[English] 日本語
Yorodumi
- PDB-8pmp: Structure of the human nuclear cap-binding complex bound to ARS2[... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8pmp
TitleStructure of the human nuclear cap-binding complex bound to ARS2[147-871] and m7GTP
Components
  • Nuclear cap-binding protein subunit 1
  • Nuclear cap-binding protein subunit 2
  • Serrate RNA effector molecule homolog
KeywordsRNA BINDING PROTEIN / Nuclear cap-binding complex / ARS2 / Pol II transcript metabolism
Function / homology
Function and homology information


mRNA cap binding complex binding / 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 RNA export from nucleus / positive regulation of mRNA 3'-end processing / cap-dependent translational initiation ...mRNA cap binding complex binding / 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 RNA export from nucleus / positive regulation of mRNA 3'-end processing / cap-dependent translational initiation / Processing of Intronless Pre-mRNAs / snRNA binding / RNA cap binding / neuronal stem cell population maintenance / alternative mRNA splicing, via spliceosome / miRNA-mediated post-transcriptional gene silencing / primary miRNA processing / SLBP independent Processing of Histone Pre-mRNAs / SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs / regulation of mRNA processing / regulatory ncRNA-mediated post-transcriptional gene silencing / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / RNA 7-methylguanosine cap binding / response to arsenic-containing substance / 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 / Transport of Mature mRNA derived from an Intron-Containing Transcript / RNA catabolic process / regulation of translational initiation / positive regulation of neurogenesis / RNA Polymerase II Transcription Termination / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / Abortive elongation of HIV-1 transcript in the absence of Tat / 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 / mRNA processing / snRNP Assembly / positive regulation of cell growth / protein-macromolecule adaptor activity / defense response to virus / molecular adaptor activity / nuclear body / ciliary basal body / ribonucleoprotein complex / mRNA binding / regulation of DNA-templated transcription / protein-containing complex / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
SERRATE/Ars2 , C-terminal / SERRATE/Ars2, N-terminal / SERRATE/Ars2 / Arsenite-resistance protein 2 / SERRATE/Ars2, N-terminal domain / MIF4G-like, type 1 / MIF4G-like, type 2 / Nuclear cap-binding protein subunit 1 / MIF4G like / MIF4G like ...SERRATE/Ars2 , C-terminal / SERRATE/Ars2, N-terminal / SERRATE/Ars2 / Arsenite-resistance protein 2 / SERRATE/Ars2, N-terminal domain / 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'-TRIPHOSPHATE / Nuclear cap-binding protein subunit 2 / Nuclear cap-binding protein subunit 1 / Serrate RNA effector molecule homolog
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.43 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
DepositionJun 29, 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
D: Serrate RNA effector molecule homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,4114
Polymers190,8713
Non-polymers5391
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area7300 Å2
ΔGint-27 kcal/mol
Surface area40290 Å2

-
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
Details: Additional GA at the N-terminus / Source: (gene. exp.) Homo sapiens (human) / Gene: NCBP2, CBP20, PIG55 / Production host: Escherichia coli (E. coli) / References: UniProt: P52298
#3: Protein Serrate RNA effector molecule homolog / Arsenite-resistance protein 2


Mass: 83061.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ARS2 has N-terminal 147 residues deleted and replaced by a methionine
Source: (gene. exp.) Homo sapiens (human) / Gene: SRRT, ARS2, ASR2 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9BXP5
#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 ARS2[147-871] and m7GTP
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 FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 40.13 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

-
Processing

EM softwareName: PHENIX / Version: 1.20.1_4487: / Category: model fitting
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 84474 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0037937
ELECTRON MICROSCOPYf_angle_d0.65110747
ELECTRON MICROSCOPYf_dihedral_angle_d9.0841091
ELECTRON MICROSCOPYf_chiral_restr0.0391169
ELECTRON MICROSCOPYf_plane_restr0.0081375

+
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