[English] 日本語
Yorodumi
- PDB-7znl: Structure of the human TREX core THO-UAP56 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7znl
TitleStructure of the human TREX core THO-UAP56 complex
Components
  • (THO complex subunit ...) x 6
  • Spliceosome RNA helicase DDX39B
KeywordsGENE REGULATION / transcription and export complex / TREX / RNA export / RNA packaging / RNA binding protein / gene expression
Function / homology
Function and homology information


THO complex / THO complex part of transcription export complex / transcription export complex / primitive hemopoiesis / regulation of mRNA export from nucleus / U6 snRNP / RNA secondary structure unwinding / stem cell division / ATP-dependent protein binding / mRNA 3'-end processing ...THO complex / THO complex part of transcription export complex / transcription export complex / primitive hemopoiesis / regulation of mRNA export from nucleus / U6 snRNP / RNA secondary structure unwinding / stem cell division / ATP-dependent protein binding / mRNA 3'-end processing / ATP-dependent activity, acting on RNA / U4 snRNA binding / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / U4 snRNP / RNA Polymerase II Transcription Termination / poly(A)+ mRNA export from nucleus / generation of neurons / spliceosomal complex assembly / monocyte differentiation / blastocyst development / RHOBTB2 GTPase cycle / mRNA export from nucleus / neuron development / U6 snRNA binding / mRNA Splicing - Major Pathway / RNA splicing / central nervous system development / spliceosomal complex / cell morphogenesis / mRNA splicing, via spliceosome / nuclear matrix / mRNA processing / Signaling by CSF1 (M-CSF) in myeloid cells / negative regulation of neuron projection development / regulation of gene expression / RNA helicase activity / nuclear body / RNA helicase / nuclear speck / mRNA binding / apoptotic process / signal transduction / ATP hydrolysis activity / DNA binding / RNA binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
THO complex, subunit 5 / THO complex subunit 6 / Fms-interacting protein/Thoc5 / TREX component Tex1/THOC3 / THO complex subunit 7/Mft1 / THO complex, subunitTHOC2, C-terminal / THO complex, subunitTHOC2, N-terminal / THO complex subunit 2, N-terminal domain / THO complex subunit 2 / Tho complex subunit 7 ...THO complex, subunit 5 / THO complex subunit 6 / Fms-interacting protein/Thoc5 / TREX component Tex1/THOC3 / THO complex subunit 7/Mft1 / THO complex, subunitTHOC2, C-terminal / THO complex, subunitTHOC2, N-terminal / THO complex subunit 2, N-terminal domain / THO complex subunit 2 / Tho complex subunit 7 / Transcription factor/nuclear export subunit protein 2 / Transcription- and export-related complex subunit / THO complex subunit 2 N-terminus / THO complex, subunit THOC1 / THO complex subunit 1 transcription elongation factor / WD40-like beta propeller / WD40-like Beta Propeller Repeat / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / Death domain profile. / DEATH domain, found in proteins involved in cell death (apoptosis). / Death domain / Death domain / RNA helicase, DEAD-box type, Q motif / DEAD-box RNA helicase Q motif profile. / Death-like domain superfamily / DEAD/DEAH box helicase domain / DEAD/DEAH box helicase / Helicase conserved C-terminal domain / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
THO complex subunit 5 / Spliceosome RNA helicase DDX39B / THO complex subunit 7 / THO complex subunit 6 / THO complex subunit 2 / THO complex subunit 1 / THO complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.45 Å
AuthorsPacheco-Fiallos, F.B. / Vorlaender, M.K. / Plaschka, C.
Funding supportEuropean Union, 2items
OrganizationGrant numberCountry
European Research Council (ERC)949081European Union
European Molecular Biology Organization (EMBO)623-2020European Union
CitationJournal: Nature / Year: 2023
Title: mRNA recognition and packaging by the human transcription-export complex.
Authors: Belén Pacheco-Fiallos / Matthias K Vorländer / Daria Riabov-Bassat / Laura Fin / Francis J O'Reilly / Farja I Ayala / Ulla Schellhaas / Juri Rappsilber / Clemens Plaschka /
Abstract: Newly made mRNAs are processed and packaged into mature ribonucleoprotein complexes (mRNPs) and are recognized by the essential transcription-export complex (TREX) for nuclear export. However, the ...Newly made mRNAs are processed and packaged into mature ribonucleoprotein complexes (mRNPs) and are recognized by the essential transcription-export complex (TREX) for nuclear export. However, the mechanisms of mRNP recognition and three-dimensional mRNP organization are poorly understood. Here we report cryo-electron microscopy and tomography structures of reconstituted and endogenous human mRNPs bound to the 2-MDa TREX complex. We show that mRNPs are recognized through multivalent interactions between the TREX subunit ALYREF and mRNP-bound exon junction complexes. Exon junction complexes can multimerize through ALYREF, which suggests a mechanism for mRNP organization. Endogenous mRNPs form compact globules that are coated by multiple TREX complexes. These results reveal how TREX may simultaneously recognize, compact and protect mRNAs to promote their packaging for nuclear export. The organization of mRNP globules provides a framework to understand how mRNP architecture facilitates mRNA biogenesis and export.
History
DepositionApr 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1May 24, 2023Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jul 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
A: THO complex subunit 1
B: THO complex subunit 2
C: THO complex subunit 3
E: THO complex subunit 5 homolog
F: THO complex subunit 6 homolog
G: THO complex subunit 7 homolog
H: Spliceosome RNA helicase DDX39B
I: THO complex subunit 1
J: THO complex subunit 2
K: THO complex subunit 3
M: THO complex subunit 5 homolog
N: THO complex subunit 6 homolog
O: THO complex subunit 7 homolog
P: Spliceosome RNA helicase DDX39B
a: THO complex subunit 1
b: THO complex subunit 2
c: THO complex subunit 3
e: THO complex subunit 5 homolog
f: THO complex subunit 6 homolog
g: THO complex subunit 7 homolog
h: Spliceosome RNA helicase DDX39B
i: THO complex subunit 1
j: THO complex subunit 2
k: THO complex subunit 3
m: THO complex subunit 5 homolog
n: THO complex subunit 6 homolog
o: THO complex subunit 7 homolog
p: Spliceosome RNA helicase DDX39B


Theoretical massNumber of molelcules
Total (without water)1,946,79428
Polymers1,946,79428
Non-polymers00
Water00
1


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

-
Components

-
THO complex subunit ... , 6 types, 24 molecules AIaiBJbjCKckEMemFNfnGOgo

#1: Protein
THO complex subunit 1 / Tho1 / Nuclear matrix protein p84 / p84N5 / hTREX84


Mass: 75752.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THOC1, HPR1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96FV9
#2: Protein
THO complex subunit 2 / Tho2 / hTREX120


Mass: 183087.734 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THOC2, CXorf3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q8NI27
#3: Protein
THO complex subunit 3 / Tho3 / TEX1 homolog / hTREX45


Mass: 38817.617 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THOC3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q96J01
#4: Protein
THO complex subunit 5 homolog / Functional spliceosome-associated protein 79 / fSAP79 / NF2/meningioma region protein pK1.3 / ...Functional spliceosome-associated protein 79 / fSAP79 / NF2/meningioma region protein pK1.3 / Placental protein 39.2 / PP39.2 / hTREX90


Mass: 78624.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THOC5, C22orf19, KIAA0983 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13769
#5: Protein
THO complex subunit 6 homolog / Functional spliceosome-associated protein 35 / fSAP35 / WD repeat-containing protein 58


Mass: 37577.875 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THOC6, WDR58, PSEC0006 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q86W42
#6: Protein
THO complex subunit 7 homolog / Functional spliceosome-associated protein 24 / fSAP24 / Ngg1-interacting factor 3-like protein 1- ...Functional spliceosome-associated protein 24 / fSAP24 / Ngg1-interacting factor 3-like protein 1-binding protein 1 / NIF3L1-binding protein 1 / hTREX30


Mass: 23782.014 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: THOC7, NIF3L1BP1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q6I9Y2

-
Protein , 1 types, 4 molecules HPhp

#7: Protein
Spliceosome RNA helicase DDX39B / 56 kDa U2AF65-associated protein / ATP-dependent RNA helicase p47 / DEAD box protein UAP56 / HLA-B- ...56 kDa U2AF65-associated protein / ATP-dependent RNA helicase p47 / DEAD box protein UAP56 / HLA-B-associated transcript 1 protein


Mass: 49056.250 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DDX39B, BAT1, UAP56 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13838, RNA helicase

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: THO-UAP56 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 1.8 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 7.9
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: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3700 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.45 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 246457 / 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