[English] 日本語
Yorodumi
- PDB-8pnt: Structure of the human nuclear cap-binding complex bound to PHAX ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8pnt
TitleStructure of the human nuclear cap-binding complex bound to PHAX and m7G-capped RNA
Components
  • Nuclear cap-binding protein subunit 1
  • Nuclear cap-binding protein subunit 2
  • Phosphorylated adapter RNA export protein
KeywordsRNA BINDING PROTEIN / Nuclear cap-binding complex / PHAX / Pol II transcript metabolism
Function / homology
Function and homology information


mRNA cap binding complex binding / snRNA export from nucleus / nuclear cap binding complex / mRNA metabolic process / RNA cap binding complex / histone mRNA metabolic process / RNA stabilization / positive regulation of mRNA 3'-end processing / positive regulation of RNA export from nucleus / cap-dependent translational initiation ...mRNA cap binding complex binding / snRNA export from nucleus / nuclear cap binding complex / mRNA metabolic process / RNA cap binding complex / histone mRNA metabolic process / RNA stabilization / 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 / positive regulation of RNA binding / RNA cap binding / alternative mRNA splicing, via spliceosome / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / regulation of mRNA processing / primary miRNA processing / regulatory ncRNA-mediated post-transcriptional gene silencing / miRNA-mediated post-transcriptional gene silencing / : / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / RNA 7-methylguanosine cap binding / mRNA 3'-end processing / mRNA 3'-end processing / Transport of Mature mRNA Derived from an Intronless Transcript / mRNA cis splicing, via spliceosome / positive regulation of mRNA splicing, via spliceosome / RNA catabolic process / Transport of Mature mRNA derived from an Intron-Containing Transcript / Abortive elongation of HIV-1 transcript in the absence of Tat / FGFR2 alternative splicing / regulation of translational initiation / RNA Polymerase II Transcription Termination / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Signaling by FGFR2 IIIa TM / spliceosomal complex assembly / Formation of the Early Elongation Complex / Formation of the HIV-1 Early Elongation Complex / mRNA Capping / mRNA Splicing - Minor Pathway / 7-methylguanosine mRNA capping / Processing of Capped Intron-Containing Pre-mRNA / RNA polymerase II transcribes snRNA genes / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / toxic substance binding / Formation of HIV-1 elongation complex containing HIV-1 Tat / Cajal body / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Formation of HIV elongation complex in the absence of HIV Tat / mRNA export from nucleus / 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 / protein transport / snRNP Assembly / positive regulation of cell growth / defense response to virus / molecular adaptor activity / ribonucleoprotein complex / mRNA binding / neuronal cell body / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Phosphorylated adapter RNA export protein / Phosphorylated adapter RNA export protein, RNA-binding domain / Phosphorylated adapter RNA export protein, RNA-binding domain superfamily / Phosphorylated adapter RNA export protein, RNA-binding domain / Nuclear cap-binding protein subunit 2 / NCBP2, RNA recognition motif / MIF4G-like, type 1 / MIF4G-like, type 2 / Nuclear cap-binding protein subunit 1 / MIF4G like ...Phosphorylated adapter RNA export protein / Phosphorylated adapter RNA export protein, RNA-binding domain / Phosphorylated adapter RNA export protein, RNA-binding domain superfamily / Phosphorylated adapter RNA export protein, RNA-binding domain / Nuclear cap-binding protein subunit 2 / NCBP2, RNA recognition motif / MIF4G-like, type 1 / MIF4G-like, type 2 / Nuclear cap-binding protein subunit 1 / MIF4G like / MIF4G like / 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'-TRIPHOSPHATE / Nuclear cap-binding protein subunit 2 / Nuclear cap-binding protein subunit 1 / Phosphorylated adapter RNA export protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.46 Å
AuthorsDubiez, E. / Pellegrini, E. / Foucher, A.E. / Cusack, S. / Kadlec, J.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR) France
CitationJournal: Cell Rep / Year: 2024
Title: Structural basis for competitive binding of productive and degradative co-transcriptional effectors to the nuclear cap-binding complex.
Authors: Etienne Dubiez / Erika Pellegrini / Maja Finderup Brask / William Garland / Anne-Emmanuelle Foucher / Karine Huard / Torben Heick Jensen / Stephen Cusack / Jan Kadlec /
Abstract: The nuclear cap-binding complex (CBC) coordinates co-transcriptional maturation, transport, or degradation of nascent RNA polymerase II (Pol II) transcripts. CBC with its partner ARS2 forms mutually ...The nuclear cap-binding complex (CBC) coordinates co-transcriptional maturation, transport, or degradation of nascent RNA polymerase II (Pol II) transcripts. CBC with its partner ARS2 forms mutually exclusive complexes with diverse "effectors" that promote either productive or destructive outcomes. Combining AlphaFold predictions with structural and biochemical validation, we show how effectors NCBP3, NELF-E, ARS2, PHAX, and ZC3H18 form competing binary complexes with CBC and how PHAX, NCBP3, ZC3H18, and other effectors compete for binding to ARS2. In ternary CBC-ARS2 complexes with PHAX, NCBP3, or ZC3H18, ARS2 is responsible for the initial effector recruitment but inhibits their direct binding to the CBC. We show that in vivo ZC3H18 binding to both CBC and ARS2 is required for nuclear RNA degradation. We propose that recruitment of PHAX to CBC-ARS2 can lead, with appropriate cues, to competitive displacement of ARS2 and ZC3H18 from the CBC, thus promoting a productive rather than a degradative RNA fate.
History
DepositionJul 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release

-
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: Phosphorylated adapter RNA export protein
D: Phosphorylated adapter RNA export protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,2865
Polymers196,7474
Non-polymers5391
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
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: 89781.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CBP80 construct has the N-terminal 20 residues (containing the NLS) deleted and replaced by a methionine
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: Escherichia coli (E. coli) / References: UniProt: P52298
#3: Protein Phosphorylated adapter RNA export protein / RNA U small nuclear RNA export adapter protein


Mass: 44468.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PHAX, RNUXA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H814
#4: Chemical ChemComp-MGT / 7N-METHYL-8-HYDROGUANOSINE-5'-TRIPHOSPHATE


Mass: 539.223 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20N5O14P3 / 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: Structure of the human nuclear cap-binding complex bound to PHAX and m7G-capped RNA
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

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 FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 41.67 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.46 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 193335 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0027787
ELECTRON MICROSCOPYf_angle_d0.47210542
ELECTRON MICROSCOPYf_dihedral_angle_d4.6541031
ELECTRON MICROSCOPYf_chiral_restr0.0351151
ELECTRON MICROSCOPYf_plane_restr0.0041350

+
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