DA)(DC)(DA)(DC)(DT)(DA)(DG)(DG)(DC) (DA)(DC)(DT)(DG)(DG)(DA) ...Sequence:
(DA)(DG)(DA)(DA)(DG)(DT)(DC)(DT)(DG)(DA) (DC)(DA)(DT)(DC)(DC)(DT)(DT)(DA)(DC)(DT) (DC)(DA)(DG)(DC)(DC)(DA)(DG)(DC)(DC)(DC) (DC)(DA)(DC)(DA)(DC)(DT)(DA)(DG)(DG)(DC) (DA)(DC)(DT)(DG)(DG)(DA)(DA)(DG)(DG)(DT) (DG)(DA)(DG)(DT)(DC)(DA)(DC)(DT)(DC)(DT) (DG)(DG)(DT)(DG)(DA)(DG)(DG)(DC)(DG)(DA) (DT)(DT)(DG)(DC)(DG)(DA)(DT)(DT)(DG)(DG) (DG)(DT)(DG)(DA)(DG)
MassTheoretical: 26.326807 kDa
SourceSpecies: Homo sapiens (human)

+
Component #42: nucleic-acid, DNA (85-MER)

nucleic acidName: DNA (85-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DC)(DT)(DC)(DA)(DC)(DC)(DC)(DA)(DA)(DT) (DC)(DG)(DC)(DA)(DA)(DT)(DC)(DG)(DC)(DC) (DT)(DC)(DA)(DC)(DC)(DA)(DG)(DA)(DG)(DT) (DG)(DA)(DC)(DT)(DC)(DA)(DC)(DC)(DT)(DT) (DC)(DC)(DA)(DG)(DT)(DG) ...Sequence:
(DC)(DT)(DC)(DA)(DC)(DC)(DC)(DA)(DA)(DT) (DC)(DG)(DC)(DA)(DA)(DT)(DC)(DG)(DC)(DC) (DT)(DC)(DA)(DC)(DC)(DA)(DG)(DA)(DG)(DT) (DG)(DA)(DC)(DT)(DC)(DA)(DC)(DC)(DT)(DT) (DC)(DC)(DA)(DG)(DT)(DG)(DC)(DC)(DT)(DA) (DG)(DT)(DG)(DT)(DG)(DG)(DG)(DG)(DC)(DT) (DG)(DG)(DC)(DT)(DG)(DA)(DG)(DT)(DA)(DA) (DG)(DG)(DA)(DT)(DG)(DT)(DC)(DA)(DG)(DA) (DC)(DT)(DT)(DC)(DT)
MassTheoretical: 26.108658 kDa
SourceSpecies: Homo sapiens (human)

+
Component #43: protein, DNA-directed RNA polymerase II subunit RPB7

ProteinName: DNA-directed RNA polymerase II subunit RPB7Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 19.314283 kDa
SourceSpecies: Pig (pig)

+
Component #44: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 10 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

+
Component #45: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.9
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 21692
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • 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. New: 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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
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.

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