[English] 日本語
Yorodumi
- PDB-8srr: Cryo-EM structure of the CBC-ALYREF complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8srr
TitleCryo-EM structure of the CBC-ALYREF complex
Components
  • Nuclear cap-binding protein subunit 1
  • Nuclear cap-binding protein subunit 2
  • RNA and export factor binding protein 2
KeywordsRNA BINDING PROTEIN / mRNA nuclear export
Function / homology
Function and homology information


positive regulation of RNA binding / snRNA export from nucleus / nuclear cap binding complex / histone mRNA metabolic process / RNA cap binding complex / mRNA metabolic process / positive regulation of mRNA 3'-end processing / positive regulation of RNA export from nucleus / cap-dependent translational initiation / Processing of Intronless Pre-mRNAs ...positive regulation of RNA binding / snRNA export from nucleus / nuclear cap binding complex / histone mRNA metabolic process / RNA cap binding complex / mRNA metabolic process / positive regulation of mRNA 3'-end processing / positive regulation of RNA export from nucleus / cap-dependent translational initiation / Processing of Intronless Pre-mRNAs / snRNA binding / RNA cap binding / alternative mRNA splicing, via spliceosome / primary miRNA processing / miRNA-mediated post-transcriptional gene silencing / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / regulatory ncRNA-mediated post-transcriptional gene silencing / regulation of mRNA processing / RNA 7-methylguanosine cap binding / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / positive regulation of mRNA splicing, via spliceosome / mRNA 3'-end processing / mRNA cis splicing, via spliceosome / RNA catabolic process / Transport of Mature mRNA derived from an Intron-Containing Transcript / regulation of translational initiation / Abortive elongation of HIV-1 transcript in the absence of Tat / RNA Polymerase II Transcription Termination / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / FGFR2 alternative splicing / Signaling by FGFR2 IIIa TM / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / spliceosomal complex assembly / mRNA Splicing - Minor Pathway / Processing of Capped Intron-Containing Pre-mRNA / RNA polymerase II transcribes snRNA genes / 7-methylguanosine mRNA capping / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Formation of HIV-1 elongation complex containing HIV-1 Tat / mRNA export from nucleus / Formation of HIV elongation complex in the absence of HIV Tat / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of RNA Pol II elongation complex / RNA Polymerase II Pre-transcription Events / mRNA Splicing - Major Pathway / RNA splicing / positive regulation of transcription elongation by RNA polymerase II / mRNA transcription by RNA polymerase II / mRNA splicing, via spliceosome / Regulation of expression of SLITs and ROBOs / snRNP Assembly / positive regulation of cell growth / molecular adaptor activity / defense response to virus / ciliary basal body / ribonucleoprotein complex / mRNA binding / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Chromatin target of PRMT1 protein, C-terminal / C-terminal duplication domain of Friend of PRMT1 / C-terminal duplication domain of Friend of PRMT1 / : / MIF4G-like, type 1 / MIF4G-like, type 2 / Nuclear cap-binding protein subunit 1 / MIF4G like / MIF4G like / Nuclear cap-binding protein subunit 2 ...Chromatin target of PRMT1 protein, C-terminal / C-terminal duplication domain of Friend of PRMT1 / C-terminal duplication domain of Friend of PRMT1 / : / MIF4G-like, type 1 / MIF4G-like, type 2 / Nuclear cap-binding protein subunit 1 / MIF4G like / MIF4G like / Nuclear cap-binding protein subunit 2 / NCBP2, RNA recognition motif / MIF4G domain / Middle domain of eukaryotic initiation factor 4G (eIF4G) / MIF4G-like, type 3 / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Armadillo-type fold / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE / Nuclear cap-binding protein subunit 2 / Nuclear cap-binding protein subunit 1 / RNA and export factor binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.22 Å
AuthorsXie, Y. / Clarke, B.P. / Ren, Y.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM133743 United States
Citation
Journal: Elife / Year: 2024
Title: Cryo-EM structure of the CBC-ALYREF complex.
Authors: Bradley P Clarke / Alexia E Angelos / Menghan Mei / Pate S Hill / Yihu Xie / Yi Ren /
Abstract: In eukaryotes, RNAs transcribed by RNA Pol II are modified at the 5' end with a 7-methylguanosine (mG) cap, which is recognized by the nuclear cap binding complex (CBC). The CBC plays multiple ...In eukaryotes, RNAs transcribed by RNA Pol II are modified at the 5' end with a 7-methylguanosine (mG) cap, which is recognized by the nuclear cap binding complex (CBC). The CBC plays multiple important roles in mRNA metabolism, including transcription, splicing, polyadenylation, and export. It promotes mRNA export through direct interaction with a key mRNA export factor, ALYREF, which in turn links the TRanscription and EXport (TREX) complex to the 5' end of mRNA. However, the molecular mechanism for CBC-mediated recruitment of the mRNA export machinery is not well understood. Here, we present the first structure of the CBC in complex with an mRNA export factor, ALYREF. The cryo-EM structure of CBC-ALYREF reveals that the RRM domain of ALYREF makes direct contact with both the NCBP1 and NCBP2 subunits of the CBC. Comparing CBC-ALYREF with other cellular complexes containing CBC and/or ALYREF components provides insights into the coordinated events during mRNA transcription, splicing, and export.
#1: Journal: Elife / Year: 2024
Title: Cryo-EM structure of the CBC-ALYREF complex
Authors: Clarke, B.P. / Angelos, A.E. / Mei, M. / Hill, P.S. / Xie, Y. / Ren, Y.
History
DepositionMay 6, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2024Group: Data collection / Database references / Category: citation / citation_author / em_admin / Item: _em_admin.last_update

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nuclear cap-binding protein subunit 1
B: Nuclear cap-binding protein subunit 2
C: RNA and export factor binding protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,9904
Polymers127,5313
Non-polymers4581
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein Nuclear cap-binding protein subunit 1 / 80 kDa nuclear cap-binding protein / CBP80 / NCBP 80 kDa subunit


Mass: 91960.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCBP1, CBP80, NCBP / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q09161
#2: Protein Nuclear cap-binding protein subunit 2 / 20 kDa nuclear cap-binding protein / Cell proliferation-inducing gene 55 protein / NCBP 20 kDa ...20 kDa nuclear cap-binding protein / Cell proliferation-inducing gene 55 protein / NCBP 20 kDa subunit / CBP20 / NCBP-interacting protein 1 / NIP1


Mass: 18028.131 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCBP2, CBP20, PIG55 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P52298
#3: Protein RNA and export factor binding protein 2


Mass: 17542.857 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Alyref2, Refbp2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q4KL64
#4: Chemical ChemComp-M7G / 7N-METHYL-8-HYDROGUANOSINE-5'-DIPHOSPHATE


Mass: 458.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O11P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Cryo-EM structure of an mRNA export factor / Type: COMPLEX / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 52 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

-
Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 241915 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 162.9 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00268160
ELECTRON MICROSCOPYf_angle_d0.406811041
ELECTRON MICROSCOPYf_chiral_restr0.03661203
ELECTRON MICROSCOPYf_plane_restr0.00291416
ELECTRON MICROSCOPYf_dihedral_angle_d9.91313057

+
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