[English] 日本語
Yorodumi
- EMDB-16321: Structure of the human nuclear cap-binding complex bound to NCBP3... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-16321
TitleStructure of the human nuclear cap-binding complex bound to NCBP3(560-620) and cap-analogue m7GpppG
Map dataprimary map
Sample
  • Complex: Ternary complex of CBP80, CBP20 and NCBP3 with bound m7GpppG
    • Protein or peptide: Nuclear cap-binding protein subunit 1
    • Protein or peptide: Nuclear cap-binding protein subunit 2
    • Protein or peptide: Nuclear cap-binding protein subunit 3
  • Ligand: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE
KeywordsNuclear cap-binding complex / NCBP3 / Pol II transcript metabolism / RNA BINDING PROTEIN
Function / homology
Function and homology information


snRNA export from nucleus / nuclear cap binding complex / mRNA metabolic process / RNA cap binding complex / histone 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 ...snRNA export from nucleus / nuclear cap binding complex / mRNA metabolic process / RNA cap binding complex / histone 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 / 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) / Formation of HIV-1 elongation complex containing HIV-1 Tat / 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 / snRNP Assembly / positive regulation of cell growth / defense response to virus / molecular adaptor activity / nuclear speck / ribonucleoprotein complex / mRNA binding / mitochondrion / DNA binding / RNA binding / nucleoplasm / nucleus / cytosol / cytoplasm
Similarity search - Function
Nuclear cap-binding protein subunit 3 / Nuclear cap-binding protein subunit 3 / 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 ...Nuclear cap-binding protein subunit 3 / Nuclear cap-binding protein subunit 3 / 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
Nuclear cap-binding protein subunit 2 / Nuclear cap-binding protein subunit 1 / Nuclear cap-binding protein subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsDubiez E / Pellegrini E / Foucher AE / Cusack S / Kadlec J
Funding support France, 1 items
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
DepositionDec 12, 2022-
Header (metadata) releaseJan 24, 2024-
Map releaseJan 24, 2024-
UpdateJan 31, 2024-
Current statusJan 31, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_16321.png

Downloads & links

-
Map

FileDownload / File: emd_16321.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 300 pix.
= 248.1 Å		0.83 Å/pix.
x 300 pix.
= 248.1 Å		0.83 Å/pix.
x 300 pix.
= 248.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.1957389 - 0.41728508
Average (Standard dev.)0.00017795419 (±0.011694301)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 248.1 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_16321_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: locally filtered and sharpened map (-100 A2)

Fileemd_16321_additional_1.map
Annotationlocally filtered and sharpened map (-100 A2)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A

Fileemd_16321_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B

Fileemd_16321_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Ternary complex of CBP80, CBP20 and NCBP3 with bound m7GpppG

EntireName: Ternary complex of CBP80, CBP20 and NCBP3 with bound m7GpppG
Components
  • Complex: Ternary complex of CBP80, CBP20 and NCBP3 with bound m7GpppG
    • Protein or peptide: Nuclear cap-binding protein subunit 1
    • Protein or peptide: Nuclear cap-binding protein subunit 2
    • Protein or peptide: Nuclear cap-binding protein subunit 3
  • Ligand: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE

-
Supramolecule #1: Ternary complex of CBP80, CBP20 and NCBP3 with bound m7GpppG

SupramoleculeName: Ternary complex of CBP80, CBP20 and NCBP3 with bound m7GpppG
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Nuclear cap-binding protein subunit 1

MacromoleculeName: Nuclear cap-binding protein subunit 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 89.809984 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MKTSDANETE DHLESLICKV GEKSACSLES NLEGLAGVLE ADLPNYKSKI LRLLCTVARL LPEKLTIYTT LVGLLNARNY NFGGEFVEA MIRQLKESLK ANNYNEAVYL VRFLSDLVNC HVIAAPSMVA MFENFVSVTQ EEDVPQVRRD WYVYAFLSSL P WVGKELYE ...String:
MKTSDANETE DHLESLICKV GEKSACSLES NLEGLAGVLE ADLPNYKSKI LRLLCTVARL LPEKLTIYTT LVGLLNARNY NFGGEFVEA MIRQLKESLK ANNYNEAVYL VRFLSDLVNC HVIAAPSMVA MFENFVSVTQ EEDVPQVRRD WYVYAFLSSL P WVGKELYE KKDAEMDRIF ANTESYLKRR QKTHVPMLQV WTADKPHPQE EYLDCLWAQI QKLKKDRWQE RHILRPYLAF DS ILCEALQ HNLPPFTPPP HTEDSVYPMP RVIFRMFDYT DDPEGPVMPG SHSVERFVIE ENLHCIIKSH WKERKTCAAQ LVS YPGKNK IPLNYHIVEV IFAELFQLPA PPHIDVMYTT LLIELCKLQP GSLPQVLAQA TEMLYMRLDT MNTTCVDRFI NWFS HHLSN FQFRWSWEDW SDCLSQDPES PKPKFVREVL EKCMRLSYHQ RILDIVPPTF SALCPVNPTC IYKYGDESSN SLPGH SVAL CLAVAFKSKA TNDEIFSILK DVPNPNQDDD DDEGFSFNPL KIEVFVQTLL HLAAKSFSHS FSALAKFHEV FKTLAE SDE GKLHVLRVMF EVWRNHPQMI AVLVDKMIRT QIVDCAAVAN WIFSSELSRD FTRLFVWEIL HSTIRKMNKH VLKIQKE LE EAKEKLARQH KRRSDDDDRS SDRKDGVLEE QIERLQEKVE SAQSEQKNLF LVIFQRFIMI LTEHLVRCET DGTSVLTP W YKNCIERLQQ IFLQHHQIIQ QYMVTLENLL FTAELDPHIL AVFQQFCALQ A

UniProtKB: Nuclear cap-binding protein subunit 1

-
Macromolecule #2: Nuclear cap-binding protein subunit 2

MacromoleculeName: Nuclear cap-binding protein subunit 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.15626 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GAMSGGLLKA LRSDSYVELS QYRDQHFRGD NEEQEKLLKK SCTLYVGNLS FYTTEEQIYE LFSKSGDIKK IIMGLDKMKK TACGFCFVE YYSRADAENA MRYINGTRLD DRIIRTDWDA GFKEGRQYGR GRSGGQVRDE YRQDYDAGRG GYGKLAQNQ

UniProtKB: Nuclear cap-binding protein subunit 2

-
Macromolecule #3: Nuclear cap-binding protein subunit 3

MacromoleculeName: Nuclear cap-binding protein subunit 3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6.734328 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KKVDHRAPGA EEDDSELQRA WGALIKEKEQ SRQKKSRLDN LPSLQIEVSR ESSSGSEAES

UniProtKB: Nuclear cap-binding protein subunit 3

-
Macromolecule #4: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE

MacromoleculeName: 7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE / type: ligand / ID: 4 / Number of copies: 1 / Formula: GTG
Molecular weightTheoretical: 803.44 Da
Chemical component information

ChemComp-GTG:
7-METHYL-GUANOSINE-5'-TRIPHOSPHATE-5'-GUANOSINE

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5oo6

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 152563
FSC plot (resolution estimation)

+
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