[English] 日本語
Yorodumi
- PDB-7zwc: Structure of SNAPc:TBP-TFIIA-TFIIB sub-complex bound to U5 snRNA ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7zwc
TitleStructure of SNAPc:TBP-TFIIA-TFIIB sub-complex bound to U5 snRNA promoter
Components
  • (Transcription initiation factor IIA subunit ...) x 2
  • (snRNA-activating protein complex subunit ...) x 4
  • Non-template strand
  • TATA-box-binding protein
  • Template strand
  • Transcription initiation factor IIB
KeywordsTRANSCRIPTION / RNA polymerase II / Pol II / PIC / SNAPc / snRNA / U5 promoter
Function / homology
Function and homology information


snRNA-activating protein complex / snRNA transcription / snRNA transcription by RNA polymerase III / bent DNA binding / positive regulation of core promoter binding / RNA polymerase II core complex assembly / RNA polymerase III type 3 promoter sequence-specific DNA binding / RNA polymerase transcription factor SL1 complex / meiotic sister chromatid cohesion / snRNA transcription by RNA polymerase II ...snRNA-activating protein complex / snRNA transcription / snRNA transcription by RNA polymerase III / bent DNA binding / positive regulation of core promoter binding / RNA polymerase II core complex assembly / RNA polymerase III type 3 promoter sequence-specific DNA binding / RNA polymerase transcription factor SL1 complex / meiotic sister chromatid cohesion / snRNA transcription by RNA polymerase II / RNA polymerase III general transcription initiation factor activity / transcriptional start site selection at RNA polymerase II promoter / RNA polymerase I core promoter sequence-specific DNA binding / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Transcription Initiation From Type 3 Promoter / transcription factor TFIIA complex / female germ cell nucleus / RNA Polymerase III Abortive And Retractive Initiation / male pronucleus / female pronucleus / germinal vesicle / RNA polymerase II general transcription initiation factor binding / nuclear thyroid hormone receptor binding / RNA Polymerase I Transcription Termination / transcription preinitiation complex / protein acetylation / cell division site / RNA polymerase II general transcription initiation factor activity / transcription factor TFIID complex / HIV Transcription Initiation / RNA Polymerase II HIV Promoter Escape / Transcription of the HIV genome / 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 / acetyltransferase activity / transcription initiation at RNA polymerase III promoter / RNA polymerase II complex binding / aryl hydrocarbon receptor binding / viral transcription / TFIIB-class transcription factor binding / RNA Polymerase I Transcription Initiation / RNA polymerase II transcribes snRNA genes / positive regulation of transcription initiation by RNA polymerase II / transcription by RNA polymerase III / core promoter sequence-specific DNA binding / RNA polymerase II core promoter sequence-specific DNA binding / histone H4K16 acetyltransferase activity / histone H3K56 acetyltransferase activity / histone H3K23 acetyltransferase activity / histone H2AK5 acetyltransferase activity / histone H2AK9 acetyltransferase activity / histone H2BK5 acetyltransferase activity / histone H2BK12 acetyltransferase activity / histone H3K4 acetyltransferase activity / histone H3K27 acetyltransferase activity / histone H3K36 acetyltransferase activity / histone H3K122 acetyltransferase activity / histone H3K18 acetyltransferase activity / histone H3K9 acetyltransferase activity / histone H3K14 acetyltransferase activity / histone H4K5 acetyltransferase activity / histone H4K8 acetyltransferase activity / histone H4K12 acetyltransferase activity / RNA polymerase II preinitiation complex assembly / spindle assembly / histone acetyltransferase / RNA Polymerase II Pre-transcription Events / TBP-class protein binding / male germ cell nucleus / SIRT1 negatively regulates rRNA expression / transcription initiation at RNA polymerase II promoter / RNA Polymerase I Promoter Escape / DNA-templated transcription initiation / promoter-specific chromatin binding / mRNA transcription by RNA polymerase II / euchromatin / protein-DNA complex / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / kinetochore / RNA polymerase II transcription regulator complex / chromosome / DNA-binding transcription factor binding / spermatogenesis / Regulation of TP53 Activity through Phosphorylation / Estrogen-dependent gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / transcription cis-regulatory region binding / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / chromatin / nucleolus / enzyme binding / protein homodimerization activity
Similarity search - Function
snRNA-activating protein complex subunit 5 / snRNA-activating protein complex subunit 19, SNAPc subunit 19 / snRNA-activating protein complex subunit 1 / snRNA-activating protein complex, subunit 3 / Small nuclear RNA activating complex (SNAPc), subunit 1 / snRNA-activating protein complex (SNAPc), subunit 3 / : / Myb-like domain profile. / Myb-like DNA-binding domain / Transcription factor IIA, alpha/beta subunit ...snRNA-activating protein complex subunit 5 / snRNA-activating protein complex subunit 19, SNAPc subunit 19 / snRNA-activating protein complex subunit 1 / snRNA-activating protein complex, subunit 3 / Small nuclear RNA activating complex (SNAPc), subunit 1 / snRNA-activating protein complex (SNAPc), subunit 3 / : / Myb-like domain profile. / Myb-like DNA-binding domain / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription factor IIA, alpha/beta subunit / Transcription initiation factor IIA, gamma subunit / Transcription factor IIA, alpha-helical domain / Transcription factor IIA, beta-barrel / Transcription initiation factor IIA, gamma subunit, C-terminal / Transcription initiation factor IIA, gamma subunit, N-terminal / Transcription initiation factor IIA, gamma subunit, helical domain / Transcription initiation factor IIA, gamma subunit / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Cyclin-like / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / Zinc finger, TFIIB-type / TFIIB zinc-binding / Myb-type HTH DNA-binding domain profile. / TATA-box binding protein, eukaryotic / TATA-box binding protein / TATA-box binding protein, conserved site / Transcription factor TFIID (or TATA-binding protein, TBP) / Transcription factor TFIID repeat signature. / Myb domain / SANT domain / Cyclin A; domain 1 / TBP domain superfamily / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / Cyclin-like superfamily / SANT/Myb domain / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / snRNA-activating protein complex subunit 5 / TATA-box-binding protein / Transcription initiation factor IIA subunit 1 / Transcription initiation factor IIA subunit 2 / Transcription initiation factor IIB / snRNA-activating protein complex subunit 1 / snRNA-activating protein complex subunit 4 / snRNA-activating protein complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsRengachari, S. / Schilbach, S. / Kaliyappan, T. / Gouge, J. / Zumer, K. / Schwarz, J. / Urlaub, H. / Dienemann, C. / Vannini, A. / Cramer, P.
Funding support Germany, United Kingdom, 4items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB860 Germany
German Research Foundation (DFG)EXC 2067/1 39072994 Germany
Cancer Research UKCR-UK C47547/A21536 United Kingdom
Wellcome Trust200818/Z/16/Z United Kingdom
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: Structural basis of SNAPc-dependent snRNA transcription initiation by RNA polymerase II.
Authors: Srinivasan Rengachari / Sandra Schilbach / Thangavelu Kaliyappan / Jerome Gouge / Kristina Zumer / Juliane Schwarz / Henning Urlaub / Christian Dienemann / Alessandro Vannini / Patrick Cramer /
Abstract: RNA polymerase II (Pol II) carries out transcription of both protein-coding and non-coding genes. Whereas Pol II initiation at protein-coding genes has been studied in detail, Pol II initiation at ...RNA polymerase II (Pol II) carries out transcription of both protein-coding and non-coding genes. Whereas Pol II initiation at protein-coding genes has been studied in detail, Pol II initiation at non-coding genes, such as small nuclear RNA (snRNA) genes, is less well understood at the structural level. Here, we study Pol II initiation at snRNA gene promoters and show that the snRNA-activating protein complex (SNAPc) enables DNA opening and transcription initiation independent of TFIIE and TFIIH in vitro. We then resolve cryo-EM structures of the SNAPc-containing Pol IIpre-initiation complex (PIC) assembled on U1 and U5 snRNA promoters. The core of SNAPc binds two turns of DNA and recognizes the snRNA promoter-specific proximal sequence element (PSE), located upstream of the TATA box-binding protein TBP. Two extensions of SNAPc, called wing-1 and wing-2, bind TFIIA and TFIIB, respectively, explaining how SNAPc directs Pol II to snRNA promoters. Comparison of structures of closed and open promoter complexes elucidates TFIIH-independent DNA opening. These results provide the structural basis of Pol II initiation at non-coding RNA gene promoters.
History
DepositionMay 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Dec 28, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jul 24, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
M: Transcription initiation factor IIB
O: TATA-box-binding protein
U: Transcription initiation factor IIA subunit 1
V: Transcription initiation factor IIA subunit 2
a: snRNA-activating protein complex subunit 1
b: snRNA-activating protein complex subunit 3
c: snRNA-activating protein complex subunit 4
d: snRNA-activating protein complex subunit 5
N: Non-template strand
T: Template strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)446,85012
Polymers446,71910
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

-
Components

-
Protein , 2 types, 2 molecules MO

#1: Protein Transcription initiation factor IIB / General transcription factor TFIIB / S300-II


Mass: 34877.949 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2B, TF2B, TFIIB / Production host: Escherichia coli (E. coli) / References: UniProt: Q00403, histone acetyltransferase
#2: Protein TATA-box-binding protein / TATA sequence-binding protein / TATA-binding factor / TATA-box factor / Transcription initiation ...TATA sequence-binding protein / TATA-binding factor / TATA-box factor / Transcription initiation factor TFIID TBP subunit


Mass: 37729.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TBP, GTF2D1, TF2D, TFIID / Production host: Escherichia coli (E. coli) / References: UniProt: P20226

-
Transcription initiation factor IIA subunit ... , 2 types, 2 molecules UV

#3: Protein Transcription initiation factor IIA subunit 1 / General transcription factor IIA subunit 1 / TFIIAL / Transcription initiation factor TFIIA 42 kDa ...General transcription factor IIA subunit 1 / TFIIAL / Transcription initiation factor TFIIA 42 kDa subunit / TFIIA-42


Mass: 41544.551 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2A1, TF2A1 / Production host: Escherichia coli (E. coli) / References: UniProt: P52655
#4: Protein Transcription initiation factor IIA subunit 2 / General transcription factor IIA subunit 2 / TFIIA p12 subunit / TFIIA-12 / TFIIAS / Transcription ...General transcription factor IIA subunit 2 / TFIIA p12 subunit / TFIIA-12 / TFIIAS / Transcription initiation factor IIA gamma chain / TFIIA-gamma


Mass: 12469.091 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF2A2, TF2A2 / Production host: Escherichia coli (E. coli) / References: UniProt: P52657

-
SnRNA-activating protein complex subunit ... , 4 types, 4 molecules abcd

#5: Protein snRNA-activating protein complex subunit 1 / SNAPc subunit 1 / Proximal sequence element-binding transcription factor subunit gamma / PSE- ...SNAPc subunit 1 / Proximal sequence element-binding transcription factor subunit gamma / PSE-binding factor subunit gamma / PTF subunit gamma / Small nuclear RNA-activating complex polypeptide 1 / snRNA-activating protein complex 43 kDa subunit / SNAPc 43 kDa subunit


Mass: 43074.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNAPC1, SNAP43 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q16533
#6: Protein snRNA-activating protein complex subunit 3 / SNAPc subunit 3 / Proximal sequence element-binding transcription factor subunit beta / PSE-binding ...SNAPc subunit 3 / Proximal sequence element-binding transcription factor subunit beta / PSE-binding factor subunit beta / PTF subunit beta / Small nuclear RNA-activating complex polypeptide 3 / snRNA-activating protein complex 50 kDa subunit / SNAPc 50 kDa subunit


Mass: 46812.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNAPC3, SNAP50 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q92966
#7: Protein snRNA-activating protein complex subunit 4 / SNAPc subunit 4 / Proximal sequence element-binding transcription factor subunit alpha / PSE- ...SNAPc subunit 4 / Proximal sequence element-binding transcription factor subunit alpha / PSE-binding factor subunit alpha / PTF subunit alpha / snRNA-activating protein complex 190 kDa subunit / SNAPc 190 kDa subunit


Mass: 159645.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNAPC4, SNAP190 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5SXM2
#8: Protein snRNA-activating protein complex subunit 5 / SNAPc subunit 5 / Small nuclear RNA-activating complex polypeptide 5 / snRNA-activating protein ...SNAPc subunit 5 / Small nuclear RNA-activating complex polypeptide 5 / snRNA-activating protein complex 19 kDa subunit / SNAPc 19 kDa subunit


Mass: 11343.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SNAPC5, SNAP19 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: O75971

-
DNA chain , 2 types, 2 molecules NT

#9: DNA chain Non-template strand


Mass: 29678.027 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#10: DNA chain Template strand


Mass: 29543.893 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

-
Non-polymers , 1 types, 2 molecules

#11: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1General transcription factors and SNAPc bound to U5 promoterCOMPLEX#1-#100MULTIPLE SOURCES
2SNAPcCOMPLEX#2, #5-#81RECOMBINANT
3TATA-box-binding protein and transcription factorsCOMPLEX#1, #3-#41RECOMBINANT
4PromoterCOMPLEX#9-#101RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
44Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Trichoplusia ni (cabbage looper)7111
33Escherichia coli (E. coli)562
44Synthetic construct (others)32630
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 300 nm
Image recordingElectron dose: 51.93 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 85787 / Symmetry type: POINT

+
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